Lead Optimization of 3,5-Disubstituted-7-Azaindoles for the Treatment of Human African Trypanosomiasis

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Lead Optimization of 3,5-Disubstituted-7-Azaindoles for the

Treatment of Human African Trypanosomiasis

Dana M. Klug, Eftychia M. Mavrogiannaki, Katherine C. Forbes, Lisseth Silva, Rosario Diaz-Gonzalez,

Guiomar P é rez-Moreno, Gloria Ceballos-P é rez, Raquel Garcia-Hern á ndez, Cristina Bosch-Navarrete,

̃

Carlos Cord ó n-Obras, Claudia G ó mez-Lin á n, Andreu Saura, Jeremiah D. Momper,

Maria Santos Martinez-Martinez, Pilar Manzano, Ali Syed, Nelly El-Sakkary, Conor R. Ca ﬀ rey,

Francisco Gamarro, Luis Miguel Ruiz-Perez, Dolores Gonzalez Pacanowska, Lori Ferrins,*

Miguel Navarro, and Michael P. Pollastri

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ABSTRACT: Neglected tropical diseases such as human African

trypanosomiasis (HAT) are prevalent primarily in tropical climates

and among populations living in poverty. Historically, the lack of

economic incentive to develop new treatments for these diseases

has meant that existing therapeutics have serious shortcomings in

terms of safety, eﬃcacy, and administration, and better therapeutics

are needed. We now report a series of 3,5-disubstituted-7-

azaindoles identiﬁed as growth inhibitors of Trypanosoma brucei,

the parasite that causes HAT, through a high-throughput screen.

We describe the hit-to-lead optimization of this series and the

development and preclinical investigation of 29d, a potent

antitrypanosomal compound with promising pharmacokinetic

(PK) parameters. This compound was ultimately not progressed beyond in vivo PK studies due to its inability to penetrate the

blood−brain barrier (BBB), critical for stage 2 HAT treatments.

fexinidazole has been approved to treat both stages of T. brucei

gambiense HAT and has been added to the WHO treatment

guidelines;⁴and acoziborole, formerly known as SCYX-7158,

has been advanced to Phase II/III clinical trials for HAT.^5,6

However, as with any infectious disease, resistance to current

therapies may develop, and it is important to ﬁll the pipeline

with backup compounds. As much of the drug discovery for

NTDs is done by academic laboratories with limited resources,

repurposing strategies (including but not limited to drug

repurposing)⁷are used to quickly identify chemical matter that

may be suitable for further development. Such strategies take

advantage of target function shared between human and

parasite and assess compounds that were optimized against

human targets as starting points for antiparasitic agents. In this

instance, we exploited the fact that trypanosomes are known to

express essential kinases by repurposing compounds originally

INTRODUCTION

■

Human African trypanosomiasis (HAT) is designated by the

World Health Organization as a neglected tropical disease

(NTD), one of a group of 20 communicable diseases that are

prevalent in tropical climates and disproportionately aﬀect

populations living in poverty.¹HAT is caused by infection with

either of two subspecies of the parasite Trypanosoma brucei (T.

brucei gambiense or T. brucei rhodesiense) and is fatal if

untreated.²The disease proceeds in two stages; in the ﬁrst

stage, patients exhibit milder, ﬂu-like symptoms and thus often

go undiagnosed. In the second stage, the parasite crosses the

blood−brain barrier (BBB) and causes more serious neuro-

logical symptoms, such as the severe disruption of sleep

patterns from which the disease takes the colloquial name

“African sleeping sickness.”²Historically, the treatments

available for HAT have been suboptimal in terms of eﬃcacy,

safety, and route of administration.³Recent advances include a

combination therapy called nifurtimox−eﬂornithine combina-

tion therapy (NECT), which reduces the dose requirement for

eﬂornithine, a repurposed cancer drug requiring hours-long

intravenous infusions to administer, by combining it with

nifurtimox, an oral treatment ﬁrst used to treat Chagas disease

(a related NTD).³Even more recently, the orally available drug

Received: April 13, 2021

Published: June 22, 2021

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a

Table 1. Targeted versus Measured and Calculated Values for the Properties of Interest

a

nd = no data. Values highlighted in green meet or exceed targeted values; values highlighted in yellow indicate acceptable values, and values

†

highlighted in red indicate values that are well outside the target. Kinetic aqueous solubility.

designed as inhibitors of human kinases.⁸⁻¹⁰A high-

throughput screen (HTS) of over 40 000 kinase inhibitors,

drawn largely from the published kinase inhibitor set (PKIS)

and in-house GSK compounds, was undertaken and resulted in

the identiﬁcation of 797 compounds that showed Trypanosoma

brucei growth inhibition (pEC₅₀> 6.0) and 100× selectivity

over HepG2 cells.¹¹These hits were then clustered by

structural similarity, and the most promising were selected

for further optimization.

Due to a patient population that is likely to have limited

access to health care facilities and the lack of eﬀective

therapeutics for stage 2 HAT, we sought a lead compound

likely to be orally available and brain penetrant. Therefore, in

Figure 1. Plasma concentrations of NEU-1207 over time after a 5

addition to potency against T. brucei and mammalian cell

toxicity, physicochemical properties and metrics such as the

lipophilic ligand eﬃciency (LLE) and central nervous system-

multiparameter optimization (CNS-MPO) score were used to

prioritize clusters for further optimization.^12,13One of the

clusters identiﬁed through this HTS comprised a series of 3,5-

disubstituted-7-azaindoles. Table 1 highlights the properties of

three compounds in this series: NEU-1207, −1208, and

−1209. Both NEU-1207 and NEU-1208 display pEC₅₀> 7.0

against T. brucei; NEU-1209 is ≥0.5 log units less potent. The

longer aliphatic chain and primary amine of NEU-1209

translate to suboptimal physicochemical properties, such as

high molecular weight and topological polar surface area

(TPSA), and a low CNS-MPO score; however, the other two

compounds had properties in acceptable ranges, and we felt

the series warranted further investigation.

In addition to these data, we also obtained pharmacokinetic

(PK) data for NEU-1207. Figure 1 shows the plasma

concentration of this compound over time following a 5 mg/

kg oral dose. The compound concentration was below the

lower limit of quantitation after an average of 4.7 h in vivo,

which is consistent with the observed high in vitro human liver

microsome intrinsic clearance (HLM Cl_int) for this compound

(190 μg/min/mg protein). Metabolism was therefore identi-

ﬁed as a key liability of this series going forward. Given the

mg/kg oral dose.

data on the initial hits and the PK proﬁle of NEU-1207, our

major goals for the series were to maintain or improve potency

against T. brucei while improving the ADME properties of

NEU-1207 (in particular, its clearance and solubility) to

develop an eﬀective, orally available HAT therapeutic.

RESULTS AND DISCUSSION

■

We ﬁrst sought to establish structure−activity relationships

(SAR) around the 7-azaindole core of the series. The biological

activity of these analogues is shown in Table 2 (preparation

described in Schemes S1 −S5). Methylation (1) or tosylation

(2) of the indole −NH resulted in a loss of activity against T.

brucei, as did replacing the azaindole with a pyridofuran (3) or

indole (4). These analogues demonstrated that the hydrogen

bond donor/acceptor pair of the azaindole core was required

for potency. The methylated-core analogue 5, which we

anticipated might increase solubility by virtue of breaking the

planarity of the molecule, maintained potency without any

improvement in clearance or solubility. The substituents at the

3- and 5-positions of the core were interchangeable without

sacriﬁcing substantial activity (6 vs NEU-1207), while

removing either one (7 and 8) rendered the compound

inactive.

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a

Table 2. Biological Activity of Core-Replacement Analogues

a

nd = no data. All pEC₅₀SD within 0.17.

The HLM Cl_intof the core-replacement analogues was also

assessed, but only compound 2 showed a signiﬁcant reduction

compared to NEU-1207. To better understand the high

clearance of these compounds, predictive software was used to

determine likely sites of metabolism. Figure 2 shows the most

aﬀord intermediate 7. This compound was iodinated using NIS

and subsequently tosylated to aﬀord intermediate 11, which

could then undergo a second Suzuki reaction with the desired

boronic acid or ester to aﬀord the protected products 12.

Under basic conditions, the tosyl group was removed to aﬀord

the ﬁnal products 13a-aa.

The T. brucei activity, in vitro clearance, and thermodynamic

aqueous solubility of the aromatic benzonitrile replacements

are shown in Table 3. Moving the nitrile to the 2- (13a) or 4-

(13b) position of the benzene ring resulted in ∼10-fold

reduction in potency; an unsubstituted benzene ring (13c) was

slightly more potent. 4-Chloro, -methyl, and -triﬂuoromethyl

substituents (13d−f, 13i) were detrimental to antitrypanoso-

mal activity compared to the parent compound, while the

methoxy group (13g) fared slightly better. A series of

ﬂuorinated analogues (13j−o), both with and without a nitrile

group, maintained submicromolar potency, but only two of

these compounds, 3-ﬂuoro (13j) and 3-cyano-5-ﬂuoro (13n),

were equipotent to NEU-1207. Although some of these

compounds did show improved clearance over NEU-1207, all

of them remain in the “high clearance” category (see the

Supporting Information, Table S1) and only a few were soluble

at concentrations >10 μM.

Figure 2. Predicted metabolites of NEU-1207 using MetaSite

software.¹⁴

likely metabolites for NEU-1207 as predicted by MetaSite 5.0

(Molecular Discovery Ltd.). Both are the products of oxidation

at substituents on either the 3- or 5-position substituents of the

7-azaindole core, consistent with the clearance data presented

in Table 2. We therefore focused further eﬀorts on varying

substituents at these positions.

Further nitrile replacements included the amide (13p),

carboxylic acid (13q), amine (13r), and nitro (13t) groups. In

addition, the 4-N,N-dimethylmethanamine (13s) and 4-

hydroxy (13u) substituents, both included in another

azaindole-derived HTS cluster, were synthesized. Of these

The synthesis of analogues varied at the 3-position is shown

in Scheme 1. By maintaining the pyrazole at the 5-position, we

employed a parallel-enabled synthetic route. The pyrazole was

installed by reacting 5-bromo-7-azaindole 9 with 1-methyl-4-

pyrazoleboronic acid pinacol ester under Suzuki conditions to

a

Scheme 1. Synthesis of 3-Position Analogues

a

Reagents and reaction conditions: (a) 1-methyl-4-pyrazoleboronic acid pinacol ester, K₂CO₃, PdCl₂(dppf)·CH₂Cl₂, 3:1 dioxane/water, 85 °C, 4 h

(93%). (b) NIS, acetonitrile, 50 °C, 2 h (69%). (c) Tosyl chloride, 4-dimethylaminopyridine (DMAP), triethylamine (TEA), dichloromethane

(DCM), rt, 12 h (89%). (d) Aryl boronic acid or pinacol ester, K₂CO₃, PdCl₂(dppf)·CH₂Cl₂, 3:1 dioxane/water, 120 °C, μw, 30 min (24−85%).

(e) NaOH (2 M aq), dioxane, 150 °C, μw, 1−10 min (10−83%). Ar = aryl group.

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a

Table 3. Biological Activity, HLM Cl_int, and Aqueous Solubility of Aromatic Benzonitrile Replacement Analogues

a

nd = no data. All pEC₅₀SD within 0.17.

analogues, the amine and hydroxy substituents were

equipotent to NEU-1207, and the nitro substituent showed

an increase in potency (pEC₅₀7.6). Although 13r showed

vastly improved solubility, the HLM Cl_intremained problem-

atic, and both 13t and 13u showed signs of toxicity in

mammalian cells (a known liability of nitrobenzenes and

phenols; see the Supporting Information, Table S2). The

benzoxadiazole (13v) and indole (13w) were designed as

bioisosteres of the nitro and hydroxy groups, respectively, in an

attempt to recapitulate the improved potency and solubility of

the parent compounds; however, both resulted in decreased

activity against trypanosomes.

In a ﬁnal attempt to improve the ADME properties by

modiﬁcation of the benzonitrile substituent, insertion of a

heteroatom led to 3-pyridyl (13x) and 4-pyridyl (13y)

analogues. Although these compounds did show a decrease

in HLM Cl_intand an increase in solubility as compared to

NEU-1207, they had lower antitrypanosomal activity. Seeking

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a

Scheme 2. Synthesis of Aliphatic 3-Position Analogues

a

Reagents and reaction conditions: (a) NIS, acetonitrile, 50 °C, 2 h (83%). (b) Tosyl chloride, Et₃N, DMAP, DCM, rt, 12 h (78%). (c) Boronic

ester, PdCl₂(dppf)·CH₂Cl₂, K₂CO₃, 3:1 dioxane/water, 80 °C, 10 min, μw (56−73%). (d) 1-Methyl-4-pyrazoleboronic acid pinacol ester, K₂CO₃,

PdCl₂(dppf)·CH₂Cl₂, 3:1 dioxane/water, 85 °C, 4 h (83−93%). (e) NH₄COO, 10% Pd/C, EtOH, 85 °C, 1.5 h (59−68%). (f) 2 M aq NaOH,

dioxane, 150 °C, 15 min, μw (44−75%). (g) HCl, dioxane, 1−3 h, rt (78−97%).

a

Table 4. Biological Activity, HLM Cl_int, and Aqueous Solubility of Aliphatic Benzonitrile Replacement Analogues

a

All pEC₅₀SD within 0.17.

additive SAR, we synthesized nitrile-substituted pyridyl groups

(13z-aa) based on the previous SAR (cf. NEU-1207 vs 13c).

However, these analogues lost activity compared to the

unsubstituted pyridyl compounds and the beneﬁcial ADME

properties were lost as well. Although 13y showed the best

combination of potency, clearance, and solubility, none of the

aromatic groups installed at the 3-position had values within

the desirable range for all three properties simultaneously.

In addition to aromatic substituents, aliphatic groups were

also installed at the 3-position. The synthesis of these

analogues is shown in Scheme 2. The 5-bromo-7-azaindole

starting material 9 was converted to the dihalide 14 and

subsequently tosylated to aﬀord intermediate 15. A Suzuki

reaction with 5- and 6-membered cyclic amine boronic acids

produced the oleﬁn compounds 16, and a second Suzuki

reaction to install N-methylpyrazole at the 5-position aﬀorded

disubstituted intermediates 17. The oleﬁn was reduced via

transfer hydrogenation using ammonium formate to produce

intermediates 18, which were subsequently deprotected to

aﬀord the ﬁnal products 19a−c and 20a−c.

The biological activity, clearance, and solubility of analogues

containing an aliphatic group at the 3-position are shown in

Table 4. These compounds were designed to increase the Fsp³,

a known strategy to increase the solubility of highly aromatic,

“ﬂat” compounds.¹⁵None of these compounds displayed

submicromolar activity against T. brucei, indicating that

aromaticity in this position is essential for antitrypanosomal

activity. However, those compounds that possessed a basic

amine showed a consistent and dramatic improvement in

HLM Cl_intand aqueous solubility, the latter likely due to

increased ionization at physiological pH.

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a

Scheme 3. Synthesis of 5-Position Aromatic and Cyclic Amine Analogues

a

Reagents and reaction conditions: (a) (3-cyanophenyl)boronic acid, K₂CO₃, PdCl₂(dppf)·CH₂Cl₂, 3:1 dioxane/water, 120 °C, μw, 5 min (60%).

(b) Aryl boronic acid or pinacol ester, K₂CO₃, PdCl₂(dppf)·CH₂Cl₂, 3:1 dioxane/water, 85 °C, 4 h (31−84%). (c) NaOH (2 M aq), dioxane, 150

°C, μw, 1−10 min (10−83%). (d) Amine, LiHMDS (1.0 M in tetrahydrofuran (THF)), RuPhos, RuPhos Pd G1, 65 °C, 5 h (12−30%).

a

Table 5. Biological Activity, HLM Cl_int, and Aqueous Solubility of Aromatic and Aliphatic Pyrazole Replacement Analogues

a

nd = no data. All pEC₅₀SD within 0.17.

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a

Table 6. Biological Activity, HLM Cl_int, and Aqueous Solubility of Substituted Pyrazoles and Related Analogues

a

All pEC₅₀SD within 0.17.

We next turned our attention to the pyrazole at the 5-

position of the azaindole, also identiﬁed as a potential

metabolic hotspot. Aromatic substituents were installed

according to Scheme 3 using the advanced intermediate 15.

Short reaction times in a microwave reactor enabled selective

Suzuki coupling of the aryl iodide with (3-cyanophenyl)-

boronic acid to aﬀord intermediate 21. A second Suzuki

reaction at the 5-position yielded intermediates 22, which were

detosylated to aﬀord ﬁnal products 23a−f. Alternatively,

intermediate 21 was subjected to palladium-mediated coupling

conditions to aﬀord 5-amino-substituted azaindoles 24, where

the tosyl group was deprotected under the reaction conditions.

The syntheses of compounds 25−28 are presented in Schemes

S7 and S8.

The biological activity, clearance, and solubility data of the

pyrazole replacement analogues are shown in Table 5. Many of

the analogues with aromatic substituents (23a,b, 23d, and

23f), as well as compounds with an intervening N atom (27,

28), were approximately equipotent with respect to NEU-

1207, although the trisubstituted pyrazole (23c) and

pyrimidine (23e) were almost 10-fold less potent. In general,

aliphatic replacements of the pyrazole were inactive, except for

the methylsulfonylpiperazine analogue (25).

The clearance of pyrazoles 23a−c remained quite high,

whereas replacement with methylsulfonyl benzene or pyr-

imidine signiﬁcantly lowered the clearance, though poor

aqueous solubility was still generally an issue, with 23a being

the exception (aqueous solubility: 26 μM). In addition, most

aliphatic substituents also had improved clearance over NEU-

1207. Insertion of an intervening −NH resulted in improved

solubility of compound 27. This was thought to be due to the

inclusion of an ionizable group, although 28 was no more

soluble than its matched pair 23d. Aliphatic substituents

containing a basic nitrogen distal to the azaindole core (24c,

24e, and 26) resulted in signiﬁcantly improved solubility;

aliphatic substituents without this feature (24a, b) or those

where the basicity of the distal nitrogen was attenuated by

further substitution (24d, 25) did not show similar improve-

ment.

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Finally, we explored a variety of substituted pyrazoles at the

5-position, including tetrahydropyran (29a), N-boc-piperidine

(29b), and N-methyl piperidine (29c). The synthesis of these

compounds is shown in Scheme S9. Of these, 29a showed a

signiﬁcant (10-fold) improvement in potency, becoming the

most potent compound to date for this series, which was

reﬂected in its high LLE. In addition, both 29a and 29c

showed a signiﬁcant reduction in HLM Cl_int, suggesting that

the N-alkyl pyrazole moiety constitutes the major metabolic

liability of this chemotype. This reduction in clearance

represented a major step forward in resolving a critical issue

for this series. However, all three of these substituted pyrazoles

displayed poor solubility (<10 μM), prompting further

optimization eﬀorts.

We sought to improve the solubility of 29a using insights

from the established SAR. Previously, both pyridyl and

saturated groups at the 5-position had resulted in higher

solubility. The synthesis of these compounds with the

tetrahydropyran-substituted pyrazole in the 5-position is

shown in Schemes S10 and S11. In this case, the inclusion

of the pyridine (30) did not result in signiﬁcant solubility

improvement, and the inclusion of a saturated group (31)

while improving both solubility and HLM clearance, was

signiﬁcantly detrimental to potency, despite the presence of the

N-tetrahydropyran-2-yl (THP)-substituted pyrazole. Replace-

ment of the tetrahydropyran moiety with a piperidinyl group

(29d) to incorporate an additional H-bond donor resulted in a

compound with the best combination of potency, solubility,

and clearance thus far.

pEC₅₀of 7.2, this compound is nontoxic in MRC5 cells (see

the Supporting Information, Table S2), has an LLE of 4.8, and

a CNS-MPO score of 4.4, indicating a likelihood of brain

penetration. In addition, it is stable in mouse plasma and its

plasma protein binding is below the threshold of 95%. The

major potential liabilities with this compound continue to be

related to metabolism: although its HLM Cl_intis low, the

clearance in rat hepatocytes and mouse liver microsomes

(MLM) is higher, and this discrepancy could potentially pose

issues when evaluating safety and eﬃcacy in rodent animal

models.

Despite the concerns about rodent clearance, we felt that the

potency of 29d combined with its other, more favorable

ADME properties, justiﬁed the progression of this compound

to in vivo pharmacokinetic (PK) studies. Continuous sampling

at a 10 mg/kg intraperitoneal (ip) dose showed an average

C

_maxof 4413.3 ng/mL 1 h after dosing (Figure 3). Calculation

In a ﬁnal eﬀort to improve the ADME properties of 29a, we

returned to the strategy of making further modiﬁcations to the

core (Table 6; synthesis shown in Scheme S12). It was

hypothesized that increasing the polarity of the azaindole may

improve clearance and solubility; as such, the azaindole core

was replaced with a pyrazolopyridine (32). In addition, ortho-

methylation is known to improve the aqueous solubility of

compounds,¹⁶and we had previously demonstrated that this

change did not impact the potency of the series (cf. compound

5). We reasoned that the installation of methyl at the 4-

position of 29d (compound 33) could increase aqueous

solubility due to a steric clash with the tetrahydropyran that

would twist the substituent out of plane. However, neither of

these modiﬁcations produced the desired improvement in

ADME properties.

Figure 3. Plasma concentration versus time proﬁle of 29d in mice (n

= 3) following a single 10 mg/kg ip dose. The blue dashed line shows

the average concentration and the shaded area represents the standard

deviation.

of the protein-binding-adjusted EC₅₀(EC₅₀/f_u, 256 ng/mL)

reveals that exposure over the adjusted EC₅₀is maintained for

∼8 h, which is a marked improvement over NEU-1207

(which, when accounting for PPB, did not achieve levels over

the EC₅₀(378 ng/mL) for the duration of the study).

However, as shown in Table 8, compound 29d is not

Table 8. Sparse Sampling Brain and Plasma Concentration

a

of 29d after a 10 mg/kg, ip Dose

time

(h)

mean plasma concentration

(ng/mL)

mean brain concentration

(ng/mg)

Given its combination of high potency, improved LLE, low

clearance, and reasonable (>10 μM) solubility, we obtained

additional data on compound 29d (Table 7). In addition to its

0.5

4

3193.7

426.3

<LLOQ

0.22

a

LLOQ = 9.77 ng/mL.

Table 7. Overall Proﬁle of 29d

appreciably brain penetrant. We sought to gain a better

understanding of the permeability and eﬄux of 29d using a

Caco-2 assay (see the Supporting Information, Table S3),

which revealed that 29d had low permeability and is likely a

substrate for P-gp or other active transporters. Given this

information and the PK data, we concluded that the series was

not likely to yield a compound appropriate for treating stage 2

HAT and did not undertake further optimization or pursue

eﬃcacy studies on compound 29d.

It should be noted that a lack of CNS penetration was

observed for another compound in this series (see the

Supporting Information, Table S4), which also had a high

CNS-MPO score (>5; see the Supporting Information, Table

targeted value

29d

7.2

256

4.9

4.8

4.4

25

<3

19

T.b.b. pEC₅₀

protein-binding-adjusted T.b.b. EC₅₀(ng/mL)

MRC5 pTC₅₀

≥7

≤5

≥4

>10

<9

LLE

CNS-MPO score

aq. sol. (μM)

HLM Cl_int(μL/min/mg protein)

rat hepatocyte Cl_int(μL/min/10⁶cells)

mouse plasma stability t_1/2(min)

MLM t_1/2(min)

<5

>120

34

91

>60

<95

PPB

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S5). Although unavailable to us at the time, we have since

calculated a BBB score¹⁷for both compounds, according to

which neither compound is predicted to penetrate the CNS

(see the Supporting Information, Table S6). The BBB score

diﬀers from the CNS-MPO score in the properties it takes into

account, the functions used to assign T0 values to those

properties, and the weight given to each, and higher sensitivity

and speciﬁcity have been reported for the BBB score over the

CNS-MPO score.¹⁷

For compound 29d, the components that are most

detrimental to the overall BBB score are the number of

aromatic rings, which is not factored into the CNS-MPO score

calculation, and the TPSA, which gives a T0 of 1 using the

CNS-MPO calculator and a T0 of 0.43 using the BBB

calculator. Thus, analysis of the BBB score of 29d would

suggest that a reduction in the number of aromatic rings and a

reduction in the TPSA would improve its brain penetration,

although it is unclear whether this would be eﬀective if 29d is

indeed a P-gp substrate. One limitation of both metrics in our

hands is the use of predicted pK_avalues, which can vary

depending on the programs used to calculate them. Another is

the general lack of guidance for the physicochemical properties

required for therapeutics that are both orally available and

brain penetrant, of great importance for stage 2 HAT

therapeutics. However, it appears that the BBB score is a

better predictor of brain penetration than the CNS-MPO score

for this series and may be of greater use for HAT drug

discovery going forward.

Finally, as part of an ongoing cross-screening eﬀort by our

group, the compounds synthesized during this optimization

campaign were screened against Trypanosoma cruzi, Leishmania

donovani, and Schistosoma mansoni, the causative parasites of

Chagas disease, leishmaniasis, and schistosomiasis, respectively.

Although compounds active against T. brucei are not assumed

to have broad antiparasitic activity, we have had some success

with this approach as a way of generating new lead series

against other pathogens by screening all compounds

synthesized as part of our HAT medicinal chemistry campaigns

against multiple parasites.¹⁸The data are presented in the

Supporting Information (Tables S7 and S8). None of the

compounds in this series showed activity against L. donovani,

and only one showed submicromolar activity against T. cruzi.

To adjudicate the potency of compounds against adult S.

mansoni, we employed a severity scoring system (0−4

(severest)),¹⁹⁻²²which encapsulates many phenotypic changes

(e.g., motility, density, shape, and inability to adhere to the

bottom of the assay dish) that this parasite is capable of as a

function of time and compound concentration.²³At 10 μM for

48 h, compounds 1 and 13o demonstrated modest activity,

whereby both yielded a severity score of 2.

the resulting low brain concentrations mean that the

compounds would not be eﬀective in the target tissue for

stage 2 of the disease. Similar limitations were observed for a

related compound and, therefore, work on the series

discontinued for HAT. Cross-screening against T. cruzi, L.

donovani, and S. mansoni did not result in potent inhibitors

against any of these pathogens.

EXPERIMENTAL SECTION

■

In Vitro Biology. To determine the T. b. brucei EC₅₀values, 4 μL

per well from compound master plates was dispensed into a new

plate, and 96 μL of HMI-9 per well was added to generate a 4%

dimethyl sulfoxide (DMSO) intermediate plate. Mid-log phase

growth T. b. brucei was diluted to a working cell density of 2750

cells/mL, and 90 μL/well was dispensed into 96-well ﬂat-bottom

transparent assay plates (Nunc). From intermediate plates, 10 μL/

well was added so that the ﬁnal cell concentration was 2500 cells/mL,

and the ﬁnal top concentration of compounds was 40 μM in 0.4%

DMSO per well. Assay plates were incubated for 72 h at 37 °C and

5% CO₂. Four hours prior to the end of the incubation, 20 μL of a

440 μM resazurin solution in prewarmed HMI-9 was added to each

well and incubated for another 4 h. Fluorescence was then measured

in an Inﬁnite F200 plate reader (Tecan) at 550 nm (excitation ﬁlter)

and 590 nm (emission ﬁlter). A four-parameter equation was

employed to ﬁt the dose−response curves and determine the EC₅₀

value using SigmaPlot 13.0 software. Assays were performed in

duplicate at least twice to achieve a minimal n = 2 per dose−response.

Pharmacokinetic Protocols. In vivo pharmacokinetics were

evaluated in BALB/c mice (n = 3). Each mouse received a 10 mg/

kg dose of the test compound by intraperitoneal injection. Blood

samples (50 μL) were taken via retro-orbital bleeds at 0.083, 0.25, 0.5,

1, 2, 4, 8, and 24 h postdose. Plasma concentrations were determined

using liquid chromatography with tandem mass spectrometry

(LCMS-MS).

Animal studies for NEU-1207 were ethically reviewed and carried

out in accordance with European Directive 2010/63/EEC and the

GSK Policy on the Care, Welfare and Treatment of Animals;

meanwhile, the study for 29d was conducted under animal use

protocols approved by the University of California, San Diego

Institutional Animal Care and Use Committee.

General Chemistry. Reagents purchased were used as received

unless otherwise noted. Puriﬁcation of intermediates and ﬁnal

compounds was performed using silica gel chromatography using

the Biotage Isolera One ﬂash puriﬁcation system. When required,

preparative high-performance liquid chromatography (HPLC) was

conducted for ﬁnal compounds on a Waters FractionLynx system

using acetonitrile/water and 0.1% formic acid gradient and collected

based on UV monitoring at 254 nm. LCMS analysis was performed

using a Waters Alliance reverse phase HPLC (columns Waters

SunFire C18 4.6 × 50 mm², 3.5 μm, or Waters SunFire C8 4.6 × 50

mm², 3.5 μm), using a multiwavelength photodiode array detector

from 210 to 600 nm and Waters Micromass ZQ detector

(electrospray ionization). All compounds tested had a purity of

>95% as measured by LCMS unless otherwise noted. ¹H NMR

spectra were obtained with Varian NMR systems, operating at either

400 or 500 MHz at room temperature, using solvents from

Cambridge Isotope Laboratories. Chemical shifts (δ, ppm) are

reported relative to the solvent peak (CDCl₃: 7.26 [¹H]; DMSO-d₆:

CONCLUSIONS

■

Using a lead repurposing approach, we identiﬁed a series of

3,5-disubstituted-7-azaindoles with antitrypanosomal activity

through an HTS of human kinase inhibitor chemotypes.

Through a detailed SAR study, we identiﬁed 29d which

retained submicromolar activity againstT. brucei while showing

improved aqueous solubility and dramatically improved HLM

Cl_intover the original HTS hit. This compound was progressed

to in vivo PK studies and maintained a free plasma

concentration greater than or equal to EC₅₀for ∼8 h after a

10 mg/kg ip dose. However, the low brain penetration of this

series precluded it from progression as a HAT therapeutic, as

1

2.50 [¹H]; acetone-d₆: 2.05; or CD₃OD: 3.31 [¹H]). Data for H

NMR spectra are reported as follows: chemical shift (ppm),

multiplicity (s for singlet, d for doublet, t for triplet, dd for doublet

of doublet, m for multiplet), coupling constant (Hz), and integration.

Compounds obtained from GSK in-house library were not

resynthesized unless otherwise noted.

General Procedure A (For the Synthesis of 5-(1-Methyl-1H-

pyrazol-4-yl)-3-aryl-1-tosyl-1H-pyrrolo[2,3-b]pyridines). Intermedi-

ate 11 (1.0 equiv), desired boronic acid or ester (2.5 equiv), and

PdCl₂(dppf)·CH₂Cl₂(10 mol %) were combined in a microwave vial

that was purged with nitrogen and evacuated three times. Dioxane

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(0.26 M) and 2 M K₂CO₃(3.0 equiv) were added, and the reaction

mixture was degassed for ∼10 min. The reaction was run in the

microwave at 120 °C for 30 min. The reaction mixture was diluted

with EtOAc, ﬁltered through Celite, and concentrated under reduced

pressure, and the title compound was puriﬁed by the stated method to

aﬀord the title compounds.

General Procedure B (For the Synthesis of 3-(5-Aryl-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitriles). 3-(5-Bromo-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (1 equiv), the desired boronic

acid or ester (1.1 equiv), and PdCl₂(dppf)·CH₂Cl₂(0.1 equiv) were

combined in a reaction vial that was ﬁlled with nitrogen and evacuated

three times. Dioxane (0.17 M) and 2 M K₂CO₃(5 equiv) were added,

and the reaction mixture was degassed. The reaction mixture was

heated at 85 °C for ∼4−5 h, then diluted with EtOAc, ﬁltered

through Celite, and concentrated under reduced pressure. The crude

material was puriﬁed by the stated method to aﬀord the ﬁnal

compounds.

General Procedure C (For the Synthesis of 3-(5-Amino-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitriles). 3-(5-Bromo-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (1 equiv), RuPhos (0.05

equiv), and RuPhos Pd G1 (0.05 equiv) were combined in a vial

that was ﬁlled with nitrogen and evacuated three times. Then, 1.0 M

LiHMDS in THF (2.5 equiv) was added, followed by the addition of

the desired amine (1.8 equiv). The reaction mixture was heated at 65

°C for ∼5 h, then quenched by the addition of 1 M HCl, diluted with

EtOAc, and poured over sat. aq. NaHCO₃. The aqueous layer was

extracted three times with EtOAc, and the combined organic layers

were washed once with brine, dried with sodium sulfate, and

concentrated under reduced pressure. The crude residue was puriﬁed

by the stated method to aﬀord the title compounds.

General Procedure D (For the Synthesis of Detosylated 3,5-

Disubstituted-1H-pyrrolo[2,3-b]pyridines). The tosylated azaindole

starting material (1.0 equiv) was suspended in dioxane (0.10 M), and

2 M NaOH (3.5−5.0 equiv) was added. The reaction was run in the

microwave at 150 °C for the speciﬁed amount of time. The solvent

was removed by rotovap, and the crude material was puriﬁed by the

stated method to aﬀord the title compounds.

compound as a light orange solid (135 mg, 71%). LCMS [M +

H]⁺454.16 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 8.70 (d, J =

2.0 Hz, 1H), 8.42 (d, J = 2.0 Hz, 1H), 8.40 (s, 1H), 8.34 (t, J = 1.5

Hz, 1H), 8.31 (s, 1H), 8.20 (dt, J = 7.8, 1.5 Hz, 1H), 8.06 (s, 1H),

8.04 (d, J = 3.4 Hz, 2H), 7.85 (dt, J = 7.8, 1.0 Hz, 1H), 7.70 (t, J = 7.8

Hz, 1H), 7.44 (d, J = 8.8 Hz, 2H), 3.88 (s, 3H), 2.35 (s, 3H).

5-(1-Methyl-1H-pyrazol-4-yl)furo[2,3-b]pyridine (S2). 5-

Bromofuro[2,3-b]pyridine S1 (177 mg, 0.893 mmol), 1-methyl-4-

(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole (205 mg,

0.985 mmol), and PdCl₂(dppf)·CH₂Cl₂(37 mg, 0.045 mmol) were

combined in a reaction vial that was ﬁlled with nitrogen and evacuated

three times. Dioxane (5.2 mL, 0.17 M) and 2 M K₂CO₃(1.3 mL, 2.60

mmol) were added, and the reaction mixture was degassed for 10 min.

The reaction mixture was heated at 85 °C for ∼4.5 h. The reaction

mixture was diluted with MeOH and ﬁltered through Celite. The

ﬁltrate was puriﬁed by ﬂash chromatography (20−50% EtOAc/Hex)

to aﬀord the title compound as an oﬀ-white solid (140 mg, 79%).

LCMS [M + H]⁺199.95 m/z; ¹H NMR (500 MHz, chloroform-d): δ

ppm 8.46 (s, 1H), 7.99 (d, J = 2.0 Hz, 1H), 7.79 (s, 1H), 7.72 (d, J =

2.0 Hz, 1H), 7.67 (s, 1H), 6.79 (d, J = 2.4 Hz, 1H), 3.99 (s, 3H).

3-Bromo-5-(1-methyl-1H-pyrazol-4-yl)furo[2,3-b]pyridine (S3).

5-(1-Methyl-1H-pyrazol-4-yl)furo[2,3-b]pyridine S2 (70 mg, 0.351

mmol) was dissolved in DCM (4.2 mL, 0.09 M) and cooled to 0 °C.

Bromine (0.4 M in DCM, 0.95 mL, 0.380 mmol) was added dropwise

to the reaction mixture. The reaction mixture was stirred at 0 °C for 1

h. The reaction mixture was concentrated, redissolved in THF (∼5

mL), and treated dropwise with 1 M KOH in MeOH (∼1 mL), upon

which the reaction mixture turned cloudy. The reaction mixture was

stirred at room temperature for ∼10 min, then poured over water, and

extracted three times with EtOAc. The combined organic layers were

washed once with brine, dried with sodium sulfate, and concentrated

under reduced pressure. The crude material was puriﬁed by ﬂash

chromatography (20−40% EtOAc/Hex) to aﬀord the title compound

as an oﬀ-white solid (34 mg, 35%). 278.04 m/z (⁷⁹Br), 279.99 m/z

1

(⁸¹Br); H NMR (500 MHz, chloroform-d): δ ppm 8.50 (d, J = 2.0

Hz, 1H), 7.93 (d, J = 2.0 Hz, 1H), 7.83 (s, 1H), 7.77 (s, 1H), 7.72 (s,

1H), 4.00 (s, 3H).

General Procedure E (For the Synthesis of Aryl 4,4,5,5-

Tetramethyl-1,3,2-dioxaborolanes). The desired aryl halide (1.0

equiv), bis(pinacolato)diboron (1.5 equiv), potassium acetate (3.5

equiv), and PdCl₂(dppf)·CH₂Cl₂(0.05 equiv) were combined in a

microwave vial that was ﬁlled with nitrogen and evacuated three

times. Dry, degassed dioxane (0.13 M) was added and the reaction

was run in the microwave (145 °C) for 30 min. The reaction mixture

was diluted with MeOH, ﬁltered through Celite, and concentrated.

The crude material was puriﬁed by the stated method to aﬀord the

title compounds.

3-(5-(1-Methyl-1H-pyrazol-4-yl)furo[2,3-b]pyridin-3-yl)-

benzonitrile (3). 3-Bromo-5-(1-methyl-1H-pyrazol-4-yl)furo[2,3-b]-

pyridine S3 (34 mg, 0.122 mmol), (3-cyanophenyl)boronic acid (26

mg, 0.176 mmol), and PdCl₂(dppf)·CH₂Cl₂(6 mg, 0.007 mmol)

were combined in a microwave vial that was purged with nitrogen and

evacuated three times. Dioxane (0.60 mL, 0.21 M) and 2 M K₂CO₃

(0.30 mL, 0.600 mmol) were added, and the reaction mixture was

degassed for ∼10 min. The reaction was run in the microwave (120

°C) for 5 min. The reaction mixture was diluted with EtOAc, ﬁltered

through Celite, and concentrated under reduced pressure. The crude

material was puriﬁed by ﬂash chromatography (1% MeOH/DCM)

and then repuriﬁed by ﬂash chromatography (30−50% EtOAc/

hexanes) to aﬀord the title compound as an oﬀ-white solid (59%).

LCMS [M + H]⁺301.15 m/z; ¹H NMR (500 MHz, chloroform-d): δ

ppm 8.53 (d, J = 2.0 Hz, 1H), 8.13 (d, J = 2.4 Hz, 1H), 7.95 (s, 1H),

7.91 (s, 1H), 7.86 (d, J = 7.8 Hz, 1H), 7.82 (s, 1H), 7.73 (s, 1H), 7.70

(d, J = 7.8 Hz, 1H), 7.63 (t, J = 8.3 Hz, 1H), 4.00 (s, 3H).

3-(1-Methyl-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (1). 3-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile NEU-1207 (58 mg, 0.194

mmol) was dissolved in dry dimethylformamide (DMF; 0.30 mL,

0.65 M). The reaction mixture was cooled to 0 °C, and sodium

hydride (81 mg, 0.387 mmol) was added. The reaction mixture was

stirred at 0 °C for ∼1 h before the addition of methyl iodide (25 μL,

0.401 mmol). The reaction mixture was allowed to warm to room

temperature and stirred overnight. The reaction mixture was diluted

with EtOAc, poured over cold water, and extracted twice. The

combined organic layers were washed once with brine, dried with

sodium sulfate, and concentrated under reduced pressure. The crude

residue was puriﬁed by ﬂash chromatography (0−10% MeOH/

EtOAc) to aﬀord the title compound as an oﬀ-white solid (41 mg,

5-(1-Methyl-1H-pyrazol-4-yl)-1H-indole (S5). 5-Bromo-1H-indole

S4 (251 mg, 1.28 mmol), 1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-

dioxaborolan-2-yl)-1H-pyrazole (293 mg, 1.41 mmol), and

PdCl₂(dppf)·CH₂Cl₂(51 mg, 0.062 mmol) were combined in a

reaction vial that was ﬁlled with nitrogen and evacuated three times.

Dioxane (8.0 mL, 0.16 M) and 2 M K₂CO₃(2.0 mL, 4.00 mmol)

were added, and the reaction mixture was degassed for 10 min. The

reaction was run in the microwave (145 °C) for 30 min. The reaction

mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (10−40% EtOAc/Hex) to aﬀord the title

compound as an oﬀ-white solid (65 mg, 26%). LCMS [M + H]⁺

1

97%). LCMS [M + H]⁺314.16 m/z; H NMR (500 MHz, DMSO-

d₆): δ ppm 8.60 (d, J = 2.0 Hz, 1H), 8.46 (d, J = 2.0 Hz, 1H), 8.28 (s,

1H), 8.17 (s, 1H), 8.11−8.14 (m, 2H), 8.02 (s, 1H), 7.69 (s, 1H),

7.66 (d, J = 7.8 Hz, 1H), 3.89 (s, 3H), 3.88 (s, 3H).

3-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (2). The title compound was prepared

according to General Procedure A on a 199 mg scale using (3-

cyanophenyl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (20−80% EtOAc/hexanes) to aﬀord the title

1

198.00 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 11.02 (br s,

1H), 8.01 (s, 1H), 7.78 (s, 1H), 7.68−7.71 (m, 1H), 7.36 (d, J = 8.3

Hz, 1H), 7.31 (t, J = 2.7 Hz, 1H), 7.26−7.29 (m, 1H), 6.38 (dd, J =

2.7, 1.7 Hz, 1H), 3.85 (s, 3H).

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3-Iodo-5-(1-methyl-1H-pyrazol-4-yl)-1H-indole (S6). 5-(1-Meth-

yl-1H-pyrazol-4-yl)-1H-indole S5 (65 mg, 0.329 mmol) was dissolved

in DCM (6.6 mL, 0.05 M), and KOH (10 mg, 0.178 mmol) was

added. The reaction mixture was stirred at room temperature for 30

min, after which NIS (76 mg, 0.338 mmol) was added. The reaction

mixture was stirred overnight at room temperature, quenched with

Na₂S₂O₃, and extracted twice with DCM. The combined organic

layers were dried with sodium sulfate and concentrated under reduced

pressure to aﬀord the title compound as a dark purple solid (97 mg,

nitrogen and evacuated three times. Degassed THF (3.0 mL, 0.84 M)

was added, followed by the addition of degassed triethylamine (16.0

mL, 114.79 mmol) and TMS-acetylene (0.450 mL, 3.25 mmol). The

reaction was run at room temperature overnight under nitrogen. The

reaction mixture was diluted with EtOAc and washed once with water

and once with brine. The organic layer was dried with sodium sulfate

and concentrated under reduced pressure. The crude material was

puriﬁed by ﬂash chromatography (20% EtOAc/Hex) to aﬀord the

title compound as a tan solid (602 mg, 85%). LCMS [M + H]⁺

282.95 m/z (⁷⁹Br), 284.96 m/z (⁸¹Br); ¹H NMR (500 MHz, DMSO-

d₆): δ ppm 8.00 (s, 1H), 6.26 (br s, 2H), 2.35 (s, 3H), 0.25 (s, 9H).

5-Bromo-4-methyl-1H-pyrrolo[2,3-b]pyridine (S12). Potassium

tert-butoxide (525 mg, 4.68 mmol) was dissolved in NMP (16.0

mL, 0.30 M) and heated to 80 °C. 5-Bromo-4-methyl-3-

((trimethylsilyl)ethynyl)pyridin-2-amine S11 (602 mg, 2.13 mmol)

was dissolved in NMP (10 mL, 0.23 M) and added dropwise to the

KOtBu solution. The reaction mixture was stirred at 80 °C for 30 min.

The reaction mixture was diluted with EtOAc and washed ﬁve times

with water. The combined organic layers were washed once with

brine, dried with sodium sulfate, and concentrated under reduced

pressure. The crude material was puriﬁed by ﬂash chromatography

(20% EtOAc/hexanes) to aﬀord the title compound as an oﬀ-white

solid (236 mg, 53%). LCMS [M + H]⁺210.84 m/z (⁷⁹Br), 212.86 m/

1

91%). LCMS [M + H]⁺324.02 m/z; H NMR (500 MHz, DMSO-

d₆): δ ppm 11.46−11.51 (m, 1H), 8.11 (s, 1H), 7.82 (d, J = 1.0 Hz,

1H), 7.52 (d, J = 2.4 Hz, 1H), 7.35−7.40 (m, 3H), 3.86 (s, 3H).

3-Iodo-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-indole (S7). 3-

Iodo-5-(1-methyl-1H-pyrazol-4-yl)-1H-indole S6 (97 mg, 0.300

mmol) was suspended in DCM (1.5 mL, 0.21 M), and TEA (0.15

mL, 1.08 mmol), DMAP (46 mg, 0.376 mmol), and 4-

methylbenzenesulfonyl chloride (150 mg, 0.787 mmol) were added

in that order. The reaction mixture was stirred overnight at room

temperature. The reaction mixture was washed once with 1 M HCl,

once with sat. aq. NaHCO₃, and once with brine. The organic layer

was dried with sodium sulfate and concentrated under reduced

pressure. The crude material was puriﬁed by ﬂash chromatography

(50% EtOAc/Hex) to aﬀord the title compound as a dark orange oil

(102 mg, 71%). LCMS [M + H]⁺477.98 m/z; ¹H NMR (500 MHz,

DMSO-d₆): δ ppm 8.21 (s, 1H), 8.04 (s, 1H), 7.89−7.93 (m, 3H),

7.89 (s, 1H), 7.62 (dd, J = 8.8, 1.5 Hz, 1H), 7.42 (d, J = 1.5 Hz, 1H),

7.40 (d, J = 7.8 Hz, 2H), 3.86 (s, 3H), 2.32 (s, 3H).

1

z (⁸¹Br); H NMR (500 MHz, DMSO-d₆): δ ppm 11.79 (br s, 1H),

8.24 (s, 1H), 7.48 (d, J = 3.4 Hz, 1H), 6.57 (t, J = 2.7 Hz, 1H), 2.54

(d, J = 2.0 Hz, 3H).

4-Methyl-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridine (S13). 5-Bromo-4-methyl-1H-pyrrolo[2,3-b]pyridine S12

(236 mg, 1.12 mmol), 1-methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxa-

borolan-2-yl)-1H-pyrazole (258 mg, 1.24 mmol), and PdCl₂(dppf)·

CH₂Cl₂(46 mg, 0.056 mmol) were combined in a reaction vial that

was ﬁlled with nitrogen and evacuated three times. Dioxane (6.6 mL,

0.17 M) and 2 M K₂CO₃(1.7 mL, 3.40 mmol) were added, and the

reaction mixture was degassed for 10 min. The reaction mixture was

heated at 85 °C for ∼4 h. The reaction mixture was diluted with

MeOH, ﬁltered through Celite, and concentrated under reduced

pressure. The crude material was puriﬁed by ﬂash chromatography

(1−10% MeOH/DCM), then repuriﬁed by ﬂash chromatography

(100% EtOAc) to aﬀord the title compound as a tan solid (152 mg,

3-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-indol-3-yl)-

benzonitrile (S8). 3-Iodo-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-

indole S7 (100 mg, 0.210 mmol), (3-cyanophenyl)boronic acid (62

mg, 0.422 mmol), and PdCl₂(dppf)·CH₂Cl₂(20 mg, 0.025 mmol)

were combined in a microwave vial that was purged with nitrogen and

evacuated three times. Dioxane (0.85 mL, 0.25 M) and 2 M K₂CO₃

(0.40 mL, 0.800 mmol) were added, and the reaction mixture was

degassed for ∼10 min. The reaction was run in the microwave (120

°C) for 30 min. The reaction mixture was diluted with EtOAc, ﬁltered

through Celite, and concentrated under reduced pressure. The crude

material was puriﬁed by ﬂash chromatography (20−50% EtOAc/Hex)

to aﬀord the title compound as an orange solid (81 mg, 86%). LCMS

1

[M + H]⁺453.14 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm

1

64%). LCMS [M + H]⁺212.99 m/z; H NMR (500 MHz, DMSO-

8.25−8.28 (m, 2H), 8.19 (s, 1H), 8.13 (dt, J = 7.8, 1.5 Hz, 1H), 7.98

(m, J = 8.8, 3.4 Hz, 3H), 7.93 (d, J = 1.0 Hz, 1H), 7.91 (d, J = 1.0 Hz,

1H), 7.85 (dt, J = 7.8, 1.5 Hz, 1H), 7.70 (t, J = 7.8 Hz, 1H), 7.62 (dd,

J = 8.8, 1.5 Hz, 1H), 7.41 (d, J = 7.8 Hz, 2H), 3.85 (s, 3H), 2.32 (s,

3H).

d₆): δ ppm 11.54 (br. s., 1H), 8.16 (s, 1H), 7.93 (s, 1H), 7.65 (s, 1H),

7.40 (t, J = 2.7 Hz, 1H), 6.52 (dd, J = 3.4, 2.0 Hz, 1H), 3.90 (s, 3H),

2.52 (s, 3H).

3-Iodo-4-methyl-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-

b]pyridine (S14). 4-Methyl-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridine S13 (152 mg, 0.716 mmol) was dissolved in

acetonitrile (4.2 mL, 0.17 M), and N-iodosuccinimide (242 mg,

1.08 mmol) was added. The reaction mixture was stirred at 50 °C for

2 h. Upon cooling to room temperature, a dark brown precipitate was

observed and collected by vacuum ﬁltration to aﬀord the title

compound as a dark brown solid (101 mg, 42%). LCMS [M + H]⁺

3-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-indol-3-yl)benzonitrile (4).

The title compound was prepared according to General Procedure

D on an 81 mg scale using 3-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-

1H-indol-3-yl)benzonitrile S8. The reaction was run for 1 h, and the

crude material was puriﬁed by ﬂash chromatography (5% EtOAc/

DCM) to aﬀord the title compound as an oﬀ-white solid (20 mg,

1

38%). LCMS [M + H]⁺299.13 m/z; H NMR (500 MHz, DMSO-

338.93 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 12.02 (br s,

1H), 8.16 (s, 1H), 7.90 (s, 1H), 7.65 (d, J = 2.4 Hz, 1H), 7.61 (s,

1H), 3.90 (s, 3H), 2.79 (s, 3H).

d₆): δ ppm 11.53 (br s, 1H), 8.09−8.14 (m, 3H), 8.01 (s, 1H), 7.85−

7.88 (m, 2H), 7.61−7.68 (m, 2H), 7.44 (d, J = 8.8 Hz, 1H), 7.39 (dd,

J = 8.3, 2.0 Hz, 1H), 3.87 (s, 3H).

3-Iodo-4-methyl-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridine (S15). 3-Iodo-4-methyl-5-(1-methyl-1H-pyra-

zol-4-yl)-1H-pyrrolo[2,3-b]pyridine S14 (101 mg, 0.299 mmol) was

suspended in DCM (1.6 mL, 0.19 M) and TEA (0.150 mL, 1.08

mmol), DMAP (46 mg, 0.377 mmol), and 4-methylbenzenesulfonyl

chloride (142 mg, 0.745 mmol) were added in that order. The

reaction mixture was stirred overnight at room temperature. The

reaction mixture was washed once with 1 M HCl, once with sat. aq.

NaHCO₃, and once with brine. The organic layer was dried with

sodium sulfate and concentrated under reduced pressure. The crude

material was puriﬁed by ﬂash chromatography (20−100% EtOAc/

hexanes) to aﬀord the title compound as an orange solid (37 mg,

5-Bromo-3-iodo-4-methylpyridin-2-amine (S10). 5-Bromo-4-

methylpyridin-2-amine S9 (500 mg, 2.67 mmol) was dissolved in

acetic acid (3.3 mL, 0.82 M), and N-iodosuccinimide (666 mg, 2.96

mmol) was added, followed by the addition of TFA (41 μL, 0.535

mmol). The reaction mixture was stirred at 50 °C overnight. The

reaction solution was poured over ice water and neutralized with 28%

aqueous ammonia, upon which a light orange precipitate was

observed and collected by vacuum ﬁltration (washed with water) to

aﬀord the title compound as an orange solid (784 mg, 94%). LCMS

1

[M + H]⁺312.80 m/z (⁷⁹Br), 314.81 m/z (⁸¹Br); H NMR (500

MHz, DMSO-d₆): δ ppm 7.95 (s, 1H), 6.24 (br s, 2.48 (s, 3H)).

5-Bromo-4-methyl-3-((trimethylsilyl)ethynyl)pyridin-2-amine

(S11). 5-Bromo-3-iodopyridin-2-amine S10 (784 mg, 2.51 mmol),

copper iodide (26 mg, 0.137 mmol), and PdCl₂(PPh₃)₂(37 mg, 0.053

mmol) were combined in a round bottom ﬂask that was ﬁlled with

1

25%). LCMS [M + H]⁺492.90 m/z; H NMR (500 MHz, DMSO-

d₆): δ ppm 8.30 (s, 1H), 8.09 (s, 1H), 8.00 (d, J = 8.8 Hz, 2H), 7.95

(s, 1H), 7.64 (s, 1H), 7.43 (d, J = 8.3 Hz, 2H), 3.89 (s, 3H), 2.76 (s,

3H), 2.35 (s, 3H).

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3-(4-Methyl-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridin-3-yl)benzonitrile (S16). 3-Iodo-4-methyl-5-(1-methyl-

1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridine S15 (37 mg,

0.075 mmol), (3-cyanophenyl)boronic acid (15 mg, 0.102 mmol),

and PdCl₂(dppf)·CH₂Cl₂(7 mg, 0.009 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (0.40 mL, 0.21 M) and 2 M K₂CO₃(0.15 mL, 0.300

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (120 °C) for 5 min. The

reaction mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (50−100% EtOAc/hexanes) to aﬀord the

title compound as a light yellow solid (25 mg, 71%). LCMS [M + H]⁺

1H), 8.42 (d, J = 2.2 Hz, 1H), 8.13 (d, J = 1.5 Hz, 1H), 8.09 (s, 1H),

8.04 (dd, J = 8.1, 1.5 Hz, 1H), 7.86 (s, 1H), 7.71−7.75 (m, 1H), 7.68

(d, J = 7.3 Hz, 1H), 7.64 (s, 1H), 3.97 (s, 3H).

5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine (7). 5-

Bromo-1H-pyrrolo[2,3-b]pyridine 9 (686 mg, 3.48 mmol), 1-

methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole

(800 mg, 3.84 mmol), and PdCl₂(dppf)·CH₂Cl₂(147 mg, 0.180

mmol) were combined in a reaction vial that was ﬁlled with nitrogen

and evacuated three times. Dioxane (20 mL, 0.17 M) and 2 M K₂CO₃

(5.0 mL, 10.00 mmol) were added, and the reaction mixture was

degassed for 10 min. The reaction mixture was heated at 85 °C for ∼4

h. The reaction mixture was diluted with EtOAc, ﬁltered through

Celite, and concentrated under reduced pressure. The crude mixture

was puriﬁed by ﬂash chromatography (1−10% MeOH/DCM) to

aﬀord the title compound as an orange solid (640 mg, 93%). LCMS

1

468.03 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.34 (s, 1H),

8.03−8.09 (m, 3H), 7.98 (s, 1H), 7.95 (s, 1H), 7.90 (d, J = 8.8 Hz,

2H), 7.64−7.69 (m, 2H), 7.45 (d, J = 7.8 Hz, 2H), 3.88 (s, 3H), 2.36

(s, 3H), 2.18 (s, 3H).

1

[M + H]⁺199.01 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm

11.59 (br s, 1H), 8.45 (d, J = 1.95 Hz, 1H), 8.13 (s, 1H), 8.08 (d, J =

1.95 Hz, 1H), 7.88 (s, 1H), 7.44 (t, J = 2.93 Hz, 1H), 6.41 (dd, J =

3.42, 1.95 Hz, 1H), 3.87 (s, 3H).

3-(4-Methyl-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (5). The title compound was prepared

according to General Procedure D on a 25 mg scale using 3-(4-

methyl-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile S16. The reaction was run for 3 min, and the

crude material was puriﬁed by ﬂash chromatography (1−5% MeOH/

DCM), then repuriﬁed by ﬂash chromatography (50−100% EtOAc/

hexanes) to aﬀord the title compound as a beige solid (9 mg, 55%).

LCMS [M + H]⁺314.05 m/z; ¹H NMR (500 MHz, chloroform-d): δ

ppm 10.40 (br s, 1H), 8.32 (br s, 1H), 7.77 (s, 1H), 7.72 (d, J = 7.8

Hz, 1H), 7.65 (d, J = 7.8 Hz, 1H), 7.61 (s, 1H), 7.54 (t, J = 7.8 Hz,

1H), 7.48 (s, 1H), 7.32 (s, 1H), 4.01 (s, 3H), 2.32 (s, 3H).

5-Bromo-3-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-

b]pyridine (S17). 5-Bromo-3-iodo-1-tosyl-1H-pyrrolo[2,3-b]pyridine

15 (1502 mg, 0.318 mmol), (1-methyl-1H-pyrazol-4-yl)boronic acid

(43 mg, 0.341 mmol), and PdCl₂(dppf)·CH₂Cl₂(27 mg, 0.033

mmol) were combined in a microwave vial that was purged with

nitrogen and evacuated three times. Dioxane (1.3 mL, 0.24 M) and 2

M K₂CO₃(0.50 mL, 1.00 mmol) were added, and the reaction

mixture was degassed for ∼10 min. The reaction was run in the

microwave (120 °C) for 15 min. The reaction mixture was diluted

with EtOAc, ﬁltered through Celite, and concentrated under reduced

pressure. The crude material was puriﬁed by ﬂash chromatography

(20−50% EtOAc/Hex) to aﬀord the title compound as a tan solid (41

mg, 30%). LCMS [M + H]⁺430.95 m/z (⁷⁹Br), 432.91 m/z (⁸¹Br);

¹H NMR (399 MHz, DMSO-d₆): δ ppm 8.55 (d, J = 2.9 Hz, 1H),

3-Iodo-1-tosyl-1H-pyrrolo[2,3-b]pyridine (S20). 3-Iodo-1H-

pyrrolo[2,3-b]pyridine S19 (250 mg, 1.002 mmol) was suspended

in DCM (10.0 mL, 0.10 M) and TEA (0.35 mL, 2.51 mmol), DMAP

(67 mg, 0.548 mmol) and 4-methylbenzenesulfonyl chloride (403 mg,

2.11 mmol) were added in that order. Upon the addition of 4-

methylbenzenesulfonyl chloride, the reaction mixture changed from a

cloudy suspension to a clear solution. The reaction mixture was

stirred overnight at room temperature. The reaction mixture was

washed once with 1 M HCl, once with saturated aqueous NaHCO₃,

and once with brine. The organic layer was dried with sodium sulfate

and concentrated under reduced pressure to aﬀord the title

compound as an orange solid (311 mg, 76%). LCMS [M + H]⁺

1

398.97 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.41 (dd, J =

4.9, 1.5 Hz, 1H), 8.15 (s, 1H), 8.02 (d, J = 8.3 Hz, 2H), 7.79 (dd, J =

7.8, 1.5 Hz, 1H), 7.42 (d, J = 8.3 Hz, 2H), 7.39 (dd, J = 7.8, 4.9 Hz,

1H), 2.34 (s, 3H).

3-(1-Tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (S21). 3-

Iodo-1-tosyl-1H-pyrrolo[2,3-b]pyridine S20 (150 mg, 0.377 mmol),

(3-cyanophenyl)boronic acid (140 mg, 0.953 mmol), and

PdCl₂(dppf)·CH₂Cl₂(31 mg, 0.037 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (1.5 mL, 0.25 M) and 2 M K₂CO₃(0.55 mL, 1.10

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (120 °C) for 30 min,

then diluted with EtOAc, ﬁltered through Celite, and concentrated

under reduced pressure. The crude residue was puriﬁed by ﬂash

chromatography (20−40% EtOAc/Hex) to aﬀord the title compound

as an oﬀ-white solid (67 mg, 48%). LCMS [M + H]⁺374.13 m/z; ¹H

NMR (500 MHz, DMSO-d₆): δ ppm 8.43−8.47 (m, 2H), 8.40 (dd, J

= 8.3, 1.5 Hz, 1H), 8.31 (s, 1H), 8.14 (d, J = 7.8 Hz, 1H), 8.06 (d, J =

8.8 Hz, 2H), 7.84 (d, J = 8.3 Hz, 1H), 7.69 (t, J = 7.8 Hz, 1H), 7.43

(d, J = 8.8 Hz, 2H), 7.38−7.42 (m, 1H), 2.34 (s, 3H).

3-(1H-Pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (8). The title com-

pound was prepared according to General Procedure D on a 67 mg

scale using 3-(1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile S21.

The reaction was run for 2 min, and the crude material was puriﬁed

by ﬂash chromatography (1−5% MeOH/DCM) to aﬀord the title

compound as a white solid (18 mg, 45%). LCMS [M + H]⁺220.03

m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 12.09 (br s, 1H), 8.38

(d, J = 8.3 Hz, 1H), 8.30 (dd, J = 4.6, 1.2 Hz, 1H), 8.16−8.20 (m,

1H), 8.06−8.13 (m, 2H), 7.67−7.72 (m, 1H), 7.63 (t, J = 7.8 Hz,

1H), 7.19 (dd, J = 8.1, 4.6 Hz, 1H).

8.48−8.53 (m, 1H), 8.41 (s, 1H), 8.24 (s, 1H), 8.05 (s, 1H), 7.94−

8.01 (m, 2H), 7.38−7.46 (m, 2H), 3.88 (br s, 3H), 2.33 (br s, 3H).

3-(3-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-5-yl)benzonitrile (S18). 5-Bromo-3-(1-methyl-1H-pyrazol-4-

yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridine S17 (41 mg, 0.095 mmol), (3-

cyanophenyl)boronic acid (24 mg, 0.163 mmol), and PdCl₂(dppf)·

CH₂Cl₂(9 mg, 0.011 mmol) were combined in a reaction vial that

was ﬁlled with nitrogen and evacuated three times. Dioxane (0.6 mL,

0.17 M) and 2 M K₂CO₃(0.20 mL, 0.400 mmol) were added, and the

reaction mixture was degassed for 10 min. The reaction was run in the

microwave (145 °C) for 5 min. The reaction mixture was diluted with

EtOAc, ﬁltered through Celite, and concentrated under reduced

pressure. The crude material was puriﬁed by ﬂash chromatography

(50−100% EtOAc/Hex) to aﬀord the title compound as a white solid

1

(19 mg, 44%). LCMS [M + H]⁺454.03 m/z; H NMR (399 MHz,

DMSO-d₆): δ ppm 8.77 (d, J = 2.2 Hz, 1H), 8.54 (d, J = 2.2 Hz, 1H),

8.46 (s, 1H), 8.35 (s, 1H), 8.23 (s, 1H), 8.17 (d, J = 7.3 Hz, 1H), 8.12

(s, 1H), 8.02 (d, J = 8.1 Hz, 2H), 7.89 (d, J = 7.3 Hz, 1H), 7.71 (t, J =

8.1 Hz, 1H), 7.43 (d, J = 8.1 Hz, 2H), 3.91 (s, 3H), 2.34 (s, 3H).

3-(3-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl)-

benzonitrile (6). The title compound was prepared according to

General Procedure D on a 19 mg scale using 3-(3-(1-methyl-1H-

pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-5-yl)benzonitrile S18.

The reaction was run for 2 min, and the crude material was puriﬁed

by ﬂash chromatography (1−5% MeOH/DCM) to aﬀord the title

compound as a white solid (4 mg, 28%). LCMS [M + H]⁺300.12 m/

3-Iodo-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine

(10). Intermediate 7 (640 mg, 3.23 mmol) was dissolved in

acetonitrile (18 mL, 0.18 M), and N-iodosuccinimide (1.09 g, 4.84

mmol) was added. The reaction mixture was stirred at 50 °C for 2 h.

Upon cooling to room temperature, a precipitate was observed and

collected by vacuum ﬁltration (washed with acetonitrile) to aﬀord the

title compound as a light brown solid (730 mg, 69%). LCMS [M +

H]⁺324.98 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 12.06 (br s,

1

z; H NMR (399 MHz, methanol-d₄): δ ppm 8.51 (d, J = 1.5 Hz,

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1H), 8.51 (d, J = 1.95 Hz, 1H), 8.25 (s, 1H), 7.96 (s, 1H), 7.76 (d, J =

2.44 Hz, 1H), 7.69 (d, J = 2.44 Hz, 1H), 3.88 (s, 3H).

2-Fluoro-5-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile (12f). The title compound was prepared

according to General Procedure A on a 74 mg scale using 2-ﬂuoro-5-

(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzonitrile. The crude

material was puriﬁed by ﬂash chromatography (50−100% EtOAc/

hexanes) to aﬀord the title compound as an oﬀ-white solid (48 mg,

3-Iodo-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridine (11). Intermediate 10 (730 mg, 2.25 mmol) was suspended

in DCM (37 mL, 0.06 M) and TEA (1.5 mL, 10.76 mmol), DMAP

(227 mg, 1.86 mmol) and 4-methylbenzenesulfonyl chloride (1.06 g,

5.56 mmol) were added in that order. The reaction mixture was

stirred overnight at room temperature. The reaction mixture was

washed once with 1 M HCl, once with sat. aq. NaHCO₃, and once

with brine. The organic layer was dried with sodium sulfate and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (0−100% EtOAc/Hex0−10% MeOH/

DCM) to aﬀord the title compound as a light orange solid (741 mg,

1

66%). LCMS [M + H]⁺472.07 m/z; H NMR (500 MHz, DMSO-

d₆): δ ppm 8.69 (d, J = 1.95 Hz, 1H), 8.43 (dd, J = 6.35, 2.44 Hz,

1H), 8.41 (d, J = 1.95 Hz, 1H), 8.39 (s, 1H), 8.30 (s, 1H), 8.26 (m, J

= 2.40, 2.40, 2.40, 2.40, 2.40, 2.40 Hz, 1H), 8.03−8.07 (m, 3H), 7.65

(t, J = 9.03 Hz, 1H), 7.44 (d, J = 8.30 Hz, 2H), 3.88 (s, 3H), 2.34 (s,

3H).

3-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)aniline (12g). Intermediate 11 (40 mg, 0.083 mmol), (3-

aminophenyl)boronic acid (34 mg, 0.251 mmol), and PdCl₂(dppf)·

CH₂Cl₂(6 mg, 0.007 mmol) were combined in an 8 mL vial. The vial

was purged with nitrogen and evacuated three times. Dioxane (0.8

mL, 0.1 M) and 2 M aqueous K₂CO₃(0.2 mL, 0.4 mmol) were

added, and the reaction mixture was degassed for 10 min. The

reaction was run at 100 °C for 4 h, then stopped, diluted with EtOAc,

and ﬁltered through Celite. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/hexanes, step gradient) to aﬀord

the title compound as a solid (5 mg, 14%). LCMS [M + H]⁺290.16

1

69%). LCMS [M + H]⁺478.95 m/z; H NMR (500 MHz, DMSO-

d₆): δ ppm 8.66 (d, J = 1.95 Hz, 1H), 8.33 (s, 1H), 8.12 (s, 1H),

7.98−8.04 (m, 3H), 7.85 (d, J = 2.44 Hz, 1H), 7.43 (d, J = 8.79 Hz,

2H), 3.87 (s, 3H), 2.34 (s, 3H).

2-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (12a). The title compound was prepared

according to General Procedure A on a 75 mg scale using 2-

(cyanophenyl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/hexanes) to aﬀord the title

compound as a light orange solid (48 mg, 68%). LCMS [M + H]⁺

1

m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.66 (d, J = 2.0 Hz,

454.03 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.72 (d, J =

1H), 8.29 (d, J = 2.0 Hz, 1H), 8.27 (s, 1H), 8.03 (d, J = 8.8 Hz, 2H),

8.00 (s, 2H), 7.43 (d, J = 8.3 Hz, 2H), 7.14 (t, J = 7.8 Hz, 1H), 6.96−

6.98 (m, 1H), 6.89−6.93 (m, 1H), 6.59 (dd, J = 8.1, 2.2 Hz, 1H),

5.18−5.23 (m, 2H), 3.87 (s, 3H), 2.34 (s, 3H).

1.95 Hz, 1H), 8.29 (s, 1H), 8.27 (s, 1H), 8.16 (d, J = 1.95 Hz, 1H),

8.01−8.07 (m, 3H), 7.98 (s, 1H), 7.85 (d, J = 3.91 Hz, 2H), 7.64 (m,

J = 8.30, 4.20, 4.20 Hz, 1H), 7.45 (d, J = 7.81 Hz, 2H), 3.85 (s, 3H),

2.35 (s, 3H).

1-(4-Bromophenyl)-N,N-dimethylmethanamine (S23). 1-Bromo-

4-(bromomethyl)benzene S22 (499 mg 2.00 mmol) was suspended in

hexane (2.0 mL, 1.0 M), and the reaction mixture was cooled to 0 °C.

Then, 2 M dimethylamine in THF (4.00 mL, 8.00 mmol) was added

dropwise. The reaction mixture was left stirring overnight and allowed

to warm to room temperature. A precipitate was observed and

removed by ﬁltration; the ﬁltrate was concentrated to aﬀord the title

compound as an orange oil (350 mg, 82%). LCMS [M + H]⁺213.93

3-(4-Fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridine (12b). The title compound was prepared

according to General Procedure A on a 65 mg scale using (4-

ﬂuorophenyl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/hexanes) to aﬀord the title

compound as a light orange solid (42 mg, 69%). LCMS [M + H]⁺

1

447.02 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.68 (d, J =

1.95 Hz, 1H), 8.33 (d, J = 1.95 Hz, 1H), 8.30 (s, 1H), 8.19 (s, 1H),

8.04 (d, J = 8.30 Hz, 2H), 8.02 (s, 1H), 7.84−7.90 (m, 2H), 7.43 (d, J

= 7.81 Hz, 2H), 7.30−7.36 (m, 2H), 3.87 (s, 3H), 2.34 (s, 3H).

3-(3,4-Diﬂuorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridine (12c). The title compound was prepared

according to General Procedure A on a 69 mg scale using (3,4-

diﬂuorophenyl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/hexanes) to aﬀord the title

compound as a light orange solid (42 mg, 62%). LCMS [M + H]⁺

1

m/z (⁷⁹Br), 215.93 m/z (⁸¹Br); H NMR (500 MHz, DMSO-d₆): δ

ppm 7.50 (d, J = 8.30 Hz, 2H), 7.24 (d, J = 8.30 Hz, 2H), 3.34 (s,

2H), 2.12 (s, 6H).

N,N-Dimethyl-1-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-

yl)phenyl)methanamine (S24). The title compound was prepared

according to General Procedure E on a 350 mg scale using 1-(4-

bromophenyl)-N,N-dimethylmethanamine S23. The crude material

was puriﬁed by ﬂash chromatography (5−20% 5% NH₄OH/

MeOH:DCM) to aﬀord the title compound as a brown oil (176

mg, 41%). LCMS [M + H]⁺262.22 m/z; ¹H NMR (500 MHz,

DMSO-d₆): δ ppm 7.62 (d, J = 8.30 Hz, 2H), 7.30 (d, J = 8.30 Hz,

2H), 3.39 (s, 2H), 2.12 (s, 6H), 1.28 (s, 12H).

N,N-Dimethyl-1-(4-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl) phenyl)methanamine (12h). The title

compound was prepared according to General Procedure A on a 150

mg scale using N,N-dimethyl-1-(4-(4,4,5,5-tetramethyl-1,3,2-dioxa-

borolan-2-yl)phenyl)methanamine S24. The crude material was

puriﬁed by ﬂash chromatography (50−100% EtOAc/Hex0−20%

MeOH/EtOAc0−10% 5% NH₄OH/MeOH:DCM) to aﬀord the

title compound as a glassy brown solid (36 mg, 24%). LCMS [M +

H]⁺486.23 m/z; ¹H NMR (500 MHz, methanol-d₄): δ ppm 8.59 (d, J

= 1.95 Hz, 1H), 8.29 (d, J = 1.95 Hz, 1H), 8.07 (s, 1H), 8.05 (d, J =

8.30 Hz, 2H), 8.02 (s, 1H), 7.90 (s, 1H), 7.70 (d, J = 8.30 Hz, 2H),

7.48 (d, J = 8.30 Hz, 2H), 7.36 (d, J = 8.79 Hz, 2H), 3.94 (s, 3H),

3.58 (s, 2H), 2.37 (s, 3H), 2.32 (s, 6H).

5-(1-Methyl-1H-pyrazol-4-yl)-3-(3-nitrophenyl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridine (12i). Intermediate 3−4 (38 mg, 0.08 mmol),

(3-nitrophenyl)boronic acid (40 mg, 0.238 mmol), and PdCl₂(dppf)·

CH₂Cl₂(6 mg, 0.007 mmol) were combined in a 8 mL vial. The vial

was purged with nitrogen and evacuated three times. Dioxane (0.8

mL, 0.1 M) and 2 M aqueous K₂CO₃(0.2 mL, 0.4 mmol) were

added, and the reaction mixture was degassed for 10 min. The

reaction was run at 100 °C for 4 h, then stopped, diluted with EtOAc,

and ﬁltered through Celite. The crude material was puriﬁed by ﬂash

1

465.05 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.69 (d, J =

1.95 Hz, 1H), 8.37 (d, J = 1.95 Hz, 1H), 8.32 (s, 1H), 8.30 (s, 1H),

8.02−8.07 (m, 3H), 7.96 (qd, J = 8.80, 2.00 Hz, 1H), 7.68−7.73 (m,

1H), 7.51−7.59 (m, 1H), 7.44 (d, J = 8.30 Hz, 2H), 3.88 (s, 3H),

2.35 (s, 3H).

3-(2-Fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridine (12d). The title compound was prepared

according to General Procedure A on a 75 mg scale using (2-

ﬂuorophenyl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/hexanes) to aﬀord the title

compound as an oﬀ-white solid (55 mg, 78%). LCMS [M + H]⁺

1

447.08 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.70 (d, J =

1.95 Hz, 1H), 8.28 (s, 1H), 8.16 (t, J = 1.95 Hz, 1H), 8.11 (s, 1H),

8.06 (d, J = 8.30 Hz, 2H), 7.99 (s, 1H), 7.80 (td, J = 7.69, 1.71 Hz,

1H), 7.46−7.52 (m, 1H), 7.45 (d, J = 8.30 Hz, 2H), 7.34−7.43 (m,

2H), 3.86 (s, 3H), 2.35 (s, 3H).

3-Fluoro-5-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile (12e). The title compound was prepared

according to General Procedure A on a 75 mg scale using (3-cyano-5-

ﬂuorophenyl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/hexanes) to aﬀord the title

compound as an oﬀ-white solid (44 mg, 60%). LCMS [M + H]⁺

1

472.06 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.71 (d, J =

1.95 Hz, 1H), 8.49 (s, 1H), 8.45 (d, J = 2.44 Hz, 1H), 8.32 (s, 1H),

8.23 (s, 1H), 8.12 (d, J = 9.77 Hz, 1H), 8.04−8.08 (m, 3H), 7.87 (d, J

= 8.30 Hz, 1H), 7.44 (d, J = 8.79 Hz, 2H), 3.88 (s, 3H), 2.35 (s, 3H).

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chromatography (30−80% EtOAc/hexanes, step gradient) to aﬀord

1H), 8.08 (s, 1H), 8.06 (d, J = 8.30 Hz, 2H), 7.45 (d, J = 8.30 Hz,

2H), 3.89 (s, 3H), 2.35 (s, 3H).

the title compound as a solid (30 mg, 80%). LCMS [M + H]⁺320.12

1

m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.71 (d, J = 2.0 Hz,

5-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methylpyridin-4-yl)-1-tosyl-

1H-pyrrolo[2,3-b]pyridine (12p). The title compound was prepared

according to General Procedure A on a 75 mg scale using (2-

methylpyridin-4-yl)boronic acid. The crude material was puriﬁed by

ﬂash chromatography (3% MeOH/DCM) to aﬀord the title

compound as a dark orange solid (47 mg, 68%). LCMS [M + H]⁺

1H), 8.60 (t, J = 2.4 Hz, 1H), 8.48 (s, 1H), 8.41 (d, J = 2.0 Hz, 1H),

8.28−8.32 (m, 2H), 8.24 (dd, J = 8.3, 1.5 Hz, 1H), 8.08 (d, J = 8.8

Hz, 2H), 8.02 (s, 1H), 7.80 (t, J = 7.8 Hz, 1H), 7.45 (d, J = 8.3 Hz,

2H), 3.87 (s, 3H), 2.35 (s, 3H).

4-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)phenol (12j). The title compound was prepared

according to General Procedure A on a 100 mg scale using (4-

hydroxyphenyl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/Hex) to aﬀord the title

compound as a tan solid (49 mg, 52%). LCMS [M + H]⁺445.13

1

444.16 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.70 (d, J =

1.95 Hz, 1H), 8.52 (d, J = 5.37 Hz, 1H), 8.46 (s, 1H), 8.45 (d, J =

1.95 Hz, 1H), 8.33 (s, 1H), 8.03−8.08 (m, 3H), 7.74 (s, 1H), 7.68 (d,

J = 5.86 Hz, 1H), 7.44 (d, J = 8.79 Hz, 2H), 3.88 (s, 3H), 2.56 (s,

3H), 2.35 (s, 3H).

2,6-Dimethyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-

pyridine (S28). The title compound was prepared according to

General Procedure E on a 150 mg scale using 4-bromo-2,6-

dimethylpyridine S28. The dark brown crude material was carried

forward without further puriﬁcation. LCMS [M + H]⁺151.78 m/z

(boronic acid).

1

m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 9.62 (br s, 1H), 8.65

(d, J = 1.95 Hz, 1H), 8.30 (s, 1H), 8.28 (d, J = 1.46 Hz, 1H), 7.98−

8.04 (m, 4H), 7.61 (d, J = 8.30 Hz, 2H), 7.42 (d, J = 8.30 Hz, 2H),

6.89 (d, J = 8.30 Hz, 2H), 3.87 (s, 3H), 2.34 (s, 3H).

5-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)benzo[c][1,2,5]-

oxadiazole (S26). The title compound was prepared according to

General Procedure E on a 100 mg scale using 5-chlorobenzo[c]-

[1,2,5]oxadiazole S25. The dark brown crude material was carried

forward without further puriﬁcation. *Does not ionize.

3-(2,6-Dimethylpyridin-4-yl)-5-(1-methyl-1H-pyrazol-4-yl)-1-

tosyl-1H-pyrrolo[2,3-b]pyridine (12q). The title compound was

prepared according to General Procedure A on a 75 mg scale using

crude 2,6-dimethyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-

pyridine S28. The crude material was puriﬁed by ﬂash chromatog-

raphy (5% MeOH/DCM), then repuriﬁed by ﬂash chromatography

(10−100% EtOAc/DCM) to aﬀord the title compound as a tan solid

5-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzo[c][1,2,5]oxadiazole (12k). The title compound

was prepared according to General Procedure A on a 151 mg scale

using 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzo[c][1,2,5]-

oxadiazole S26. The crude material was puriﬁed by ﬂash

chromatography (20−60% EtOAc/hexanes) to aﬀord the title

compound as a white solid (109 mg, 73%). LCMS [M + H]⁺

1

(43 mg, 60%). LCMS [M + H]⁺458.14 m/z; H NMR (500 MHz,

DMSO-d₆): δ ppm 8.69 (d, J = 1.95 Hz, 1H), 8.42 (d, J = 1.46 Hz,

1H), 8.41 (s, 1H), 8.32 (s, 1H), 8.05 (m, J = 3.90, 3.90 Hz, 3H), 7.52

(s, 2H), 7.44 (d, J = 8.30 Hz, 2H), 3.88 (s, 3H), 2.51 (s, 6H), 2.35 (s,

3H).

1

471.02 m/z; H NMR (399 MHz, DMSO-d₆): δ ppm 8.74 (d, J =

2.20 Hz, 1H), 8.63 (s, 1H), 8.61 (d, J = 2.20 Hz, 1H), 8.53 (s, 1H),

8.38 (s, 1H), 8.21 (dd, J = 9.53, 1.47 Hz, 1H), 8.17 (d, J = 8.79 Hz,

1H), 8.06−8.12 (m, 3H), 7.45 (d, J = 8.79 Hz, 2H), 3.89 (s, 3H),

2.35 (s, 3H).

2-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile (13a). The title compound was prepared according to

General Procedure D on a 48 mg scale using 12a. The reaction was

run for 5 min, and the crude material was puriﬁed by ﬂash

chromatography (1−5% MeOH/DCM) and then by prep HPLC

(70−5% water/ACN) to aﬀord the title compound as a formate salt.

The resulting solid was dissolved in MeOH, and MP-carbonate was

added. The suspension was stirred overnight at room temperature,

then the solids were removed by ﬁltration, and the ﬁltrate was

concentrated to aﬀord the title compound as a white solid (9 mg,

28%). LCMS [M + H]⁺300.06 m/z; ¹H NMR (399 MHz, methanol-

d₄): δ ppm 8.51 (d, J = 2.20 Hz, 1H), 8.22 (d, J = 2.20 Hz, 1H), 8.02

(s, 1H), 7.84−7.89 (m, 2H), 7.75−7.83 (m, 3H), 7.49 (td, J = 8.06,

1.47 Hz, 1H), 3.94 (s, 3H).

3-(1H-Indol-5-yl)-5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridine (12l). The title compound was prepared

according to General Procedure A on a 76 mg scale using (1H-indol-

5-yl)boronic acid. The crude material was puriﬁed by ﬂash

chromatography (20−100% EtOAc/hexanes) to aﬀord the title

compound as a glassy orange solid (41 mg, 55%). LCMS [M +

H]⁺468.007 m/z; ¹H NMR (399 MHz, DMSO-d₆): δ ppm 11.21 (br

s, 1H), 8.67 (d, J = 1.47 Hz, 1H), 8.34 (d, J = 2.20 Hz, 1H), 8.30 (s,

1H), 8.05 (d, J = 8.79 Hz, 2H), 8.02 (s, 1H), 8.01 (s, 1H), 7.95 (s,

1H), 7.46−7.56 (m, 2H), 7.39−7.45 (m, 3H), 6.52 (br s, 1H), 3.87

(s, 3H), 2.34 (s, 3H).

4-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile (13b). Intermediate 11 (90 mg, 0.188 mmol), (4-

cyanophenyl)boronic acid (83 mg, 0.565 mmol), and PdCl₂(dppf)·

CH₂Cl₂were combined in a microwave vial, which was then purged

with nitrogen and evacuated three times. Dioxane (1.9 mL, 0.1 M)

and K₂CO₃(0.565 mL, 1.1 mmol) were added, and the reaction

mixture was then degassed for 10 min. The reaction was then run in

the microwave for 30 min at 120 °C. Then, 2 M aqueous NaOH (0.3

mL, 0.6 mmol) was then added to the ﬂask, and the solution was

microwaved for 1.5 min at 150 °C. Additional 2 M NaOH (0.1 mL,

0.2 mmol) was then added, and the reaction mixture was microwaved

for another 2.5 min at 150 °C. The crude product was then diluted

with EtOAc and ﬁltered through Celite using EtOAc to wash. The

ﬁltrate was puriﬁed by ﬂash chromatography (50−100% EtOAc/

hexanes) to aﬀord the title compound as a solid (36 mg, 64%). LCMS

5-(1-Methyl-1H-pyrazol-4-yl)-3-(pyridin-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridine (12m). The title compound was prepared according

to General Procedure A using 4-(4,4,5,5-tetramethyl-1,3,2-dioxabor-

olan-2-yl)pyridine. The crude material was carried forward without

further puriﬁcation. LCMS [M + H]⁺430.11 m/z.

5-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)nicotinonitrile (12n). The title compound was prepared

according to General Procedure A on a 75 mg scale using (5-

cyanopyridin-3-yl)boronic acid. The crude material was puriﬁed by

ﬂash chromatography (50−100% EtOAc/hexanes) to aﬀord the title

compound as a light orange solid (60 mg, 85%). LCMS [M + H]⁺

455.05 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 9.36 (t, J = 2.20

Hz, 1H), 9.03 (t, J = 1.95 Hz, 1H), 8.81 (q, J = 2.28 Hz, 1H), 8.72 (t,

J = 1.95 Hz, 1H), 8.55 (d, J = 1.95 Hz, 1H), 8.50 (t, J = 1.95 Hz, 1H),

8.33 (d, J = 0.98 Hz, 1H), 8.04−8.08 (m, 3H), 7.44 (d, J = 8.30 Hz,

2H), 3.88 (s, 3H), 2.35 (s, 3H).

1

[M + H]⁺300.12 m/z, H NMR (500 MHz, methanol-d₄): δ ppm

4-(5-(1-Methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)picolinonitrile (12o). The title compound was prepared

according to General Procedure A on a 100 mg scale using crude (2-

cyanopyridin-4-yl)boronic acid 5−26. The crude material was puriﬁed

by ﬂash chromatography (50−100% EtOAc/hexanes) to aﬀord the

title compound as a light yellow solid (34 mg, 36%). LCMS [M + H]⁺

455.12 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.80 (d, J =

5.37 Hz, 1H), 8.74 (s, 1H), 8.73 (d, J = 1.95 Hz, 1H), 8.61 (s, 1H),

8.57 (d, J = 1.95 Hz, 1H), 8.33 (s, 1H), 8.27 (dd, J = 5.86, 1.95 Hz,

8.51 (d, J = 2.0 Hz, 1H), 8.46 (d, J = 2.0 Hz, 1H), 8.08 (s, 1H), 7.94

(d, J = 5.4 Hz, 2H), 7.93 (s, 1H), 7.87 (s, 1H), 7.80 (d, J = 8.3 Hz,

2H), 3.96 (s, 3H). *The −NH peak is too rapidly exchanging to be

seen in the H NMR.

5-(1-methyl-1H-pyrazol-4-yl)-3-phenyl-1H-pyrrolo[2,3-b]-

pyridine (13c). In a microwave tube, 10 (37.3 mg, 0.115 mmol) was

added, followed by phenylboronic acid (41.5 mg, 0.340 mmol) and

PdCl₂(dppf)·CH₂Cl₂(12.70 mg, 0.016 mmol). The tube was sealed

and purged with nitrogen three times. 1,4-Dioxane (0.115 mL, 1 M)

1

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and a 2 M solution of potassium carbonate (0.517 mL, 1.035 mmol)

were then added, and the reaction mixture was degassed and run in

the microwave for 30 min at 120 °C. The reaction mixture was then

concentrated, and EtOAc was added. This solution was then washed

with water, followed by brine, and the organic layer was dried over

sodium sulfate and concentrated. The crude product was puriﬁed by

reverse phase chromatography (30−70% ACN/water gradient) to

aﬀord the title compound as a white solid (5 mg, 16%). LCMS [M +

H]⁺275.1; ¹H NMR (399 MHz, chloroform-d): δ ppm 3.99 (s, 3H),

7.30−7.38 (m, 1H), 7.45−7.55 (m, 3H), 7.63−7.71 (m, 3H), 7.82 (s,

1H), 8.28 (s, 1H), 8.52 (s, 1H), 9.49 (br s, 1H).

3-(4-Chlorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridine (13d). In a microwave tube, 10 (25 mg, 0.077 mmol)

was added, followed by (4-chlorophenyl)boronic acid (35.6 mg, 0.228

mmol) and PdCl₂(dppf)·CH₂Cl₂(8.51 mg, 10.42 μmol). The tube

was sealed and purged with nitrogen three times. 1,4-Dioxane (77 μL,

1 M) and a 2 M solution of potassium carbonate (0.347 mL, 0.695

mmol) were then added, and the reaction mixture was degassed and

run in the microwave for 30 min at 120 °C. The reaction mixture was

then concentrated, and EtOAc was added. This solution was then

washed with water, followed by brine, and the organic layer was dried

over sodium sulfate and concentrated. The crude product was puriﬁed

by reverse phase chromatography (30−70% ACN/water gradient) to

aﬀord the title compound as a white solid (10 mg, 42%). LCMS [M +

H]⁺309.1; ¹H NMR (399 MHz, chloroform-d): δ ppm 4.00 (s, 3H),

7.43−7.48 (m, 2H), 7.50 (d, J = 1.5 Hz, 1H), 7.56−7.61 (m, 2H),

7.68 (s, 1H), 7.82 (s, 1H), 8.21 (d, J = 1.5 Hz, 1H), 8.52 (s, 1H), 9.17

(br s, 1H).

3-(3,4-Dichlorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridine (13e). In a microwave tube, 10 (25 mg, 0.090 mmol)

was added, followed by (3,4-dichlorophenyl)boronic acid (19.7 mg,

0.103 mmol) and PdCl₂(dppf)·CH₂Cl₂(7.51 mg, 9.2 μmol). The

tube was sealed and purged with nitrogen three times. Tetrahy-

drofuran (0.626 mL, 0.144 M) and a 2 M solution of potassium

carbonate (0.313 mL, 0.625 mmol, 6.93 equiv) were then added, and

the reaction mixture was degassed and ran in the microwave for 30

min at 120 °C. The reaction mixture was then concentrated, and

EtOAc was added. This solution was then washed with water,

followed by brine, and the organic layer was dried over sodium sulfate

and concentrated. The crude product was puriﬁed by reverse phase

chromatography (20−95% ACN/water gradient) to aﬀord the title

compound as a white solid (3.2 mg, 10%). LCMS [M + H]⁺343.0;

¹H NMR (399 MHz, chloroform-d): δ ppm 4.01 (d, J = 1.47 Hz, 3H),

EtOAc was added. This solution was then washed with water,

followed by brine, and the organic layer was dried over sodium sulfate

and concentrated. The crude product was puriﬁed by reverse phase

chromatography (30−70% ACN/water gradient) to aﬀord the title

compound as a white solid (6.4 mg, 32%). LCMS [M + H]⁺305.2;

¹H NMR (399 MHz, chloroform-d): δ ppm 3.89 (s, 3H), 3.99 (s,

3H), 7.05 (d, J = 8.8 Hz, 2H), 7.44 (s, 1H), 7.58 (d, J = 8.1 Hz, 2H),

7.68 (s, 1H), 7.81 (s, 1H), 8.25 (s, 1H), 8.49 (br s, 1H), 9. 17 (br s,

1H).

3-(3-Methoxyphenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridine (13h). In a microwave tube, 10 (30 mg, 0.108 mmol)

was added, followed by (3-methoxyphenyl)boronic acid (28.1 mg,

0.185 mmol) and PdCl₂(dppf)·CH₂Cl₂(9.02 mg, 0.011 mmol). The

tube was sealed and purged with nitrogen three times. 1,4-Dioxane

(0.752 mL, 0.144 M) and a 2 M solution of potassium carbonate

(0.376 mL, 0.753 mmol) were then added, and the reaction mixture

was degassed and ran in the microwave for 30 min at 120 °C. The

reaction mixture was then concentrated, and EtOAc was added. This

solution was then washed with water, followed by brine, and the

organic layer was dried over sodium sulfate and concentrated. The

crude product was puriﬁed by reverse phase chromatography (20−

95% ACN/water gradient) to the title compound as a white solid (4.6

mg, 14%). LCMS [M + H]⁺305.1; ¹H NMR (399 MHz, chloroform-

d): δ ppm 3.87−3.95 (m, 3H), 3.96−4.03 (m, 3H), 6.90 (d, J = 8.8

Hz, 1H), 7.19 (d, J = 1.5 Hz, 1H), 7.25 (s, 1H), 7.42 (t, J = 8.1 Hz,

1H), 7.53 (s, 1H), 7.68 (s, 1H), 7.81 (s, 1H), 8.30 (s, 1H), 8.50 (s,

1H), 9.60 (br s, 1H).

5-(1-Methyl-1H-pyrazol-4-yl)-3-(4-(triﬂuoromethyl)phenyl)-1H-

pyrrolo[2,3-b]pyridine (13i). In a microwave tube, 10 (25.3 mg, 0.091

mmol) was added, followed by (3-triﬂuoromethylphenyl)boronic acid

(20 mg, 0.105 mmol) and PdCl₂(dppf)·CH₂Cl₂(8.9 mg, 10.9 μmol).

The tube was sealed and purged with nitrogen three times. 1,4-

Dioxane (0.634 mL, 0.144 M) and a 2 M solution of potassium

carbonate (0.313 mL, 0.626 mmol) were then added, and the reaction

mixture was degassed and ran in the microwave for 30 min at 120 °C.

The reaction mixture was then concentrated, and EtOAc was added.

This solution was then washed with water, followed by brine, and the

organic layer was dried over sodium sulfate and concentrated. The

crude product was puriﬁed by reverse phase chromatography (20−

90% ACN/water gradient) to aﬀord the title compound as a white

1

solid (4.9 mg, 15.7% yield). LCMS [M + H]⁺343.1; H NMR (399

MHz, chloroform-d): δ ppm 4.01 (s, 3H), 7.56−7.64 (m, 3H), 7.69

(br s, 1H), 7.81−7.86 (m, 2H), 7.88 (s, 1H), 8.25 (s, 1H), 8.52−8.63

(m, 1H), 9.50−9.63 (m, 1H).

7.45−7.50 (m, 1H), 7.53−7.59 (m, 2H), 7.71 (d, J = 5.86 Hz, 2H),

7.82 (s, 1H), 8.19 (s, 1H), 8.28 (s, 1H), 8.46 (br s, 1H).

3-(3-Fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-

b]pyridine (13j). In a microwave tube, 10 (60 mg, 0.217 mmol) was

added, followed by (3-ﬂuoromethylphenyl)boronic acid (33 mg,

0.236 mmol) and PdCl₂(dppf)·CH₂Cl₂(18 mg, 0.022 mmol). The

tube was sealed and purged with nitrogen three times. 1,4-Dioxane

(1.504 mL, 0.144 M) and a 2 M solution of potassium carbonate

(0.750 mL, 1.5 mmol) were then added, and the reaction mixture was

degassed and ran in the microwave for 30 min at 120 °C. The reaction

mixture was then concentrated, and EtOAc was added. This solution

was then washed with water, followed by brine, and the organic layer

was dried over sodium sulfate and concentrated. The crude product

was puriﬁed by reverse phase chromatography (30−70% ACN/water

gradient) to aﬀord the title compound as a white solid (5.4 mg, 8.5%

5-(1-Methyl-1H-pyrazol-4-yl)-3-(p-tolyl)-1H-pyrrolo[2,3-b]-

pyridine (13f). In a microwave tube, 10 (70 mg, 0.253 mmol) was

added followed by p-tolylboronic acid (37 mg, 0.275 mmol) and

PdCl₂(dppf)·CH₂Cl₂(21 mg, 0.026 mmol). The tube was sealed and

purged with nitrogen three times. 1,4-Dioxane (1.754 mL, 0.144 M)

and a 2 M solution of potassium carbonate (0.875 mL, 1.750 mmol)

were then added, and the reaction mixture was degassed and ran in

the microwave for 30 min at 120 °C. The reaction mixture was then

concentrated, and EtOAc was added. This solution was then washed

with water, followed by brine, and the organic layer was dried over

sodium sulfate and concentrated. The crude product was puriﬁed by

reverse phase chromatography (30−70% ACN/water gradient) to

aﬀord the title compound as a white solid (5.1 mg, 7%). LCMS [M +

H]⁺289.0; ¹H NMR (399 MHz, chloroform-d, D₂O): δ ppm 2.36 (s,

3H), 3.93 (s, 3H), 7.24 (d, J = 8.1 Hz, 2H), 7.43 (s, 1H), 7.48 (d, J =

8.1 Hz, 2H), 7.61 (s, 1H), 7.74 (s, 1H), 8.23 (s, 1H), 8.41 (br s, 1H).

3-(4-Methoxyphenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridine (13g). In a microwave tube, 10 (21.30 mg, 0.066

mmol) was added, followed by (4-methoxyphenyl)boronic acid (28.5

mg, 0.188 mmol, 2.85 equiv) and PdCl₂(dppf)·CH₂Cl₂(8 mg, 9.8

μmol, 0.149 equiv). The tube was sealed and purged with nitrogen

three times. 1,4-Dioxane (65.7 μL, 1 M) and a 2 M solution of

potassium carbonate (0.284 mL, 0.567 mmol) were then added, and

the reaction mixture was degassed and ran in the microwave for 30

min at 120 °C. The reaction mixture was then concentrated, and

1

yield). LCMS [M + H]⁺293.0; H NMR (399 MHz, chloroform-d):

δ ppm 4.01 (s, 3H), 7.05 (t, J = 7.7 Hz, 1H), 7.34 (d, J = 10.3 Hz,

1H), 7.41−7.48 (m, 2H), 7.58 (s, 1H), 7.71 (br s, 1H), 7.83 (s, 1H),

8.33 (s, 1H), 8.62 (br s, 1H), 9.97−10.24 (m, 1H).

3-(4-Fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-

b]pyridine (13k). The title compound was prepared according to

General Procedure D on a 42 mg scale using 12b. The reaction was

run for 1.75 h, and the crude material was puriﬁed by ﬂash

chromatography (1−5% MeOH/DCM) to aﬀord the title compound

as a tan solid (11 mg, 39%). LCMS [M + H]⁺293.17 m/z; ¹H NMR

(500 MHz, METHANOL-d₄): δ ppm 8.45 (d, J = 1.46 Hz, 1H), 8.33

(d, J = 1.95 Hz, 1H), 8.03 (s, 1H), 7.89 (d, J = 0.98 Hz, 1H), 7.67−

7.72 (m, 2H), 7.61 (s, 1H), 7.15−7.21 (m, 2H), 3.95 (s, 3H).

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3-(3,4-Diﬂuorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridine (13l). The title compound was prepared according to

General Procedure D on a 42 mg scale using 12c. The reaction was

run for 1.75 h, and the crude material was puriﬁed by ﬂash

chromatography (1−5% MeOH/DCM) to aﬀord the title compound

as a tan solid (17 mg, 59%). LCMS [M + H]⁺311.14 m/z; ¹H NMR

(500 MHz, methanol-d₄): δ ppm 8.47 (d, J = 1.95 Hz, 1H), 8.35 (d, J

= 1.95 Hz, 1H), 8.06 (s, 1H), 7.91 (s, 1H), 7.68 (s, 1H), 7.59 (ddd, J

= 11.96, 7.81, 2.20 Hz, 1H), 7.48−7.54 (m, 1H), 7.34 (m, J = 10.50,

8.40, 8.40 Hz, 1H), 3.94−3.99 (m, 3H).

3-(2-Fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-

b]pyridine (13m). The title compound was prepared according to

General Procedure D on a 55 mg scale using 12d. The reaction was

run for 6 min, and the crude material was puriﬁed by ﬂash

chromatography (1−5% MeOH/DCM) to aﬀord the title compound

as an oﬀ-white solid (23 mg, 64%). LCMS [M + H]⁺293.11 m/z; ¹H

NMR (399 MHz, DMSO-d₆): δ ppm 12.02 (br s, 1H), 8.54 (d, J =

1.47 Hz, 1H), 8.22 (s, 1H), 8.18 (s, 1H), 7.93 (s, 1H), 7.74−7.81 (m,

2H), 7.28−7.37 (m, 3H), 3.87 (s, 3H).

3-Fluoro-5-(5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (13n). The title compound was prepared

according to General Procedure D on a 44 mg scale using 12e. The

reaction was run for 2 min, and the crude material was puriﬁed by

ﬂash chromatography (5% MeOH/DCM) to aﬀord the title

compound as a white solid (22 mg, 73%). LCMS [M + H]⁺318.09

m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 12.17 (s, 1H), 8.56 (d,

J = 1.95 Hz, 1H), 8.48 (d, J = 1.46 Hz, 1H), 8.29 (s, 1H), 8.16 (s,

1H), 8.11 (s, 1H), 8.03 (s, 1H), 8.01 (d, J = 10.25 Hz, 1H), 7.68 (d, J

= 8.30 Hz, 1H), 3.90 (s, 3H).

290.19 m/z, ¹H NMR (500 MHz, DMSO-d₆): δ ppm 8.07 (d, J = 2.4

Hz, 1H), 8.04 (d, J = 2.0 Hz, 1H), 7.96−7.97 (m, 1H), 7.76 (s, 1H),

7.72 (s, 1H), 7.47−7.49 (m, 1H), 7.46 (s, 1H), 7.11 (d, J = 7.8 Hz,

2H), 6.91 (t, J = 7.6 Hz, 1H), 6.83 (d, J = 7.8 Hz, 1H), 6.14−6.20 (m,

1H), 3.86 (s, 3H).

N,N-Dimethyl-1-(4-(5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridin-3-yl)phenyl)methanamine (13s). The title compound

was prepared according to General Procedure D on a 36 mg scale

using 12h. The reaction was run for 5 min, and the crude material was

puriﬁed by ﬂash chromatography (1−10% 10% NH₄OH/

MeOH:DCM), then repuriﬁed by preparative HPLC (99−5%

water/ACN) to aﬀord the title compound as a colorless oil (6 mg,

25%). LCMS [M + H]⁺332.12 m/z; ¹H NMR (500 MHz, methanol-

d₄): δ ppm 8.46 (d, J = 1.95 Hz, 1H), 8.39 (d, J = 1.95 Hz, 1H), 8.04

(s, 1H), 7.89 (d, J = 0.98 Hz, 1H), 7.74 (d, J = 8.30 Hz, 2H), 7.69 (s,

1H), 7.46 (d, J = 8.30 Hz, 2H), 3.95 (s, 3H), 3.78 (s, 2H), 2.48 (s,

6H).

5-(1-Methyl-1H-pyrazol-4-yl)-3-(3-nitrophenyl)-1H-pyrrolo[2,3-

b]pyridine (13t). The title compound was prepared according to

General Procedure D on a 30 mg scale for 10 min using 12i. The

crude material was puriﬁed by ﬂash chromatography (3% MeOH/

DCM) to aﬀord the title compound as a solid (15 mg, 74%). LCMS

[M + H]⁺320.12 m/z, ¹H NMR (500 MHz, DMSO-d₆): δ ppm 12.13

(br s, 1H), 8.57 (d, J = 2.0 Hz, 1H), 8.49 (s, 1H), 8.42 (d, J = 2.0 Hz,

1H), 8.27 (d, J = 8.3 Hz, 1H), 8.25 (s, 1H), 8.14 (d, J = 2.4 Hz, 1H),

8.09 (dd, J = 7.8, 2.0 Hz, 1H), 7.98−7.99 (m, 1H), 7.74 (t, J = 8.1 Hz,

1H), 3.89 (s, 3H).

4-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

phenol (13u). The title compound was prepared according to General

Procedure D on a 50 mg scale using 12j. The reaction was run for 15

min, and the crude material was puriﬁed by ﬂash chromatography (1−

10% MeOH/DCM) to aﬀord the title compound as a white solid (11

mg, 33%). LCMS [M + H]⁺291.15 m/z; ¹H NMR (500 MHz,

DMSO-d₆): δ ppm 11.69 (br. s, 1H), 9.34 (br. s, 1H), 8.49 (d, J =

1.95 Hz, 1H), 8.28 (d, J = 1.95 Hz, 1H), 8.22 (s, 1H), 7.94 (d, J =

0.98 Hz, 1H), 7.66 (d, J = 2.44 Hz, 1H), 7.55 (d, J = 8.79 Hz, 2H),

6.85 (d, J = 8.30 Hz, 2H), 3.88 (s, 3H).

2-Fluoro-5-(5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (13o). The title compound was prepared

according to General Procedure D on a 48 mg scale using 12f. The

reaction was run for 1 min, and the crude material was puriﬁed by

ﬂash chromatography (1−10% MeOH/DCM, then 1−10% MeOH/

EtOAc) to aﬀord the title compound as a white solid (11 mg, 34%).

1

LCMS [M + H]⁺318.09 m/z; H NMR (399 MHz, DMSO-d₆): δ

ppm 12.07 (br s, 1H), 8.55 (d, J = 2.20 Hz, 1H), 8.43 (d, J = 1.47 Hz,

1H), 8.28 (dd, J = 5.13, 2.20 Hz, 1H), 8.26 (s, 1H), 8.16−8.23 (m,

1H), 8.02 (d, J = 2.20 Hz, 1H), 8.01 (s, 1H), 7.58 (t, J = 9.53 Hz,

1H), 3.89 (s, 3H).

5-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzo[c][1,2,5]oxadiazole (13v). The title compound was prepared

according to General Procedure D on a 109 mg scale using 12k. The

reaction was run for 5 min, and the crude reaction mixture was

neutralized with acetic acid. A precipitate was observed and collected

by vacuum ﬁltration to aﬀord the title compound as a yellow-green

4-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzamide (13p). 4-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile 13b (15 mg, 0.05 mmol) was put in a

microwave vial and dissolved in dioxane (0.1 M, 0.5 mL). Then, 2 M

aqueous NaOH was added (0.25 mL, 0.5 mmol) and the reaction was

run in the microwave at 150 °C for 40 min. The crude material was

puriﬁed by ﬂash chromatography (4−15% 5%NH₄OH/

MeOH:DCM) to aﬀord the title compound as a solid (11 mg,

1

solid (37 mg, 50%). LCMS [M + H]⁺317.11 m/z; H NMR (399

MHz, DMSO-d₆): δ ppm 12.32 (br s, 1H), 8.65 (s, 1H), 8.61 (d, J =

1.47 Hz, 1H), 8.35 (m, J = 5.10 Hz, 3H), 8.16 (d, J = 9.53 Hz, 1H),

8.06−8.10 (m, 2H), 3.91 (s, 3H).

3-(1H-Indol-5-yl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-

b]pyridine (13w). The title compound was prepared according to

General Procedure D on a 41 mg scale using 12l. The reaction was

run for 1 h, and the crude material was puriﬁed by ﬂash

chromatography (1−10% MeOH/DCM) to aﬀord the title

compound as a white solid (12 mg, 43%). LCMS [M + H]⁺314.09

m/z; ¹H NMR (399 MHz, methanol-d₄): δ ppm 8.42 (br s, 1H), 8.37

(s, 1H), 7.98 (s, 1H), 7.85 (s, 1H), 7.83 (s, 1H), 7.53 (s, 1H), 7.48

(d, J = 8.79 Hz, 1H), 7.42 (d, J = 9.53 Hz, 1H), 7.26 (d, J = 2.93 Hz,

1H), 6.51 (d, J = 2.93 Hz, 1H), 3.93 (s, 3H).

1

72%). LCMS [M + H]⁺318.15 m/z, H NMR (500 MHz, DMSO-

d₆): δ ppm 8.54 (s, 1H), 8.42 (s, 1H), 8.26 (s, 1H), 7.97−8.03 (m,

3H), 7.96 (d, J = 8.8 Hz, 2H), 7.86 (d, J = 7.8 Hz, 2H), 7.32 (s, 1H),

6.63 (s, 1H), 3.89 (s, 3H).

4-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzoic acid (13q). 4-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridin-3-yl)benzonitrile 13b (15 mg, 0.05 mmol) was put in

a microwave vial and dissolved in dioxane (0.1 M, 0.5 mL). Then, 2

M aqueous NaOH was added (1 mL, 2 mmol). The reaction was run

in the microwave at 150 °C for 30 min. The crude material was

puriﬁed by ﬂash chromatography (4−15% 5% NH₄OH/

MeOH:DCM) to aﬀord the title compound as a solid (16 mg,

100%). LCMS [M + H]⁺319.13 m/z, ¹H NMR (500 MHz,

methanol-d₄): δ ppm 8.48−8.50 (m, 1H), 8.47 (d, J = 2.0 Hz, 1H),

8.12 (d, J = 8.3 Hz, 2H), 8.08 (s, 1H), 7.93 (s, 1H), 7.85 (d, J = 8.8

Hz, 2H), 7.82 (s, 1H), 3.96 (s, 3H). *The −NH and −OH peaks are

too rapidly exchanging to be seen in the H NMR.

5-(1-Methyl-1H-pyrazol-4-yl)-3-(pyridin-3-yl)-1H-pyrrolo[2,3-b]-

pyridine (13x). Intermediate 11 (30 mg, 0.0627 mmol) was

combined with pyridin-3-ylboronic acid and PdCl₂(dppf)·CH₂Cl₂

(23 mg, 0.188 mmol) in a microwave vial, which was purged with

nitrogen and evacuated three times. Dioxane (0.6 mL, 0.1 M) and

K₂CO₃(0.25 mL, 0.5 mmol) were added and the mixture was

degassed for 10 min. The reaction was run in the microwave for 40

min at 120 °C. Aqueous NaOH (2 M, 0.3 mL, 0.6 mmol) was added,

and the solution was then microwaved for 10 min at 150 °C. The

crude product was then diluted with EtOAc and ﬁltered through

Celite using EtOAc to wash. The ﬁltrate was puriﬁed by ﬂash

chromatography (5% MeOH/DCM) to aﬀord the title compound as

3-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

aniline (13r). The title compound was prepared according to General

Procedure D on a 24 mg scale for 10 min using 12g. The crude

material was puriﬁed by ﬂash chromatography (10% MeOH/DCM)

to aﬀord the title compound as a solid (5 mg, 32%). LCMS [M + H]⁺

1

a solid (13 mg, 73%). LCMS [M + H]⁺276.14 m/z; H NMR (500

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MHz, methanol-d₄): δ ppm 8.91 (s, 1H), 8.51 (d, J = 2.0 Hz, 1H),

8.45 (d, J = 4.4 Hz, 1H), 8.40 (d, J = 2.4 Hz, 1H), 8.21 (dt, J = 8.3,

3.4 Hz, 1H), 8.07 (s, 1H), 7.92 (s, 1H), 7.82 (s, 1H), 7.54 (dd, J =

7.8, 4.9 Hz, 1H), 3.96 (s, 3H). *The −NH peak is too rapidly

exchanging to be seen in the H NMR.

aq. NaHCO₃, and once with brine. The organic layer was dried with

sodium sulfate and concentrated under reduced pressure. The crude

material was puriﬁed by ﬂash chromatography (0−50% EtOAc/Hex)

to aﬀord the title compound as a light orange solid (1.58 g, 78%).

1

LCMS [M + H]⁺476.90 m/z (⁷⁹Br), 478.92 m/z (⁸¹Br); H NMR

5-(1-Methyl-1H-pyrazol-4-yl)-3-(pyridin-4-yl)-1H-pyrrolo[2,3-b]-

pyridine (13y). The title compound was prepared according to

General Procedure D on a 40 mg scale for 20 min using crude 12m.

The crude material was puriﬁed by ﬂash chromatography (1−10%

MeOH/DCM) to aﬀord the title compound as a solid (23 mg, 92%)

(500 MHz, DMSO-d₆): δ ppm 8.51 (d, J = 1.95 Hz, 1H), 8.22 (s,

1H), 7.97−8.04 (m, 3H), 7.43 (d, J = 8.79 Hz, 2H), 2.34 (s, 3H).

tert-Butyl 4-(5-bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-

dihydropyridine-1(2H)-carboxylate (16a). Intermediate 15 (323 mg,

0.678 mmol), tert-butyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-

yl)-3,6-dihydropyridine-1(2H)-carboxylate (272 mg, 0.880 mmol),

and PdCl₂(dppf)·CH₂Cl₂(28 mg, 0.034 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (3.2 mL, 0.21 M) and 2 M K₂CO₃(1.0 mL, 2.00

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (80 °C) for 10 min. The

reaction mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (0−20% EtOAc/Hex) to aﬀord the title

compound as an oﬀ-white solid (200 mg, 56%). LCMS [M + H]⁺

532.07 m/z (⁷⁹Br), 533.96 m/z (⁸¹Br); ¹H NMR (500 MHz,

chloroform-d): δ ppm 8.46 (d, J = 2.0 Hz, 1H), 8.18 (d, J = 2.0 Hz,

1H), 8.05 (d, J = 8.3 Hz, 2H), 7.67 (s, 1H), 7.29 (d, J = 8.3 Hz, 2H),

6.11 (br s, 1H), 4.13 (br s, 2H), 3.67 (t, J = 5.4 Hz, 2H), 2.52 (br s,

2H), 2.39 (s, 3H), 1.51 (s, 9H).

1

LCMS [M + H]⁺276.15 m/z; H NMR (500 MHz, DMSO-d₆): δ

ppm 12.20 (s, 1H), 8.57 (d, J = 2.0 Hz, 1H), 8.55 (d, J = 6.3 Hz, 2H),

8.51 (d, J = 2.0 Hz, 1H), 8.30 (s, 1H), 8.21 (d, J = 2.9 Hz, 1H), 8.03

(d, J = 1.0 Hz, 1H), 7.83 (d, J = 6.3 Hz, 2H), 3.89 (s, 3H).

5-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

nicotinonitrile (13z). The title compound was prepared according to

General Procedure D on a 60 mg scale using 12n. The reaction was

run for 2 min, and the crude material was puriﬁed by ﬂash

chromatography (1−10% MeOH/DCM) to aﬀord the title

compound as a light pink solid (13 mg, 33%). LCMS [M + H]⁺

1

301.05 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 12.22 (br s,

1H), 9.33 (d, J = 1.95 Hz, 1H), 8.87 (d, J = 1.95 Hz, 1H), 8.68 (t, J =

2.20 Hz, 1H), 8.58 (d, J = 1.46 Hz, 1H), 8.53 (d, J = 1.95 Hz, 1H),

8.30 (s, 1H), 8.19 (s, 1H), 8.05 (s, 1H), 3.89 (s, 3H).

4-(5-(1-Methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

picolinonitrile (13aa). Intermediate 12o (34 mg, 0.075 mmol) was

dissolved in dioxane (1.5 mL, 0.05 M), and 2 M aq NaOH (0.10 mL,

0.200 mmol) was added. The reaction mixture was stirred at 85 °C for

1 h. The reaction mixture was puriﬁed directly by ﬂash

chromatography (0−10% MeOH/EtOAc) to aﬀord the title

compound as an oﬀ-white solid (8 mg, 34%). LCMS [M + H]⁺

tert-Butyl 3-(5-bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-2,5-

dihydro-1H-pyrrole-1-carboxylate (16b). Intermediate 15 (200 mg,

0.419 mmol), tert-butyl 3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-

yl)-2,5-dihydro-1H-pyrrole-1-carboxylate (160 mg, 0.232 mmol), and

PdCl₂(dppf)·CH₂Cl₂(19 mg, 0.023 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (2.1 mL, 0.21 M) and 2 M K₂CO₃(0.65 mL, 1.30

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (80 °C) for 15 min. The

reaction mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (0−20% EtOAc/Hex) to aﬀord the title

compound as a yellow solid (159 mg, 73%). LCMS [M + H]⁺518.09

1

301.08 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 12.41 (br s,

1H), 8.68 (d, J = 5.37 Hz, 1H), 8.60 (s, 2H), 8.46 (d, J = 1.46 Hz,

1H), 8.42 (s, 1H), 8.31 (s, 1H), 8.19 (dd, J = 4.39, 1.95 Hz, 1H), 8.06

(s, 1H), 3.90 (s, 3H).

5-(1-Methyl-1H-pyrazol-4-yl)-3-(2-methylpyridin-4-yl)-1H-

pyrrolo[2,3-b]pyridine (13ab). The title compound was prepared

according to General Procedure D on a 47 mg scale using 12p. The

reaction was run for 5 min, and the crude material was puriﬁed by

ﬂash chromatography (1−10% 5% NH₄OH/MeOH:DCM) to aﬀord

the title compound as a brown solid (19 mg, 60%). LCMS [M + H]⁺

1

m/z (⁷⁹Br), 520.10 m/z (⁸¹Br); H NMR (500 MHz, DMSO-d₆): δ

ppm 8.62 (d, J = 8.8 Hz, 1H), 8.52 (s, 1H), 8.03 (s, 1H), 8.00 (d, J =

6.8 Hz, 2H), 7.42 (d, J = 7.3 Hz, 2H), 6.58 (d, J = 18.1 Hz, 1H), 4.48

(br s, 2H), 4.22 (br s, 2H), 2.34 (s, 3H), 1.47 (d, J = 14.2 Hz, 9H).

tert-Butyl 5-(5-bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-

dihydropyridine-1(2H)-carboxylate (16c). Intermediate 15 (200 mg,

0.419 mmol), tert-butyl 5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-

yl)-3,6-dihydropyridine-1(2H)-carboxylate (169 mg, 0.546 mmol),

and PdCl₂(dppf)·CH₂Cl₂(17 mg, 0.021 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (2.1 mL, 0.20 M) and 2 M K₂CO₃(0.65 mL, 1.30

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (80 °C) for 15 min. The

reaction mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (0−20% EtOAc/Hex) to aﬀord the title

compound as an oﬀ-white solid (158 mg, 71%). LCMS [M + H]⁺

532.13 m/z (⁷⁹Br), 534.09 m/z (⁸¹Br); ¹H NMR (500 MHz, DMSO-

d₆): δ ppm 8.51 (s, 1H), 8.50 (s, 1H), 8.00 (d, J = 8.8 Hz, 2H), 7.94

(br s, 1H), 7.42 (d, J = 8.3 Hz, 2H), 6.46 (s, 1H), 4.22 (br s, 2H),

3.49 (br s, 2H), 2.34 (s, 3H), 2.28 (br s, 2H), 1.45 (s, 9H).

tert-Butyl 4-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridin-3-yl)-3,6-dihydropyridine-1(2H)-carboxylate (17a).

tert-Butyl 4-(5-bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-di-

hydropyridine-1(2H)-carboxylate 16a (200 mg, 0.376 mmol), 1-

methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole

(95 mg, 0.456 mmol), and PdCl₂(dppf)·CH₂Cl₂(15 mg, 0.018

mmol) were combined in a reaction vial that was ﬁlled with nitrogen

and evacuated three times. Dioxane (2.2 mL, 0.17 M) and 2 M

K₂CO₃(0.55 mL, 1.10 mmol) were added and the reaction mixture

was degassed for 10 min. The reaction mixture was heated at 85 °C

for ∼4 h, then the reaction mixture was diluted with EtOAc and

1

290.16 m/z; H NMR (500 MHz, methanol-d₄): δ ppm 8.45 (d, J =

1.95 Hz, 1H), 8.41 (d, J = 1.95 Hz, 1H), 8.36 (d, J = 5.37 Hz, 1H),

8.03 (s, 1H), 7.91 (s, 1H), 7.90 (s, 1H), 7.60 (s, 1H), 7.56 (dd, J =

5.37, 1.46 Hz, 1H), 3.94 (s, 3H), 2.57 (s, 3H).

3-(2,6-Dimethylpyridin-4-yl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-

pyrrolo[2,3-b]pyridine (13ac). The title compound was prepared

according to General Procedure D on a 43 mg scale using 12q. The

reaction was run for 5 min, and the crude material was puriﬁed by

ﬂash chromatography (1−10% MeOH/DCM) to aﬀord the title

compound as a tan solid (24 mg, 83%). LCMS [M + H]⁺304.21 m/z;

¹H NMR (500 MHz, DMSO-d₆): δ ppm 12.11 (br s, 1H), 8.55 (d, J =

1.95 Hz, 1H), 8.44 (d, J = 1.95 Hz, 1H), 8.27 (s, 1H), 8.11 (s, 1H),

8.02 (s, 1H), 7.45 (s, 2H), 3.90 (s, 3H), 2.49 (s, 6H).

5-Bromo-3-iodo-1H-pyrrolo[2,3-b]pyridine (14). 5-Bromo-1H-

pyrrolo[2,3-b]pyridine 9 (1.01 g, 5.13 mmol) was dissolved in

acetonitrile (30 mL, 0.17 M), and N-iodosuccinimide (1.71 g, 7.60

mmol) was added. The reaction mixture was stirred at 50 °C for 2 h.

Upon cooling to room temperature, a tan precipitate was observed

and collected by vacuum ﬁltration (washed with hexanes) to aﬀord

the title compound as a pale orange solid (1.38 g, 83%). LCMS [M +

1

H]⁺322.87 m/z (⁷⁹Br), 324.89 m/z (⁸¹Br); H NMR (500 MHz,

DMSO-d₆): δ ppm 12.35 (br s, 1H), 8.32 (d, J = 1.95 Hz, 1H), 7.87

(d, J = 2.93 Hz, 1H), 7.80 (d, J = 2.44 Hz, 1H).

5-Bromo-3-iodo-1-tosyl-1H-pyrrolo[2,3-b]pyridine (15). Inter-

mediate 14 (1.38 g, 4.27 mmol) was suspended in DCM (20 mL,

0.21 M), and TEA (1.80 mL, 12.91 mmol), DMAP (646 mg, 5.29

mmol), and 4-methylbenzenesulfonyl chloride (2.05 g, 10.75 mmol)

were added in that order. The reaction mixture was stirred overnight

at room temperature, then washed once with 1 M HCl, once with sat.

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ﬁltered through Celite. The ﬁltrate was puriﬁed by ﬂash

chromatography (50% EtOAc/Hex) to aﬀord the title compound as

a light orange solid (169 mg, 85%). LCMS [M + H]⁺534.27 m/z; ¹H

NMR (500 MHz, DMSO-d₆): δ ppm 8.64 (d, J = 1.5 Hz, 1H), 8.38

(d, J = 2.0 Hz, 1H), 8.31 (s, 1H), 8.04 (s, 1H), 7.98 (d, J = 8.3 Hz,

2H), 7.87 (s, 1H), 7.41 (d, J = 7.8 Hz, 2H), 6.45 (s, 1H), 4.08 (br s,

2H), 3.87 (s, 3H), 3.52−3.61 (m, 2H), 2.55 (br s, 2H), 2.33 (s, 3H),

1.44 (s, 9H).

achieved. Impure fractions containing the title compound were

combined to aﬀord a yellow oil (109 mg) which was taken forward

without further puriﬁcation. LCMS [M + H]⁺522.18 m/z.

tert-Butyl 3-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridin-3-yl)piperidine-1-carboxylate (18c). Intermediate

17c (147 mg, 0.275 mmol) was dissolved in EtOH (5.0 mL, 0.05

M) and 10 wt % Pd/C (27 mg, 0.025 mmol) was added. Ammonium

formate (119 mg, 1.89 mmol) was added, and the reaction mixture

was reﬂuxed at 85 °C for 1 h. The reaction mixture was diluted with

EtOAc and ﬁltered through Celite. Solids were removed from the

ﬁltrate by gravity ﬁltration and the ﬁltrate was puriﬁed by ﬂash

chromatography (2% MeOH/DCM) to aﬀord the title compound as

Tert-Butyl 3-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridin-3-yl)-2,5-dihydro-1H-pyrrole-1-carboxylate (17b).

tert-Butyl 3-(5-bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-2,5-di-

hydro-1H-pyrrole-1-carboxylate 16b (159 mg, 0.306 mmol), 1-

methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole

(77 mg, 0.370 mmol), and PdCl₂(dppf)·CH₂Cl₂(14 mg, 0.017

mmol) were combined in a reaction vial that was ﬁlled with nitrogen

and evacuated three times. Dioxane (1.8 mL, 0.17 M) and 2 M

K₂CO₃(0.45 mL, 0.900 mmol) were added, and the reaction mixture

was degassed for 10 min. The reaction mixture was heated at 85 °C

for ∼4 h. The reaction mixture was diluted with EtOAc and ﬁltered

through Celite. The ﬁltrate was puriﬁed by ﬂash chromatography

(20−50% EtOAc/Hex) to aﬀord the title compound as an oﬀ-white

1

a white solid (68%). LCMS [M + H]⁺536.23 m/z; H NMR (500

MHz, chloroform-d): δ ppm 8.54 (s, 1H), 8.06 (d, J = 7.3 Hz, 2H),

7.88 (br s, 1H), 7.75 (s, 1H), 7.64 (s, 1H), 7.51 (s, 1H), 7.29 (s, 2H),

4.04−4.14 (m, 1H), 3.98 (s, 3H), 2.91 (m, J = 11.7 Hz, 3H), 2.38 (s,

3H), 2.16 (d, J = 13.2 Hz, 1H), 1.79 (d, J = 12.2 Hz, 1H), 1.60−1.73

(m, 3H), 1.49 (s, 9H).

tert-Butyl 4-(5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)piperidine-1-carboxylate (19a). The title compound

was prepared according to General Procedure D on a 100 mg scale

using 18a. The reaction was run for 15 min, and the crude material

was puriﬁed by ﬂash chromatography (70−80% EtOAc/hexanes) to

aﬀord the title compound as a white solid (53 mg, 75%). LCMS [M +

1

solid (132 mg, 83%). LCMS [M + H]⁺520.17 m/z; H NMR (500

MHz, DMSO-d₆): δ ppm 8.67 (d, J = 2.0 Hz, 1H), 8.41 (dd, J = 8.8,

2.0 Hz, 1H), 8.34 (d, J = 3.4 Hz, 1H), 8.06 (d, J = 2.4 Hz, 1H), 8.01

(d, J = 6.8 Hz, 2H), 7.93 (s, 1H), 7.42 (d, J = 7.3 Hz, 2H), 6.66 (d, J =

24.9 Hz, 1H), 4.50 (br s, 2H), 4.27 (br s, 2H), 3.88 (s, 3H) 2.34 (s,

3H), 1.48 (d, J = 14.2 Hz, 9H).

1

H]⁺382.19 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 11.30 (s,

1H), 8.42 (d, J = 2.0 Hz, 1H), 8.16 (s, 1H), 8.11 (d, J = 2.0 Hz, 1H),

7.89 (s, 1H), 7.22 (d, J = 2.0 Hz, 1H), 3.98−4.16 (m, 2H), 3.87 (s,

3H), 2.80−3.00 (m, 3H), 1.97 (d, J = 13.7 Hz, 2H), 1.47−1.58 (m,

2H), 1.42 (s, 9H).

tert-Butyl 5-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridin-3-yl)-3,6-dihydropyridine-1(2H)-carboxylate (17c).

tert-Butyl 5-(5-bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-di-

hydropyridine-1(2H)-carboxylate 16c (158 mg, 0.297 mmol), 1-

methyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole

(75 mg, 0.360 mmol), and PdCl₂(dppf)·CH₂Cl₂(12 mg, 0.015

mmol) were combined in a reaction vial that was ﬁlled with nitrogen

and evacuated three times. Dioxane (1.7 mL, 0.17 M) and 2 M

K₂CO₃(0.50 mL, 1.00 mmol) were added and the reaction mixture

was degassed for 10 min. The reaction mixture was heated at 85 °C

for ∼4 h. The reaction mixture was diluted with EtOAc and ﬁltered

through Celite. The ﬁltrate was puriﬁed by ﬂash chromatography

(20−50% EtOAc/hexanes) to aﬀord the title compound as an oﬀ-

tert-Butyl 3-(5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)pyrrolidine-1-carboxylate (19b). The title compound

was prepared according to General Procedure D on a 109 mg scale

using 18b. The reaction was run for 15 min, and the crude material

was puriﬁed by ﬂash chromatography (2−5% MeOH/DCM, step

gradient) to aﬀord the title compound as a white solid (34 mg, 44%).

1

LCMS [M + H]⁺368.16 m/z; H NMR (500 MHz, DMSO-d₆): δ

ppm 11.39 (br s, 1H), 8.45 (d, J = 2.0 Hz, 1H), 8.13−8.20 (m, 2H),

7.92 (s, 1H), 7.30 (br s, 1H), 3.87 (s, 3H), 3.72−3.84 (m, 1H), 3.43−

3.63 (m, 2H), 3.33−3.36 (m, 1H), 3.16−3.28 (m, 1H), 2.21−2.35

(m, 1H), 1.99−2.14 (m, 1H), 1.41 (d, J = 11.7 Hz, 9H).

1

white solid (93%). LCMS [M + H]⁺534.21 m/z, H NMR (500

tert-Butyl 3-(5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)piperidine-1-carboxylate (19c). The title compound

was prepared according to General Procedure D on a 109 mg scale

using 5−28c. The reaction was run for 15 min, and the crude material

was puriﬁed by ﬂash chromatography (2−5% MeOH/DCM, step

gradient) to aﬀord the title compound as a white solid (38 mg, 54%).

LCMS [M + H]⁺382.19 m/z, ¹H NMR (500 MHz, chloroform-d): δ

ppm 8.70−8.82 (m, 1H), 8.43 (s, 1H), 8.00−8.09 (m, 1H), 7.80 (s,

1H), 7.67 (s, 1H), 7.13 (s, 1H), 4.27−4.45 (m, 1H), 3.99 (s, 3H),

2.97−3.08 (m, 1H), 2.88 (br s, 2H), 2.16−2.22 (m, 1H), 1.69−1.85

(m, 4H), 1.50 (s, 9H).

MHz, DMSO-d₆): δ ppm 8.63 (d, J = 2.0 Hz, 1H), 8.32 (s, 1H), 8.28

(s, 1H), 7.96−8.03 (m, 3H), 7.82 (s, 1H), 7.40 (d, J = 8.3 Hz, 2H),

6.54 (br s, 1H), 4.23 (br s, 2H), 3.85 (s, 3H), 3.50 (br s, 2H), 2.28−

2.34 (m, 5H), 1.44 (s, 9H).

tert-Butyl 4-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridin-3-yl)piperidine-1-carboxylate (18a). tert-Butyl 4-(5-

(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-

3,6-dihydropyridine-1(2H)-carboxylate 17a (169 mg, 0.317 mmol)

was dissolved in EtOH (6.3 mL, 0.05 M), and 10 wt % Pd/C (35 mg,

0.033 mmol) was added. Ammonium formate (160 mg, 2.54 mmol)

was added, and the reaction mixture was reﬂuxed at 85 °C for 1.5 h.

The reaction mixture was diluted with EtOAc and ﬁltered through

Celite. Solids were removed from the ﬁltrate by gravity ﬁltration and

the ﬁltrate was concentrated under reduced pressure to aﬀord the title

compound as a tan solid (100 mg, 59%). LCMS [M + H]⁺536.16 m/

z; ¹H NMR (500 MHz, chloroform-d): δ ppm 8.54 (s, 1H), 8.07 (d, J

= 8.3 Hz, 2H), 7.83 (s, 1H), 7.75 (s, 1H), 7.64 (s, 1H), 7.46 (s, 1H),

7.29 (s, 2H), 4.19−4.33 (m, 2H), 3.98 (s, 3H), 2.88 (t, J = 11.2 Hz,

2H), 2.38 (s, 3H), 1.99 (d, J = 12.7 Hz, 2H), 1.66 (qd, J = 12.7, 4.4

Hz, 2H), 1.50 (s, 9H).

tert-Butyl 3-(5-(1-methyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridin-3-yl)pyrrolidine-1-carboxylate (18b). Intermediate

17b (132 mg, 0.254 mmol) was dissolved in EtOH (5.0 mL, 0.05

M), and 10 wt % Pd/C (27 mg, 0.025 mmol) was added. Ammonium

formate (126 mg, 2.00 mmol) was added, and the reaction mixture

was reﬂuxed at 85 °C for 1.5 h. The reaction mixture was diluted with

EtOAc and ﬁltered through Celite. Solids were removed from the

ﬁltrate by gravity ﬁltration and the ﬁltrate was puriﬁed by ﬂash

chromatography (2% MeOH/DCM). However, separation was not

5-(1-Methyl-1H-pyrazol-4-yl)-3-(piperidin-4-yl)-1H-pyrrolo[2,3-

b]pyridine (20a). tert-Butyl 4-(5-(1-methyl-1H-pyrazol-4-yl)-1H-

pyrrolo[2,3-b]pyridin-3-yl)piperidine-1-carboxylate 19a (48 mg,

0.125 mmol) was taken up in 4 M HCl in dioxane (0.5 mL, 2.00

mmol). The reaction mixture was stirred at room temperature for 3 h.

The reaction mixture was concentrated under reduced pressure and

the resulting white residue was dissolved in MeOH and stirred at

room temperature with Si-carbonate overnight. The Si-carbonate was

removed by ﬁltration and the ﬁltrate was concentrated to aﬀord the

title compound as a light yellow solid (34 mg, 97%). LCMS [M + H]⁺

1

282.19 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 11.25 (br s,

1H), 8.42 (d, J = 2.0 Hz, 1H), 8.17 (s, 1H), 8.11 (s, 1H), 7.90 (s,

1H), 7.17 (s, 1H), 3.87 (s, 3H), 3.05 (d, J = 10.2 Hz, 2H), 2.86 (t, J =

13.2 Hz, 1H), 2.67 (t, J = 11.7 Hz, 2H), 1.89 (d, J = 13.7 Hz, 2H),

1.52−1.66 (m, 2H).

5-(1-Methyl-1H-pyrazol-4-yl)-3-(pyrrolidin-3-yl)-1H-pyrrolo[2,3-

b]pyridine hydrochloride (20b). tert-Butyl 3-(5-(1-methyl-1H-pyr-

azol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrrolidine-1-carboxylate

19b (22 mg, 0.060 mmol) was taken up in 4 M HCl in dioxane (0.1

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mL, 0.400 mmol). The reaction mixture was stirred at room

temperature for 1 h, then stopped and concentrated under reduced

pressure to aﬀord the title compound as a tan solid (14 mg, 78%).

3-(5-(4-(Methylsulfonyl)phenyl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (22c). The title compound was prepared

according to General Procedure B on a 30 mg scale using (4-

(methylsulfonyl)phenyl)boronic acid. The crude material was puriﬁed

by ﬂash chromatography (20−70% EtOAc/hexanes) to aﬀord the title

compound as a white solid (11 mg, 31%). LCMS [M + H]⁺528.07

1

LCMS [M + H]⁺268.19 m/z; H NMR (500 MHz, methanol-d₄): δ

ppm 8.95 (d, J = 1.5 Hz, 1H), 8.68 (d, J = 1.5 Hz, 1H), 8.27 (s, 1H),

8.06 (s, 1H), 7.71 (s, 1H), 3.99 (s, 3H), 3.94 (q, J = 8.8 Hz, 1H), 3.87

(dd, J = 11.2, 7.8 Hz, 1H), 3.59−3.67 (m, 1H), 3.47 (ddd, J = 10.7,

9.3, 7.8 Hz, 1H), 3.41 (t, J = 10.2 Hz, 1H), 2.64 (m, J = 3.9 Hz, 1H),

2.23−2.33 (m, 1H).

*The -NH peaks are too rapidly exchanging to be seen in the H

NMR in CD₃OD. 1.0 equiv HCl salt conﬁrmed by H NMR in

DMSO-d₆.

5-(1-Methyl-1H-pyrazol-4-yl)-3-(piperidin-3-yl)-1H-pyrrolo[2,3-

b]pyridine (20c). tert-Butyl 3-(5-(1-methyl-1H-pyrazol-4-yl)-1H-

pyrrolo[2,3-b]pyridin-3-yl)piperidine-1-carboxylate 19c (34 mg,

0.089 mmol) was taken up in 4 M HCl in dioxane (0.25 mL, 1.00

mmol). The reaction mixture was stirred at room temperature for 3 h,

after which the solvent was removed under reduced pressure. The

resulting yellow solid was dissolved in MeOH and Si-carbonate was

added. The mixture was stirred overnight at room temperature. The

Si-carbonate was removed by ﬁltration and the ﬁltrate was

concentrated to aﬀord the title compound as an oﬀ-white solid (20

mg, 78%). LCMS [M + H]⁺282.19 m/z; ¹H NMR (500 MHz,

methanol-d₄): δ ppm 8.40 (d, J = 2.0 Hz, 1H), 8.19 (d, J = 2.0 Hz,

1H), 8.02 (s, 1H), 7.88 (s, 1H), 7.25 (s, 1H), 3.96 (s, 3H), 3.44 (d, J

= 12.7 Hz, 1H), 3.27 (d, J = 9.8 Hz, 1H), 3.10−3.22 (m, 1H), 2.87 (t,

J = 12.2 Hz, 2H), 2.15−2.22 (m, 1H), 1.93−1.99 (m, 1H), 1.76−1.88

(m, 2H).

1

m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.81 (d, J = 1.5 Hz,

1H), 8.63 (d, J = 1.5 Hz, 1H), 8.52 (s, 1H), 8.41 (s, 1H), 8.26 (d, J =

6.8 Hz, 1H), 8.07−8.13 (m, 4H), 8.00−8.07 (m, 2H), 7.86 (d, J = 7.3

Hz, 1H), 7.71 (t, J = 7.8 Hz, 1H), 7.46 (d, J = 8.8 Hz, 2H), 3.27 (s,

3H), 2.36 (s, 3H).

3-(5-(Pyrimidin-5-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile (22d). The title compound was prepared according to

General Procedure B on a 74 mg scale using 5-(4,4,5,5-tetramethyl-

1,3,2-dioxaborolan-2-yl)pyrimidine. The crude material was puriﬁed

by ﬂash chromatography (20−100% EtOAc/Hex) to aﬀord the title

compound as an oﬀ-white solid (53 mg, 72%). LCMS [M + H]⁺

1

452.06 m/z; H NMR (399 MHz, DMSO-d₆): δ ppm 9.29 (s, 2H),

9.24 (s, 1H), 8.85 (d, J = 2.2 Hz, 1H), 8.77 (d, J = 2.2 Hz, 1H), 8.55

(s, 1H), 8.42 (s, 1H), 8.28 (d, J = 8.1 Hz, 1H), 8.09 (d, J = 8.8 Hz,

2H), 7.86 (d, J = 8.1 Hz, 1H), 7.70 (t, J = 8.1 Hz, 1H), 7.46 (d, J = 8.1

Hz, 2H), 2.35 (s, 3H).

3-(5-(Pyridin-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile (22e). The title compound was prepared according to

General Procedure B on a 74 mg scale using 4-(4,4,5,5-tetramethyl-

1,3,2-dioxaborolan-2-yl)pyridine. The crude material was puriﬁed by

ﬂash chromatography to aﬀord the title compound as an oﬀ-white

1

solid (62 mg, 84%). LCMS [M + H]⁺451.08 m/z; H NMR (399

MHz, DMSO-d₆): δ ppm 8.86 (s, 1H), 8.67 (m, J = 5.9 Hz, 3H), 8.52

(s, 1H), 8.41 (s, 1H), 8.26 (d, J = 7.3 Hz, 1H), 8.09 (d, J = 8.1 Hz,

2H), 7.84−7.91 (m, 3H), 7.71 (t, J = 8.1 Hz, 1H), 7.46 (d, J = 8.1 Hz,

2H), 2.35 (s, 3H).

3-(5-Bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(21). Intermediate 15 (575 mg, 1.21 mmol), (3-cyanophenyl)boronic

acid (176 mg, 1.20 mmol), and PdCl₂(dppf)·CH₂Cl₂(88 mg, 0.108

mmol) were combined in a microwave vial that was purged with

nitrogen and evacuated three times. Dioxane (8 mL, 0.15 M) and 2 M

K₂CO₃(2.0 mL, 4.00 mmol) were added, and the reaction mixture

was degassed for ∼10 min. The reaction was run in the microwave

(120 °C) for 5 min. The reaction mixture was diluted with EtOAc,

ﬁltered through Celite, and concentrated under reduced pressure. The

crude material was puriﬁed by ﬂash chromatography (0−20% EtOAc/

Hex) to aﬀord the title compound as a light yellow solid (322 mg,

3-(5-(1H-Pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(23a). 3-(5-Bromo-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (18

mg, 0.060 mmol), 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-

1H-pyrazole (49 mg, 0.252 mmol), potassium carbonate (25 mg,

0.181 mmol), and palladium tetrakis (3 mg, 3 μmol) were combined

in a microwave vial that was ﬁlled with nitrogen and evacuated three

times. A 4:2:1 mixture of DME/EtOH/H₂O (1.5 mL, 0.04 M) was

added and the reaction mixture was degassed and run in the

microwave (175 °C) for 15 min. The reaction mixture was diluted

with MeOH, ﬁltered through Celite, and concentrated under reduced

pressure. The ﬁltrate was puriﬁed by ﬂash chromatography (1−10%

5% NH₄OH/MeOH:DCM) to aﬀord the title compound as a white

1

59%). LCMS [M + H]⁺452.03 (⁷⁹Br), 454.04 (⁸¹Br) m/z; H NMR

(500 MHz, DMSO-d₆): δ ppm 8.65 (d, J = 1.95 Hz, 1H), 8.55 (d, J =

1.95 Hz, 1H), 8.50 (s, 1H), 8.33 (d, J = 1.46 Hz, 1H), 8.16 (dd, J =

8.06, 1.22 Hz, 1H), 8.04 (d, J = 8.30 Hz, 2H), 7.84 (dd, J = 7.81, 0.98

Hz, 1H), 7.68 (t, J = 7.32 Hz, 1H), 7.44 (d, J = 7.81 Hz, 2H), 2.35 (s,

3H).

1

solid (13 mg, 76%). LCMS [M + H]⁺286.09 m/z; H NMR (399

MHz, DMSO-d₆): δ ppm 12.98 (br s, 1H), 12.06 (br s, 1H), 8.60 (d, J

= 1.5 Hz, 1H), 8.48 (d, J = 1.5 Hz, 1H), 8.33 (br s, 1H), 8.22 (s, 1H),

8.16 (dt, J = 7.5, 1.7 Hz, 1H), 8.02−8.12 (m, 2H), 7.67−7.71 (m,

1H), 7.64 (t, J = 8.1 Hz, 1H).

3-(5-(1,3-Dimethyl-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (22a). The title compound was prepared

according to General Procedure B on a 76 mg scale using 1,3-

dimethyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyrazole.

The crude material was puriﬁed by ﬂash chromatography (20−100%

EtOAc/hexanes) to aﬀord the title compound as a light orange solid

3-(5-(1,3-Dimethyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-

yl)benzonitrile (23b). The title compound was prepared according to

General Procedure D on a 57 mg scale using 3-(5-(1,3-dimethyl-1H-

pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile. The

reaction was run for 2 min, and the crude material was puriﬁed by

ﬂash chromatography (1−10% MeOH/DCM) to aﬀord the title

compound as an oﬀ-white solid (31 mg, 81%). LCMS [M + H]⁺

1

(57 mg, 72%). LCMS [M + H]⁺468.06 m/z; H NMR (399 MHz,

DMSO-d₆): δ ppm 8.50 (d, J = 1.6 Hz, 1H), 8.43 (s, 1H), 8.33 (s,

1H), 8.26 (d, J = 1.8 Hz, 1H), 8.17 (d, J = 6.6 Hz, 1H), 8.07 (d, J =

8.4 Hz, 2H), 8.02 (s, 1H), 7.84 (d, J = 7.7 Hz, 1H), 7.69 (t, J = 8.0

Hz, 1H), 7.44 (d, J = 8.2 Hz, 2H), 3.79 (s, 3H), 2.35 (s, 3H), 2.29 (s,

3H).

1

314.09 m/z; H NMR (399 MHz, DMSO-d₆): δ ppm 12.11 (br s,

1H), 8.35 (br s, 1H), 8.27 (br s, 1H), 8.19 (br s, 1H), 8.12 (d, J =

8.06 Hz, 1H), 8.08 (br s, 1H), 7.97 (s, 1H), 7.68 (d, J = 7.33 Hz, 1H),

7.64 (t, J = 5.86 Hz, 1H), 3.81 (s, 3H), 2.31 (s, 3H).

3-(1-Tosyl-5-(1,3,5-trimethyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (22b). The title compound was prepared

according to General Procedure B on a 101 mg scale using 1,3,5-

trimethyl-4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1H-pyra-

zole. The crude material was puriﬁed by ﬂash chromatography (20−

70% EtOAc/Hex) to aﬀord the title compound as a yellow solid (67

mg, 62%). LCMS [M + H]⁺482.07 m/z; ¹H NMR (500 MHz,

DMSO-d₆): δ ppm 8.46 (s, 1H), 8.34 (d, J = 2.0 Hz, 1H), 8.31 (s,

1H), 8.18 (d, J = 2.0 Hz, 1H), 8.14 (d, J = 7.8 Hz, 1H), 8.10 (d, J =

8.3 Hz, 2H), 7.82 (d, J = 7.8 Hz, 1H), 7.67 (t, J = 7.8 Hz, 1H), 7.46

(d, J = 8.3 Hz, 2H), 3.71 (s, 3H), 2.36 (s, 3H), 2.19 (s, 3H), 2.10 (s,

3H).

3-(5-(1,3,5-Trimethyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-

3-yl)benzonitrile (23c). The title compound was prepared according

to General Procedure D on a 67 mg scale using 3-(1-tosyl-5-(1,3,5-

trimethyl-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile. The reaction was run for 2 min, and the crude material

was puriﬁed by ﬂash chromatography (5−10% MeOH/DCM) to

aﬀord the title compound as an oﬀ-white solid (17 mg, 36%). LCMS

1

[M + H]⁺328.10 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm

12.14 (s, 1H), 8.14−8.19 (m, 3H), 8.07−8.12 (m, 2H), 7.67 (d, J =

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7.8 Hz, 1H), 7.61 (t, J = 8.3 Hz, 1H), 3.73 (s, 3H), 2.22 (s, 3H), 2.13

(s, 3H).

material was puriﬁed by ﬂash chromatography (20−100% EtOAc/

hexanes) to aﬀord the title compound as a yellow solid (40 mg, 30%).

1

3-(5-(4-(Methylsulfonyl)phenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile (23d). The title compound was prepared according to

General Procedure D on an 11 mg scale using 3-(5-(4-

(methylsulfonyl)phenyl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile. The reaction was run for 2 min, and the crude material

was puriﬁed by ﬂash chromatography (2−10% MeOH/DCM) to

aﬀord the title compound as an oﬀ-white solid (7 mg, 89%). LCMS

LCMS [M + H]⁺404.21 m/z; H NMR (500 MHz, DMSO-d₆): δ

ppm 11.89 (br s, 1H), 8.16 (d, J = 2.4 Hz, 1H), 8.14 (t, J = 1.7 Hz,

1H), 8.08 (dt, J = 8.1, 1.6 Hz, 1H), 7.99 (d, J = 2.9 Hz, 1H), 7.83 (d, J

= 2.4 Hz, 1H), 7.64−7.68 (m, 1H), 7.62 (t, J = 7.8 Hz, 1H), 3.52 (m,

J = 4.9, 3.4 Hz, 4H), 3.11 (br t, J = 4.9, 4.9 Hz, 4H), 1.43 (s, 9H).

3-(5-(4-Methyl-1,4-diazepan-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile (24e). The title compound was prepared according to

General Procedure C on a 70 mg scale using 1-methyl-1,4-diazepane.

The crude material was puriﬁed by ﬂash chromatography (5−25%

MeOH/DCM) to aﬀord the title compound as a yellow solid (9 mg,

12%). LCMS [M + H]⁺332.16 m/z; ¹H NMR (500 MHz, methanol-

d₄): δ ppm 7.93−8.01 (m, 3H), 7.67 (s, 1H), 7.54−7.63 (m, 3H),

3.69 (br t, J = 4.4, 4.4 Hz, 2H), 3.55 (t, J = 6.3 Hz, 2H), 3.04 (br t, J =

4.4, 4.4 Hz, 2H), 2.90 (br t, J = 4.9, 4.9 Hz, 1H), 2.57 (s, 3H), 2.15

(quint, J = 11.1, 11.1, 11.1, 11.1, 5.9, 5.9 Hz, 2H).

1

[M + H]⁺374.03 m/z; H NMR (399 MHz, DMSO-d₆): δ ppm

12.30 (br s, 1H), 8.69 (d, J = 12.5 Hz, 1H), 8.63−8.66 (m, 1H), 8.28

(s, 1H), 8.20 (d, J = 7.3 Hz, 1H), 8.16 (s, 1H), 8.11 (d, J = 8.8 Hz,

2H), 8.03 (d, J = 8.1 Hz, 2H), 7.72 (d, J = 8.1 Hz, 1H), 7.65 (t, J = 7.3

Hz, 1H), 3.27 (s, 3H).

3-(5-(Pyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(23e). The title compound was prepared according to General

Procedure D on a 53 mg scale using 3-(5-(pyrimidin-5-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile. The reaction was run for two

minutes, then diluted with MeOH, upon which a precipitate was

observed and removed by gravity ﬁltration. The ﬁltrate was puriﬁed

by ﬂash chromatography (5% MeOH/DCM) to aﬀord the title

compound as an oﬀ-white solid (17 mg, 47%). LCMS [M + H]⁺

tert-Butyl 4-(1H-pyrrolo[2,3-b]pyridin-5-yl)piperazine-1-carboxy-

late (S29). 5-Bromo-1H-pyrrolo[2,3-b]pyridine 9 (250 mg, 1.27

mmol), 1-boc piperazine (286 mg, 1.54 mmol) RuPhos (30 mg, 0.064

mmol), and RuPhos Pd G1 (51 mg, 0.062 mmol) were combined in a

vial that was ﬁlled with nitrogen and evacuated three times. Then, 1.0

M LiHMDS in THF (3.2 mL, 3.2 mmol) was added, and the reaction

mixture was heated at 65 °C for ∼5 h. The reaction mixture was

cooled to room temperature and quenched by the addition of 1 M

HCl, then diluted with EtOAc, and poured over sat. aq. NaHCO₃.

The aqueous layer was extracted three times with EtOAc, and the

combined organic layers were washed once with brine, dried with

sodium sulfate, and concentrated under reduced pressure. The crude

residue was puriﬁed by ﬂash chromatography (50−80% EtOAc/

hexanes) to aﬀord the title compound as a light yellow solid (350 mg,

1

298.03 m/z; H NMR (399 MHz, DMSO-d₆): δ ppm 12.34 (br s,

1H), 9.31 (s, 2H), 9.21 (s, 1H), 8.77 (s, 1H), 8.71 (s, 1H), 8.30 (s,

1H), 8.23 (d, J = 8.1 Hz, 1H), 8.19 (br s, 1H), 7.71 (d, J = 7.3 Hz,

1H), 7.65 (t, J = 8.1 Hz, 1H).

3-(5-(Pyridin-4-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(23f). The title compound was prepared according to General

Procedure D on a 62 mg scale using 3-(5-(pyridin-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile. The reaction was run for two

minutes, and the crude material was puriﬁed by ﬂash chromatography

(5% MeOH/DCM) to aﬀord the title compound as an oﬀ-white solid

1

91%). LCMS [M + H]⁺303.16 m/z; H NMR (500 MHz, DMSO-

1

(36 mg, 88%). LCMS [M + H]⁺297.04 m/z; H NMR (399 MHz,

d₆): δ ppm 11.34−11.42 (m, 1H), 8.06 (d, J = 2.4 Hz, 1H), 7.51 (d, J

= 2.4 Hz, 1H), 7.37 (t, J = 2.9 Hz, 1H), 6.32 (dd, J = 3.2, 1.7 Hz, 1H),

3.49 (br t, J = 4.9, 4.9 Hz, 4H), 3.01 (br t, J = 4.9, 4.9 Hz, 4H), 1.43

(s, 9H).

DMSO-d₆): δ ppm 12.34 (br s, 1H), 8.74 (s, 1H), 8.69 (s, 1H), 8.66

(d, J = 5.1 Hz, 2H), 8.29 (s, 1H), 8.21 (d, J = 8.1 Hz, 1H), 8.17 (s,

1H), 7.90 (d, J = 5.9 Hz, 2H), 7.72 (d, J = 8.1 Hz, 1H), 7.65 (t, J = 7.3

Hz, 1H).

3-(5-(Pyrrolidin-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(24a). The title compound was prepared according to General

Procedure C on a 153 mg scale using pyrrolidine. The crude material

was puriﬁed by ﬂash chromatography (50−100% EtOAc/hexanes) to

aﬀord the title compound as a yellow solid (12 mg, 12%). LCMS [M

+ H]⁺289.12 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 11.68 (br

s, 1H), 8.11 (s, 1H), 8.06 (d, J = 6.8 Hz, 1H), 7.91 (d, J = 2.4 Hz,

1H), 7.83 (d, J = 2.4 Hz, 1H), 7.59−7.66 (m, 2H), 7.32 (s, 1H)

3.29−3.32 (m, 4H), 1.97−2.02 (m, 4H).

tert-Butyl 4-(3-iodo-1H-pyrrolo[2,3-b]pyridin-5-yl)piperazine-1-

carboxylate (S30). tert-Butyl 4-(1H-pyrrolo[2,3-b]pyridin-5-yl)-

piperazine-1-carboxylate S29 (350 mg, 1.16 mmol) was dissolved in

acetonitrile (6.5 mL, 0.18 M), and N-iodosuccinimide (314 mg, 1.40

mmol) was added. The reaction mixture was stirred at 50 °C for 2 h.

The reaction mixture was cooled to room temperature, diluted with

EtOAc, and washed three times with water and once with brine. The

organic layer was dried with sodium sulfate and concentrated under

reduced pressure. The crude residue was puriﬁed by ﬂash

chromatography (50% EtOAc/hexanes) to aﬀord the title compound

1

as a yellow solid (230 mg, 46%). LCMS [M + H]⁺429.11 m/z; H

3-(5-(Piperidin-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(24b). The title compound was prepared according to General

Procedure C on a 152 mg scale using piperidine. The crude material

was puriﬁed by ﬂash chromatography (50−100% EtOAc/hexanes) to

aﬀord the title compound as a light orange solid (20 mg, 19%). LCMS

NMR (500 MHz, DMSO-d₆): δ ppm 11.83−11.93 (m, 1H), 8.12 (d, J

= 2.9 Hz, 1H), 7.61 (d, J = 2.9 Hz, 1H), 7.13 (d, J = 2.4 Hz, 1H), 3.51

(br s, 1H), 3.07 (t, J = 4.9 Hz, 4H), 1.43 (s, 9H).

tert-Butyl 4-(3-iodo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-5-yl)-

piperazine-1-carboxylate (S31). tert-Butyl 4-(3-iodo-1H-pyrrolo-

[2,3-b]pyridin-5-yl)piperazine-1-carboxylate S30 (230 mg, 0.537

mmol) was suspended in DCM (2.7 mL, 0.21 M) and TEA (0.30

mL, 2.15 mmol), DMAP (84 mg, 0.688 mmol) and 4-

methylbenzenesulfonyl chloride (240 mg, 1.26 mmol) were added

in that order. The reaction mixture was stirred overnight at room

temperature and washed once with 1 M HCl, once with sat. aq.

NaHCO₃, and once with brine; the organic layer was dried with

sodium sulfate and concentrated under reduced pressure. The crude

residue was puriﬁed by ﬂash chromatography (20% EtOAc/Hex) to

aﬀord the title compound as an orange oil (138 mg, 44%). LCMS [M

+ H]⁺583.04 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 8.22 (t, J

= 2.4 Hz, 1H), 8.03 (d, J = 2.4 Hz, 1H), 7.95 (dd, J = 8.5, 2.2 Hz,

2H), 7.41 (d, J = 6.8 Hz, 2H), 7.13 (t, J = 2.4 Hz, 1H), 3.47 (br s,

4H), 3.14 (br s, 4H), 2.33 (s, 3H), 1.42 (s, 9H).

1

[M + H]⁺303.10 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm

11.84 (br s, 1H), 8.13 (d, J = 2.0 Hz, 2H), 8.06 (d, J = 7.3 Hz, 1H),

7.96 (d, J = 2.4 Hz, 1H), 7.76 (d, J = 2.4 Hz, 1H), 7.60−7.67 (m,

2H), 3.11 (t, J = 5.9 Hz, 4H), 1.70 (quin, J = 5.4 Hz, 4H), 1.54 (quin,

J = 5.9 Hz, 2H).

3-(5-(Piperidin-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(24c). The title compound was prepared according to General

Procedure C on a 95 mg scale using N-methylpiperazine. The crude

material was puriﬁed by ﬂash chromatography (5−10% MeOH/

DCM) to aﬀord the title compound as a light orange solid (12 mg,

18%). LCMS [M + H]⁺318.15 m/z; ¹H NMR (500 MHz,

METHANOL-d₄): δ ppm 8.13 (d, J = 2.4 Hz, 1H), 7.95−8.00 (m,

2H), 7.85 (d, J = 2.4 Hz, 1H), 7.73 (s, 1H), 7.57−7.63 (m, 2H), 3.24

(br t, J = 4.9, 4.9 Hz, 4H), 2.71 (br t, J = 4.9, 4.9 Hz, 4H), 2.39 (s,

3H).

tert-Butyl 4-(3-(3-cyanophenyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)-

piperazine-1-carboxylate (24d). The title compound was prepared

according to General Procedure C on a 150 mg scale using tert-butyl

piperazine-1-carboxylate; the reaction was run overnight. The crude

3-Iodo-5-(piperazin-1-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridine

(S32). tert-Butyl 4-(3-iodo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-5-yl)-

piperazine-1-carboxylate S31 (138 mg, 0.237 mmol) was taken up

in 4 M HCl in dioxane (0.60 mL, 2.40 mmol), and the reaction

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mixture was stirred at room temperature for 3 h. The solvent was

removed under reduced pressure, and the yellow residue (HCl salt)

was dissolved in water and poured over 1 M NaOH. The aqueous

layer (pH ∼ 13−14) was extracted three times with DCM. The

combined organic layers were dried with sodium sulfate and

concentrated under reduced pressure to aﬀord the title compound

as a yellow oil (73 mg, 64%). LCMS [M + H]⁺483.01 m/z; ¹H NMR

(500 MHz, DMSO-d₆): δ ppm 8.20 (d, J = 2.9 Hz, 1H), 8.01 (s, 1H),

7.95 (d, J = 8.3 Hz, 2H), 7.41 (d, J = 8.8 Hz, 2H), 7.05 (d, J = 2.9 Hz,

1H), 3.08 (t, J = 4.9 Hz, 4H), 2.84 (t, J = 5.4 Hz, 4H), 2.34 (s, 3H).

3-Iodo-5-(4-(methylsulfonyl)piperazin-1-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridine (S33). 3-Iodo-5-(piperazin-1-yl)-1-tosyl-1H-pyrrolo-

[2,3-b]pyridine S32 (73 mg, 0.151) was dissolved in DCM (0.5 mL,

0.32 M) and TEA (42 μL, 0.301 mmol) was added. The reaction

mixture was stirred for 10 min at room temperature before the

addition of methanesulfonyl chloride (14 μL, 0.181 mmol). The

reaction mixture was stirred overnight at room temperature. The

reaction mixture was quenched with water and extracted four times

with DCM. The combined organic layers were washed once with

brine, dried with sodium sulfate, and concentrated under reduced

pressure. The crude material was puriﬁed by ﬂash chromatography

(20−50% EtOAc/hexanes) to aﬀord the title compound as an orange

2H), 8.05−8.09 (m, 1H), 7.96 (d, J = 2.4 Hz, 1H), 7.74 (d, J = 2.4

Hz, 1H), 7.60−7.68 (m, 2H), 3.30 (br s, 1H), 3.07 (br t, J = 4.4, 4.4

Hz, 4H), 2.90 (m, J = 4.9 Hz, 4H).

3-(5-((1-Methyl-1H-pyrazol-4-yl)amino)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (27). 3-(5-Bromo-1-tosyl-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile 21 (151 mg, 0.334 mmol), BrettPhos

(19 mg, 0.035 mmol), BrettPhos Pd G1 (32 mg, 0.040 mmol), and 4-

amino-1-methylpyrazole (69 mg, 0.710 mmol) were combined in a

vial that was ﬁlled with nitrogen and evacuated three times. Then, 1.0

M LiHMDS in THF (0.800 mL, 0.800 mmol) was added and the

reaction mixture was heated at 65 °C overnight. The reaction was

quenched by the addition of 1 M HCl, then diluted with EtOAc, and

poured over sat. aq. NaHCO₃. The aqueous layer was extracted three

times with EtOAc, and the combined organic layers were washed once

with brine, dried with sodium sulfate, and concentrated under

reduced pressure. The crude material was puriﬁed by ﬂash

chromatography (20−100% EtOAc/Hex1−5% MeOH/EtOAc)

and then repuriﬁed by preparative HPLC (95−5% water/ACN) to

aﬀord the title compound (0.5 equiv formate salt) as a dark orange

1

residue (5 mg, 8%). LCMS [M + H]⁺315.19 m/z; H NMR (500

MHz, methanol-d₄): δ ppm 8.46−8.65 (m, 0 H), 7.95−7.98 (m, 1H),

7.93−7.95 (m, 1H), 7.91 (dt, J = 6.8, 2.0 Hz, 1H), 7.71 (d, J = 2.4 Hz,

1H), 7.69 (s, 1H), 7.54−7.61 (m, 3H), 7.41 (d, J = 1.0 Hz, 1H), 3.88

(s, 3H).

1

solid (68 mg, 80%). LCMS [M + H]⁺560.98 m/z; H NMR (500

MHz, DMSO-d₆): δ ppm 8.25 (d, J = 2.4 Hz, 1H), 8.04 (s, 1H), 7.96

(d, J = 8.3 Hz, 2H), 7.41 (d, J = 8.3 Hz, 2H), 7.17 (d, J = 2.9 Hz, 1H),

3.28−3.32 (m, 4H), 3.24−3.28 (m, 4H), 2.93 (s, 3H), 2.34 (s, 3H).

3-(5-(4-(Methylsulfonyl)piperazin-1-yl)-1-tosyl-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile (S34). 3-Iodo-5-(4-(methylsulfonyl)-

piperazin-1-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridine S33 (68 mg, 0.121

mmol), (3-cyanophenyl)boronic acid (36 mg, 0.245 mmol), and

PdCl₂(dppf)·CH₂Cl₂(10 mg, 0.012 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (0.50 mL, 0.25 M) and 2 M K₂CO₃(0.20 mL, 0.400

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (120 °C) for 5 min, then

diluted with EtOAc, ﬁltered through Celite, and concentrated under

reduced pressure. The crude residue was puriﬁed by ﬂash

chromatography (50% EtOAc/Hex) to aﬀord the title compound as

a dull red glassy solid (41 mg, 63%). LCMS [M + H]⁺536.10 m/z;

¹H NMR (500 MHz, DMSO-d₆): δ ppm 8.31 (s, 1H), 8.28 (s, 1H),

N-(4-(Methylsulfonyl)phenyl)-1H-pyrrolo[2,3-b]pyridin-5-amine

(S35). 5-Bromo-1H-pyrrolo[2,3-b]pyridine 9 (250 mg, 1.27 mmol), 4-

(methylsulfonyl)aniline (264 mg, 1.54 mmol), BrettPhos (34 mg,

0.063 mmol), and BrettPhos Pd G1 (51 mg, 0.064 mmol) were

combined in a vial that was ﬁlled with nitrogen and evacuated three

times. Then, 1.0 M LiHMDS in THF (3.2 mL, 3.2 mmol) was added

and the reaction mixture was heated at 65 °C for ∼5 h. The reaction

was quenched by the addition of 1 M HCl, then diluted with EtOAc,

and poured over sat. aq. NaHCO₃. The aqueous layer was extracted

three times with EtOAc, and the combined organic layers were

washed once with brine, dried with sodium sulfate, and concentrated

under reduced pressure. The crude material was puriﬁed by ﬂash

chromatography (50−100% EtOAc/Hex) to aﬀord the title

compound as a light yellow solid (146 mg, 40%). LCMS [M + H]⁺

1

288.08 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 11.65 (br s,

1H), 8.69 (s, 1H), 8.09 (d, J = 2.4 Hz, 1H), 7.82 (d, J = 2.0 Hz, 1H),

7.63 (d, J = 8.8 Hz, 2H), 7.49 (t, J = 2.9 Hz, 1H), 6.91 (d, J = 8.8 Hz,

2H), 6.43 (dd, J = 3.2, 1.7 Hz, 1H), 3.07 (s, 3H).

8.28 (s, 1H), 8.10−8.15 (m, 1H), 8.01 (d, J = 8.3 Hz, 2H), 7.83 (d, J

= 7.8 Hz, 1H), 7.76 (d, J = 2.4 Hz, 1H), 7.68 (t, J = 7.8 Hz, 1H), 7.42

(d, J = 8.8 Hz, 2H), 3.29−3.31 (m, 4H), 3.26 (m, J = 5.9 Hz, 4H),

2.93 (s, 3H), 2.34 (s, 3H).

3-Iodo-N-(4-(methylsulfonyl)phenyl)-1H-pyrrolo[2,3-b]pyridin-5-

amine (S36). N-(4-(methylsulfonyl)phenyl)-1H-pyrrolo[2,3-b]-

pyridin-5-amine S35 (146 mg, 0.508 mmol) was dissolved in

acetonitrile (2.8 mL 0.18 M) and N-iodosuccinimide (138 mg,

0.613 mmol) was added. The reaction mixture was stirred at 50 °C for

5 h. Upon cooling, a dark brown precipitate was observed and

collected by vacuum ﬁltration to aﬀord the title compound as a red-

brown solid (110 mg, 52%). LCMS [M + H]⁺413.99 m/z; ¹H NMR

(500 MHz, DMSO-d₆): δ ppm 12.13 (br s, 1H), 8.80 (s, 1H), 8.15 (d,

J = 2.4 Hz, 1H), 7.74 (d, J = 2.4 Hz, 1H), 7.67 (d, J = 8.8 Hz, 2H),

7.47 (d, J = 2.0 Hz, 1H), 6.97 (d, J = 8.8 Hz, 2H), 3.08 (s, 3H).

3-Iodo-N-(4-(methylsulfonyl)phenyl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-5-amine (S37). 3-Iodo-N-(4-(methylsulfonyl)phenyl)-1H-

pyrrolo[2,3-b]pyridin-5-amine S36 (110 mg, 0.266 mmol) was

suspended in DCM (1.3 mL, 0.21 M) and TEA (0.15 mL, 1.08

mmol), DMAP (43 mg, 0.352 mmol) and 4-methylbenzenesulfonyl

chloride (129 mg, 0.677 mmol) were added in that order. The

reaction mixture was stirred overnight at room temperature and

washed once with 1 M HCl, once with sat. aq. NaHCO₃, and once

with brine; the organic layer was dried with sodium sulfate and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (20−50% EtOAc/Hex) to aﬀord the title

compound as an oﬀ-white solid (66 mg, 44%). LCMS [M + H]⁺

3-(5-(4-(Methylsulfonyl)piperazin-1-yl)-1H-pyrrolo[2,3-b]pyridin-

3-yl)benzonitrile (25). The title compound was prepared according to

General Procedure D on a 45 mg scale using 3-(5-(4-

(methylsulfonyl)piperazin-1-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-

yl)benzonitrile S34. The reaction was run for 45 min, and the crude

material was puriﬁed by ﬂash chromatography (50−100% EtOAc/

hexanes) to aﬀord the title compound as a white solid (15 mg, 53%).

1

LCMS [M + H]⁺382.13 m/z; H NMR (500 MHz, DMSO-d₆): δ

ppm 11.92 (s, 1H), 8.18 (d, J = 2.4 Hz, 1H), 8.15 (s, 1H), 8.09 (d, J =

7.8 Hz, 1H), 8.00 (s, 1H), 7.86 (d, J = 2.0 Hz, 1H), 7.66 (d, J = 7.3

Hz, 1H), 7.63 (t, J = 7.8 Hz, 1H), 3.29−3.32 (m, 4H), 3.27 (m, J =

5.9 Hz, 4H), 2.95 (s, 3H).

3-(5-(Piperazin-1-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

(26). tert-Butyl 4-(3-(3-cyanophenyl)-1H-pyrrolo[2,3-b]pyridin-5-yl)-

piperazine-1-carboxylate 24d (40 mg, 0.099 mmol) was taken up in 4

M HCl in dioxane (0.25 mL, 1.00 mmol), and the reaction mixture

was stirred at room temperature for 2 h. The solvent was removed

under reduced pressure, and the yellow residue (HCl salt) was

dissolved in water and poured over sat. aq. NaHCO₃. The aqueous

layer (pH ∼ 8) was extracted three times with DCM. The pH of the

aqueous layer was increased to ∼13−14 by the addition of 1 M

NaOH, and the aqueous layer was extracted once more with DCM.

The combined organic layers were dried with sodium sulfate and

concentrated under reduced pressure to aﬀord the title compound as

a yellow solid (19 mg, 62%). LCMS [M + H]⁺304.17 m/z; ¹H NMR

(500 MHz, DMSO-d₆): δ ppm 11.84 (br s, 1H), 8.13 (d, J = 2.0 Hz,

1

567.90 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 9.03 (s, 1H),

8.27 (d, J = 2.4 Hz, 1H), 8.13 (s, 1H), 8.01 (d, J = 8.3 Hz, 2H), 7.71

(d, J = 8.8 Hz, 2H), 7.50 (d, J = 2.4 Hz, 1H), 7.44 (d, J = 8.8 Hz, 2H),

7.10 (d, J = 8.8 Hz, 2H), 3.11 (s, 3H), 2.35 (s, 3H).

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Article

3-(5-((4-(Methylsulfonyl)phenyl)amino)-1-tosyl-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile (S38). 3-Iodo-N-(4-(methylsulfonyl)-

phenyl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-5-amine S37 (65 mg,

0.114 mmol), (3-cyanophenyl)boronic acid (35 mg, 0.238 mmol),

and PdCl₂(dppf)·CH₂Cl₂(9 mg, 0.011 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (0.50 mL, 0.25 M) and 2 M K₂CO₃(0.20 mL, 0.400

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (120 °C) for 5 min. The

reaction mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The crude residue was puriﬁed

by ﬂash chromatography (20−75% EtOAc/Hex) to aﬀord the title

compound as a dark orange solid (46 mg, 74%). LCMS [M + H]⁺

4-Bromo-1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazole (S41a). 4-

Bromo-1H-pyrazole (200 mg, 1.36 mmol) was dissolved in DMF

(1.7 mL, 0.81 M) and cooled to 0 °C. NaH (165 mg, 4.13 mmol) was

added portionwise, and the reaction mixture was stirred for 1 h at 0

°C. Tetrahydro-2H-pyran-4-yl methanesulfonate S40a (317 mg, 1.76

mmol) was added. The reaction was mixture was gradually heated to

100 °C and stirred overnight. The reaction mixture was quenched

with water and extracted twice with EtOAc. The combined organic

layers were washed with brine, dried with sodium sulfate, and

concentrated under reduced pressure. The product was puriﬁed by

ﬂash chromatography (2% 5% NH₄OH/MeOH:DCM) to aﬀord the

title compound as an oﬀ-white solid (191 mg, 61%). LCMS [M + H]⁺

230.93 m/z (⁷⁹Br), 232.92 m/z (⁸¹Br); ¹H NMR (500 MHz, DMSO-

d₆): δ ppm 8.06 (s, 1H), 7.55 (s, 1H), 4.39 (tt, J = 10.6, 5.2 Hz, 1H),

3.94 (d, J = 12.7 Hz, 2H), 3.44 (td, J = 11.5, 2.9 Hz, 2H), 1.85−1.98

(m, 4H).

1

543.03 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.99 (s, 1H),

8.42 (s, 1H), 8.33 (d, J = 2.4 Hz, 1H), 8.29 (t, J = 1.5 Hz, 1H), 8.13

(d, J = 2.4 Hz, 1H), 8.11 (dt, J = 8.3, 1.5 Hz, 1H), 8.06 (d, J = 8.3 Hz,

2H), 7.82 (dt, J = 7.8, 1.5 Hz, 1H), 7.65−7.70 (m, 3H), 7.45 (d, J =

8.3 Hz, 2H), 7.09 (d, J = 8.8 Hz, 2H), 3.09 (s, 3H), 2.36 (s, 3H).

3-(5-((4-(Methylsulfonyl)phenyl)amino)-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile (28). The title compound was prepared

according to General Procedure D on a 46 mg scale using 3-(5-((4-

(methylsulfonyl)phenyl)amino)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-

yl)benzonitrile S38. The reaction was run for 80 min, and the crude

material was puriﬁed by ﬂash chromatography (50% EtOAc/hexanes)

to aﬀord the title compound as a white solid (15 mg, 46%). LCMS

tert-Butyl 4-(4-bromo-1H-pyrazol-1-yl)piperidine-1-carboxylate

(S41b). 4-Bromo-1H-pyrazole (200 mg, 1.36 mmol) was dissolved

in DMF (1.7 mL, 0.81 M) and cooled to 0 °C. NaH (166 mg, 4.15

mmol) was added portionwise, and the reaction mixture was stirred

for 1 h at 0 °C. tert-Butyl 4-((methylsulfonyl)oxy)piperidine-1-

carboxylate S40b (497 mg, 1.78 mmol) was added, and the reaction

mixture was gradually heated to 100 °C and stirred overnight. The

reaction mixture was quenched with water and extracted twice with

EtOAc. The combined organic layers were washed with brine, dried

with sodium sulfate, and concentrated under reduced pressure. The

product was puriﬁed by ﬂash chromatography (0−50% EtOAc/Hex)

to aﬀord the title compound as a colorless oil (282 mg, 36%). LCMS

1

[M + H]⁺389.12 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm

12.13−12.20 (m, 1H), 8.79 (s, 1H), 8.20 (dd, J = 11.5, 2.2 Hz, 2H),

8.16 (s, 1H), 8.11 (s, 1H), 8.06 (d, J = 7.8 Hz, 1H), 7.60−7.69 (m,

4H), 6.97 (d, J = 9.3 Hz, 2H), 3.08 (s, 3H).

1

[M + H]⁺273.94 m/z (⁷⁹Br), 275.96 m/z (⁸¹Br); H NMR (500

MHz, chloroform-d): δ ppm 7.47 (s, 1H), 7.44 (s, 1H), 4.16−4.41

(m, 3H), 2.76−2.97 (m, 2H), 2.10 (d, J = 12.2 Hz, 2H), 1.87 (qd, J =

12.2, 3.9 Hz, 2H), 1.47 (s, 9H).

Tetrahydro-2H-pyran-4-yl methanesulfonate (S40a). Tetrahy-

dro-2H-pyran-4-ol S39a (0.500 mL, 5.24 mmol) was dissolved in

DCM (9.0 mL, 0.60 M) and TEA (0.750 mL, 5.38 mmol) was added,

followed by the addition of DMAP (128 mg, 1.05 mmol). The

solution was cooled to 0 °C, and MsCl (0.410 mL, 5.30 mmol) was

added dropwise, upon which the reaction mixture turned opaque. The

reaction was run at 0 °C for 4 h, after which water was added and the

reaction mixture was transferred to a separatory funnel. The organic

layer was washed once with brine, dried with sodium sulfate, and

concentrated under reduced pressure to aﬀord the title compound as

4-(4-Bromo-1H-pyrazol-1-yl)-1-methylpiperidine (S41c). 4-

Bromo-1H-pyrazole (200 mg, 1.36 mmol) was dissolved in dry

DMF (1.7 mL, 0.81 M) and cooled to 0 °C. NaH (168 mg, 4.20

mmol) was added portionwise, and the reaction mixture was stirred

for 1 h at 0 °C, after which 1-methylpiperidin-4-yl methanesulfonate

406c (444 mg, 2.30 mmol) was dissolved in dry DMF (1.4 mL, 1.7

M) added. The reaction mixture was gradually heated to 100 °C and

stirred for 2 days. The reaction mixture was quenched with water and

extracted twice with EtOAc. The combined organic layers were

washed with brine, dried with sodium sulfate, and concentrated under

reduced pressure. The crude material was puriﬁed by ﬂash

chromatography (3% 5% NH₄OH/MeOH:DCM) to aﬀord the title

compound as an oﬀ-white solid (80 mg, 24%). LCMS [M + H]⁺

243.97 m/z (⁷⁹Br), 245.98 m/z (⁸¹Br); ¹H NMR (500 MHz, DMSO-

d₆): δ ppm 8.04 (s, 1H), 7.53 (s, 1H), 4.09 (dt, J = 10.5, 5.0 Hz, 1H),

2.82 (d, J = 11.7 Hz, 2H), 2.18 (s, 3H), 1.96−2.07 (m, 2H), 1.85−

1.95 (m, 4H).

3-(5-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (S42). The title compound

was prepared according to General Procedure E on a 600 mg scale

using 3-(5-bromo-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

21. The crude material was puriﬁed by ﬂash chromatography (0−

20% EtOAc/Hex) and then repuriﬁed by ﬂash chromatography (1%

MeOH/DCM) to aﬀord the title compound as a white solid (148 mg,

22%). LCMS [M + H]⁺500.08 m/z; ¹H NMR (500 MHz,

chloroform-d): δ ppm 8.86 (s, 1H), 8.40 (s, 1H), 8.15 (d, J = 8.3

Hz, 2H), 7.92 (s, 1H), 7.89 (s, 1H), 7.85 (d, J = 7.8 Hz, 1H), 7.67 (d,

J = 7.8 Hz, 1H), 7.61 (t, J = 7.8 Hz, 1H), 7.29 (d, J = 8.3 Hz, 2H),

2.39 (s, 3H), 1.36 (s, 12H).

1

an oﬀ-white solid (770 mg, 82%). H NMR (500 MHz, chloroform-

d): δ ppm 4.92 (spt, J = 4.2 Hz, 1H), 3.92−4.00 (m, 2H), 3.56 (td, J =

10.2, 8.8 Hz, 2H), 3.05 (s, 3H), 2.02−2.10 (m, 2H), 1.84−1.95 (m,

2H). *Does not ionize.

tert-Butyl 4-((methylsulfonyl)oxy)piperidine-1-carboxylate

(S40b). tert-Butyl 4-hydroxypiperidine-1-carboxylate S39b (2.00 g,

9.94 mmol) was dissolved in DCM (20 mL, 0.5 M), and the reaction

mixture was cooled to 0−5. TEA (3.0 mL, 21.52 mmol) was slowly

added, followed by the slow addition of methanesulfonyl chloride (1.0

mL, 12.92 mmol). The reaction mixture was stirred for 1 h at room

temperature. The reaction mixture was puriﬁed by ﬂash chromatog-

raphy (10% EtOAc/hexanes) to aﬀord the title compound as a white

solid (1.7 g, 61%). LCMS [M + H]⁺223.95 m/z (loss of t-Bu group);

¹H NMR (500 MHz, DMSO-d₆): δ ppm 4.82 (tt, J = 8.1, 3.8 Hz, 1H),

3.60 (tt, J = 5.9, 4.4 Hz, 2H), 3.20 (s, 3H), 3.12−3.19 (m, 2H), 1.86−

1.94 (m, 2H), 1.60 (dtd, J = 13.0, 8.8, 8.8, 4.1 Hz, 2H), 1.40 (s, 9H).

1-Methylpiperidin-4-yl methanesulfonate (S40c). 1-Methylpiper-

idin-4-ol S39c (0.500 mL, 4.25 mmol) was dissolved in DCM (7.0

mL, 0.60 M), and TEA (0.600 mL, 4.30 mmol) was added, followed

by the addition of DMAP (103 mg, 0.843 mmol). The solution was

cooled to 0 °C, and MsCl (0.330 mL, 4.26 mmol) was added

dropwise, upon which the reaction mixture turned opaque. The

reaction was run at 0 °C for 5 h. Water was added, and the reaction

mixture was transferred to a separatory funnel. The organic layer was

washed once more with water, once with brine, dried with sodium

sulfate, and concentrated under reduced pressure to aﬀord the title

compound as a yellow oil (444 mg, 54%). LCMS [M + H]⁺193.97

3-(5-(1-(Tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (S43a). 4-Bromo-1-(tetrahy-

dro-2H-pyran-4-yl)-1H-pyrazole S41a (44 mg, 0.190 mmol) and

PdCl₂(dppf)·CH₂Cl₂(14 mg, 0.017 mmol) were combined in a

reaction vial that was ﬁlled with nitrogen and evacuated three times.

Crude 3-(5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile S42 (84 mg, 0.168 mmol) was

dissolved in dioxane (1.0 mL, 0.17 M) and added to the reaction

mixture, followed by the addition of 2 M K₂CO₃(0.40 mL, 0.800

1

m/z; H NMR (500 MHz, chloroform-d): δ ppm 4.75 (br s, 1H),

3.03 (s, 3H), 2.67 (br s, 2H), 2.21−2.35 (m, 5H), 1.99−2.07 (m,

2H), 1.88−1.97 (m, 2H).

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mmol). The reaction mixture was degassed and run in the microwave

(145 °C) for 5 min. The reaction mixture was diluted with EtOAc,

ﬁltered through Celite, and concentrated under reduced pressure. The

crude material was puriﬁed by ﬂash chromatography (20−75%

EtOAc/Hex) to aﬀord the title compound as a pale yellow solid (37

mg, 43%). LCMS [M + H]⁺524.07 m/z; ¹H NMR (500 MHz,

DMSO-d₆): δ ppm 8.72 (s, 1H), 8.44 (m, J = 6.3 Hz, 2H), 8.40 (s,

1H), 8.34 (s, 1H), 8.19 (d, J = 8.3 Hz, 1H), 8.03−8.10 (m, 3H), 7.86

(d, J = 7.3 Hz, 1H), 7.71 (t, J = 8.3 Hz, 1H), 7.44 (d, J = 7.8 Hz, 2H),

4.37−4.46 (m, 1H), 3.97 (d, J = 12.7 Hz, 2H), 3.48 (t, J = 10.7 Hz,

2H), 2.35 (s, 3H), 1.88−2.06 (m, 4H).

tert-Butyl 4-(4-(3-(3-cyanophenyl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-5-yl)-1H-pyrazol-1-yl)piperidine-1-carboxylate (S43b). tert-

Butyl 4-(4-bromo-1H-pyrazol-1-yl)piperidine-1-carboxylate S41b

(282 mg, 0.854 mmol) and PdCl₂(dppf)·CH₂Cl₂(54 mg, 0.066

mmol) were combined in a reaction vial that was ﬁlled with nitrogen

and evacuated three times. Crude 3-(5-(4,4,5,5-tetramethyl-1,3,2-

dioxaborolan-2-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile

S42 (332 mg, 0.665 mmol) was dissolved in dioxane (3.5 mL, 0.17

M) and added to the reaction mixture, followed by the addition of 2

M K₂CO₃(1.3 mL, 2.60 mmol). The reaction mixture was degassed

and run in the microwave (145 °C) for 25 min. The reaction mixture

was diluted with EtOAc, ﬁltered through Celite, and concentrated

under reduced pressure. The crude material was puriﬁed by ﬂash

chromatography (20−40−60% EtOAc/Hex, step gradient) to aﬀord

the title compound as a pale yellow solid (180 mg, 43%). LCMS [M +

H]⁺623.07 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 8.71 (d, J =

1.5 Hz, 1H), 8.44 (s, 1H), 8.43 (d, J = 1.5 Hz, 1H), 8.40 (s, 1H), 8.34

(s, 1H), 8.18 (d, J = 7.8 Hz, 1H), 8.03−8.09 (m, 3H), 7.85 (d, J = 7.8

Hz, 1H), 7.71 (t, J = 8.3 Hz, 1H), 7.43 (d, J = 7.8 Hz, 2H), 4.34−4.42

(m, 1H), 4.02 (br s, 2H), 2.93 (br s, 2H), 2.34 (s, 3H), 2.04 (d, J =

10.7 Hz, 2H), 1.79 (dd, J = 12.2, 3.9 Hz, 2H), 1.42 (s, 9H).

reaction was run for 10 min, and the crude material was puriﬁed by

ﬂash chromatography (3% 5% NH₄OH/MeOH:DCM) to aﬀord the

title compound as a light yellow solid (21 mg, 55%). LCMS [M + H]⁺

1

469.10 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 12.07 (br s,

1H), 8.57 (d, J = 1.5 Hz, 1H), 8.46 (s, 1H), 8.41 (s, 1H), 8.21 (s,

1H), 8.16 (d, J = 7.3 Hz, 1H), 8.06 (d, J = 2.4 Hz, 1H), 8.04 (s, 1H),

7.69 (d, J = 8.3 Hz, 1H), 7.66 (t, J = 7.8 Hz, 1H), 4.34−4.44 (m, 1H),

4.01−4.16 (m, 2H), 2.81−3.06 (m, 2H), 2.05 (d, J = 10.7 Hz, 2H),

1.83 (qd, J = 14.2, 12.2 Hz, 2H), 1.43 (s, 9H).

3-(5-(1-(1-Methylpiperidin-4-yl)-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile (29c). The title compound was prepared

according to General Procedure D on a 45 mg scale using 3-(5-(1-(1-

methylpiperidin-4-yl)-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]-

pyridin-3-yl)benzonitrile S43c. The reaction was run for 5 min, and

the crude material was puriﬁed by ﬂash chromatography (5−10% 5%

NH₄OH/MeOH:DCM) to aﬀord the title compound as an oﬀ-white

1

solid (19 mg, 59%). LCMS [M + H]⁺383.12 m/z; H NMR (500

MHz, DMSO-d₆): δ ppm 12.06 (br s, 1H), 8.57 (d, J = 1.5 Hz, 1H),

8.45 (d, J = 1.5 Hz, 1H), 8.38 (s, 1H), 8.21 (s, 1H), 8.16 (d, J = 7.8

Hz, 1H), 8.06 (d, J = 2.4 Hz, 1H), 8.02 (s, 1H), 7.69 (d, J = 7.8 Hz,

1H), 7.65 (t, J = 7.8 Hz, 1H), 4.13 (s, 1H), 2.88 (d, J = 10.7 Hz, 2H),

2.22 (s, 3H), 1.95−2.11 (m, 6H).

5-Bromo-1-(4-(methylsulfonyl)phenyl)-3-(pyridin-4-yl)-1H-

pyrrolo[2,3-b]pyridine (S44). Intermediate 15 (200 mg, 0.419

mmol), pyridin-4-ylboronic acid (52 mg, 0.423 mmol), and

PdCl₂(dppf)·CH₂Cl₂(36 mg, 0.044 mmol) were combined in a

microwave vial that was purged with nitrogen and evacuated three

times. Dioxane (2.8 mL, 0.15 M) and 2 M K₂CO₃(0.70 mL, 1.40

mmol) were added, and the reaction mixture was degassed for ∼10

min. The reaction was run in the microwave (120 °C) for 5 min. The

reaction mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The crude material was puriﬁed

by ﬂash chromatography (20−60% EtOAc/Hex) to aﬀord the title

compound as a light yellow solid (116 mg, 65%). LCMS [M + H]⁺

427.85 m/z (⁷⁹Br), 429.86 m/z (⁸¹Br); ¹H NMR (500 MHz, DMSO-

d₆): δ ppm 8.67 (d, J = 2.0 Hz, 1H), 8.65 (d, J = 5.9 Hz, 2H), 8.61 (s,

1H), 8.57 (d, J = 2.0 Hz, 1H), 8.06 (d, J = 8.3 Hz, 2H), 7.86 (d, J =

5.9 Hz, 2H), 7.45 (d, J = 7.8 Hz, 2H), 2.36 (s, 3H).

1-(4-(Methylsulfonyl)phenyl)-3-(pyridin-4-yl)-5-(4,4,5,5-tetra-

methyl-1,3,2-dioxaborolan-2-yl)-1H-pyrrolo[2,3-b]pyridine (S45).

The title compound was prepared according to General Procedure

E on a 115 mg scale using 5-bromo-3-(pyridin-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridine S44. The resulting crude dark brown solid was

used in the next reaction without further puriﬁcation. LCMS [M +

H]⁺476.09 m/z.

1-(4-(Methylsulfonyl)phenyl)-3-(pyridin-4-yl)-5-(1-(tetrahydro-

2H-pyran-4-yl)-1H-pyrazol-4-yl)-1H-pyrrolo[2,3-b]pyridine (S46). 4-

Bromo-1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazole S41a (50 mg,

0.216 mmol) and PdCl₂(dppf)·CH₂Cl₂(23 mg, 0.028 mmol) were

combined in a reaction vial that was ﬁlled with nitrogen and evacuated

three times. Crude 3-(pyridin-4-yl)-5-(4,4,5,5-tetramethyl-1,3,2-diox-

aborolan-2-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridine S45 (129 mg, 0.271

mmol) was dissolved in dioxane (1.6 mL, 0.17 M) and added to the

reaction mixture, followed by the addition of 2 M K₂CO₃(0.60 mL,

1.20 mmol). The reaction mixture was degassed and run in the

microwave (145 °C) for 10 min. The reaction mixture was diluted

with EtOAc/MeOH, ﬁltered through Celite, and concentrated under

reduced pressure. The crude material was puriﬁed by ﬂash

chromatography (1−10% MeOH/EtOAc) to aﬀord the title

compound as a dark red residue (31 mg, 23%). LCMS [M + H]⁺

500.02 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 8.74 (d, J = 2.0

Hz, 1H), 8.67 (d, J = 6.3 Hz, 2H), 8.51 (s, 1H), 8.50 (d, J = 2.0 Hz,

1H), 8.48 (s, 1H), 8.09 (s, 1H), 8.07 (d, J = 8.3 Hz, 2H), 7.90 (d, J =

5.9 Hz, 2H), 7.44 (d, J = 8.3 Hz, 2H), 4.38−4.47 (m, 1H), 3.98 (d, J

= 10.2 Hz, 2H), 3.93 (s, 3H), 3.49 (td, J = 11.7, 2.0 Hz, 2H), 1.93−

2.07 (m, 4H).

3-(5-(1-(1-Methylpiperidin-4-yl)-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (S43c). 3-(5-(4,4,5,5-Tetra-

methyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-

yl)benzonitrile S42 (64 mg, 0.128 mmol), 4-(4-bromo-1H-pyrazol-1-

yl)-1-methylpiperidine S41c (40 mg, 0.164 mmol), and PdCl₂(dppf)·

CH₂Cl₂(11 mg, 0.013 mmol) were combined in a reaction vial that

was ﬁlled with nitrogen and evacuated three times. Dioxane (1.0 mL,

0.17 M) was added to the reaction mixture, followed by the addition

of 2 M K₂CO₃(0.30 mL, 0.600 mmol). The reaction mixture was

degassed and run in the microwave (145 °C) for 5 min. The reaction

mixture was diluted with EtOAc, ﬁltered through Celite, and

concentrated under reduced pressure. The product was puriﬁed by

ﬂash chromatography (1−10% MeOH/DCM) to aﬀord the title

compound as an orange residue (45 mg, 65%). LCMS [M + H]⁺

1

537.11 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 8.71 (s, 1H),

8.43 (s, 2H), 8.40 (s, 1H), 8.34 (s, 1H), 8.19 (d, J = 7.3 Hz, 1H),

8.02−8.09 (m, 3H), 7.86 (d, J = 7.8 Hz, 1H), 7.71 (t, J = 7.8 Hz, 1H),

7.44 (d, J = 8.3 Hz, 2H), 4.05−4.17 (m, 1H), 2.83−2.91 (m, 2H),

2.35 (s, 3H), 2.20 (s, 3H), 1.96−2.07 (m, 6H).

3-(5-(1-(Tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1H-pyrrolo-

[2,3-b]pyridin-3-yl)benzonitrile (29a). The title compound was

prepared according to General Procedure D on a 37 mg scale using

3-(5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-tosyl-1H-

pyrrolo[2,3-b]pyridin-3-yl)benzonitrile S43a. The reaction was run

for 6 min, and the crude material was puriﬁed by ﬂash

chromatography (1−10% MeOH/DCM) to aﬀord the title

compound as an oﬀ-white solid (13 mg, 49%). LCMS [M + H]⁺

1

370.10 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 12.07 (br s,

1H), 8.58 (d, J = 1.5 Hz, 1H), 8.46 (s, 1H), 8.40 (s, 1H), 8.21 (s,

1H), 8.16 (d, J = 7.8 Hz, 1H), 8.06 (d, J = 2.4 Hz, 1H), 8.04 (s, 1H),

7.70 (d, J = 7.8 Hz, 1H), 7.65 (t, J = 7.8 Hz, 1H), 4.43 (tquin, J = 6.3,

6.3, 4.9, 4.9, 4.9, 4.9 Hz, 1H), 3.99 (d, J = 11.7 Hz, 2H), 3.49 (td, J =

10.7, 2.4 Hz, 2H), 1.94−2.08 (m, 4H).

tert-Butyl 4-(4-(3-(3-cyanophenyl)-1H-pyrrolo[2,3-b]pyridin-5-

yl)-1H-pyrazol-1-yl)piperidine-1-carboxylate (29b). The title com-

pound was prepared according to General Procedure D on a 50 mg

scale using tert-butyl 4-(4-(3-(3-cyanophenyl)-1-tosyl-1H-pyrrolo[2,3-

b]pyridin-5-yl)-1H-pyrazol-1-yl)piperidine-1-carboxylate S43b. The

3-(Pyridin-4-yl)-5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-

yl)-1H-pyrrolo[2,3-b]pyridine (30). The title compound was prepared

according to General Procedure D on a 31 mg scale using 3-(pyridin-

4-yl)-5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-tosyl-1H-

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pyrrolo[2,3-b]pyridine S46. The reaction was run for 5 min, and the

crude material was puriﬁed by ﬂash chromatography (5−10% 5%

NH₄OH/MeOH:DCM) to aﬀord the title compound as an orange

= 12.0 Hz, 2H), 2.96−3.09 (m, 1H), 3.59 (td, J = 11.5, 2.9 Hz, 2H),

4.16 (d, J = 11.7 Hz, 2H), 4.42 (spt, J = 5.4 Hz, 1H), 7.13 (d, J = 1.5

Hz, 1H), 7.74 (s, 1H), 7.83 (s, 1H), 8.02 (br s, 1H), 8.46 (br s, 1H),

8.81 (br s, 1H).

1

solid (12 mg, 57%). LCMS [M + H]⁺346.11 m/z; H NMR (500

3-(Piperidin-3-yl)-5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-

yl)-1H-pyrrolo[2,3-b]pyridine (31). tert-Butyl 3-(5-(1-(tetrahydro-

2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-

yl)piperidine-1-carboxylate S50 (17 mg, 0.028 mmol) was dissolved

in dioxane (0.300 mL, 0.10 M), and 4 M HCl in dioxane (0.05 mL,

0.200 mmol) was added. The reaction mixture was stirred at room

temperature for 3 h. The reaction mixture was concentrated under

reduced pressure and the resulting light yellow residue was dissolved

in MeOH. Si-carbonate was added and the reaction mixture was

stirred at room temperature overnight. The Si-carbonate was ﬁltered

oﬀ and the ﬁltrate was puriﬁed by ﬂash chromatography (10−25% 5%

NH₄OH/MeOH:DCM, stepwise gradient) to aﬀord the title

compound as a white solid (9 mg, 72%). LCMS [M + H]⁺352.1

MHz, DMSO-d₆): δ ppm 12.20 (br s, 1H), 8.60 (d, J = 2.0 Hz, 1H),

8.56 (d, J = 5.9 Hz, 2H), 8.53 (d, J = 2.0 Hz, 1H), 8.44 (s, 1H), 8.21

(s, 1H), 8.06 (s, 1H), 7.83 (d, J = 5.9 Hz, 2H), 4.43 (spt, J = 6.3 Hz,

1H), 3.99 (d, J = 11.2 Hz, 2H), 3.50 (td, J = 10.7, 2.4 Hz, 2H), 1.96−

2.08 (m, 4H).

tert-Butyl 5-(5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-

tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-dihydropyridine-1(2H)-car-

boxylate (S47). The title compound was prepared according to

General Procedure E on a 320 mg scale using tert-butyl 5-(5-bromo-1-

tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-dihydropyridine-1(2H)-car-

boxylate 16c. The product was puriﬁed by ﬂash chromatography

(10−20% EtOAc/Hex) to aﬀord the title compound as an oﬀ-white

1

solid (156 mg, 45%). LCMS [M + H]⁺580.1 m/z; H NMR (500

1

MHz, DMSO-d₆): δ ppm 1.30 (s, 12H), 1.45 (s, 9H), 2.28−2.32 (m,

2H), 2.33 (s, 3H), 3.49 (t, J = 4.9 Hz, 2H), 4.24 (br s, 2H), 6.37 (br s,

1H), 7.40 (d, J = 8.3 Hz, 2H), 7.89−7.93 (m, 1H), 8.02 (d, J = 8.3

Hz, 2H), 8.32−8.36 (m, 1H), 8.57 (s, 1H)

m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 1.77 (qd, J = 7.8, 3.9

Hz, 1H), 1.82−1.94 (m, 2H), 1.94−2.10 (m, 5H), 2.95 (td, J = 12.1,

3.7 Hz, 1H), 3.03 (t, J = 12.2 Hz, 1H), 3.23−3.32 (m, 3H), 3.42−3.54

(m, 3H), 3.98 (d, J = 11.2 Hz, 2H), 4.42 (spt, J = 4.9 Hz, 1H), 7.33

(s, 1H), 7.95 (s, 1H), 8.19 (s, 1H), 8.31 (s, 1H), 8.49 (d, J = 1.5 Hz,

1H), 11.51 (br s, 1H).

5-Bromo-3-iodo-1H-pyrazolo[3,4-b]pyridine (S52a). 5-Bromo-

1H-pyrazolo[3,4-b]pyridine S51a (300 mg, 1.51 mmol) was

suspended in DCE (6.6 mL, 0.23 M) and NIS (511 mg, 2.27

mmol) was added. The reaction mixture was reﬂuxed at 80 °C

overnight. An oﬀ-white precipitate was observed and collected by

vacuum ﬁltration (washed with DCE) to aﬀord the title compound as

an ivory solid (465 mg, 95%). LCMS [M + H]⁺323.7 m/z (⁷⁹Br),

325.8 m/z (⁸¹Br); ¹H NMR (500 MHz, DMSO-d₆): δ ppm 8.21 (d, J

= 1.1 Hz, 1H), 8.65 (d, J = 2.2 Hz, 1H), 14.31 (s, 1H).

5-Bromo-3-iodo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-

pyrazolo[3,4-b]pyridine (S53a). 5-Bromo-3-iodo-1H-pyrazolo[3,4-

b]pyridine S52a (465 mg, 1.44 mmol) was dissolved in DMF (3.7

mL, 0.039 M), and the reaction mixture was cooled to 0 °C. NaH

(178 mg, 4.45 mmol) was added, and the reaction mixture was stirred

at 0 °C. After stirring for a few minutes, the reaction mixture changed

from a cloudy oﬀ-white suspension to a bright orange solution. After

30 min, 2-(trimethylsilyl)ethoxymethyl chloride (0.300 mL, 1.70

mmol) was added and the reaction turned bright yellow. The reaction

mixture was left stirring at 0 °C for another 2 h. The reaction was

quenched with water and extracted three times with EtOAc. The

combined organic layers were washed once with brine, dried with

sodium sulfate, and concentrated. The crude material was dried under

high vacuum overnight to aﬀord the title compound as a beige solid

(564 mg, 87%). LCMS [M + H]⁺453.8 m/z (⁷⁹Br), 455.8 m/z (⁸¹Br);

¹H NMR (500 MHz, DMSO-d₆): δ ppm −0.13 to −0.10 (m, 9H),

tert-Butyl 5-(5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-

tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-dihydropyridine-1(2H)-car-

boxylate (S48). tert-Butyl 5-(5-(4,4,5,5-tetramethyl-1,3,2-dioxaboro-

lan-2-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-dihydropyridine-

1(2H)-carboxylate S47 (156 mg, 0.269 mmol), 4-bromo-1-(tetrahy-

dro-2H-pyran-4-yl)-1H-pyrazole S41a (93 mg, 0.402 mmol), and

PdCl2(dppf)·CH₂Cl₂(22 mg, 0.027 mmol) were combined in a

reaction vial that was ﬁlled with nitrogen and evacuated three times.

Dioxane (1.6 mL, 0.17 M) was added to the reaction mixture,

followed by the addition of 2 M K₂CO₃(0.4 mL, 0.800 mmol). The

reaction mixture was degassed and run in the microwave (145 °C, H

abs) for 10 min. The reaction mixture was diluted with EtOAc,

ﬁltered through Celite, and concentrated. The crude material was

puriﬁed by ﬂash chromatography (0−70% EtOAc/Hex) to aﬀord the

title compound as a dull orange solid (48 mg, 30%). LCMS [M + H]⁺

1

604.1 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 1.45 (s, 9H),

1.91−2.07 (m, 4H), 2.30−2.39 (m, 5H), 3.44−3.57 (m, 4H), 3.94−

4.00 (m, 2H), 4.25 (br s, 2H), 4.37−4.46 (m, 1H), 6.56 (br s, 1H),

7.42 (d, J = 7.8 Hz, 2H), 7.84 (s, 1H), 8.01 (d, J = 8.3 Hz, 2H), 8.05

(s, 1H), 8.36 (s, 1H), 8.44 (s, 1H), 8.67 (d, J = 2.0 Hz, 1H).

tert-Butyl 3-(5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-

tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)piperidine-1-carboxylate (S49).

tert-Butyl 5-(5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-

tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3,6-dihydropyridine-1(2H)-car-

boxylate S48 (48 mg, 0.080 mmol) was dissolved in EtOH (1.6 mL,

0.05 M) and 10 wt % Pd/C (8 mg, 0.008 mmol) was added.

Ammonium formate (34 mg, 0.539 mmol) was added, and the

reaction mixture was reﬂuxed at 85 °C overnight. An additional

catalyst (16 mg 5 wt % Pd/C, 0.008 mmol) was added and the

reaction was monitored by LCMS. Upon completion, the reaction was

stopped and cooled to room temperature. The reaction mixture was

diluted with EtOAc, ﬁltered through Celite, and concentrated to

aﬀord the title compound as a yellow solid (46 mg, 95%). LCMS [M

+ H]⁺606.1 m/z; ¹H NMR (500 MHz, DMSO-d₆): δ ppm 1.40 (br s,

9H), 1.57−1.79 (m, 2H), 1.88−2.09 (m, 6H), 2.33 (s, 3H), 2.88−

3.08 (m, 2H), 3.10−3.22 (m, 1H), 3.48 (t, J = 11.0 Hz, 2H), 3.76−

3.88 (m, 1H), 3.97 (m, J = 7.3 Hz, 3H), 4.35−4.46 (m, 1H), 7.41 (d,

J = 7.8 Hz, 2H), 7.67 (s, 1H), 7.96 (d, J = 7.8 Hz, 2H), 8.00 (s, 1H),

8.21−8.26 (m, 1H), 8.38 (s, 1H), 8.63 (s, 1H).

0.80 (t, J = 7.8 Hz, 2H), 3.58 (t, J = 8.1 Hz, 2H), 5.74 (s, 2H), 8.28

(d, J = 2.4 Hz, 1H), 8.74 (d, J = 2.4 Hz, 1H).

3-(5-Bromo-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazolo-

[3,4-b]pyridin-3-yl)benzonitrile (S54a). 5-Bromo-3-iodo-1-((2-

(trimethylsilyl)ethoxy)methyl)-1H-pyrazolo[3,4-b]pyridine S53a

(564 mg, 1.24 mmol), (3-cyanophenyl)boronic acid (184 mg, 1.25

mmol), and PdCl2(dppf)·CH₂Cl₂(101 mg, 0.124 mmol) were

combined in a microwave vial that was purged with nitrogen and

evacuated three times. Dioxane (7.0 mL, 0.18 M) was added, followed

by the addition of 2 M K₂CO₃(1.5 mL, 3.00 mmol). The reaction

mixture was degassed for ∼10 min and the reaction was run in the

microwave (80 °C, 15 min). The reaction mixture was diluted with

EtOAc, ﬁltered through Celite, and concentrated. The crude material

was puriﬁed by ﬂash chromatography (0−20% EtOAc/Hex) to aﬀord

the title compound as a light yellow solid (259 mg, 49%). LCMS [M

tert-Butyl 3-(5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-

1H-pyrrolo[2,3-b]pyridin-3-yl)piperidine-1-carboxylate (S50). The

title compound was prepared according to General Procedure D on a

46 mg scale using tert-butyl 3-(5-(1-(tetrahydro-2H-pyran-4-yl)-1H-

pyrazol-4-yl)-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)piperidine-1-car-

boxylate S49. The reaction was run for 2 mins and the crude material

was puriﬁed by ﬂash chromatography (2−5% MeOH/DCM) to

aﬀord the title compound as a pale yellow solid (17 mg, 51%). LCMS

1

+ H]⁺428.98 m/z (⁷⁹Br), 431.0 m/z (⁸¹Br); H NMR (500 MHz,

DMSO-d₆): δ ppm −0.11 (s, 9H), 0.84 (t, J = 7.8 Hz, 2H), 3.66 (t, J

= 8.1 Hz, 2H), 5.85 (s, 2H), 7.75 (t, J = 7.8 Hz, 1H), 7.94 (d, J = 7.8

Hz, 1H), 8.39 (d, J = 8.3 Hz, 1H), 8.48 (s, 1H), 8.77 (d, J = 2.0 Hz,

1H), 9.11 (d, J = 2.0 Hz, 1H).

3-(5-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-yl)-1-((2-

(trimethylsilyl)ethoxy)methyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)-

1

[M + H]⁺452.2 m/z; H NMR (500 MHz, chloroform-d): δ ppm

1.50 (s, 9H), 1.72 (m, J = 10.7 Hz, 4H), 2.06−2.26 (m, 6H), 2.88 (t, J

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benzonitrile (S55a). The title compound was prepared according to

General Procedure E on a 140 mg scale using 3-(5-bromo-1-((2-

(trimethylsilyl)ethoxy)methyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)-

benzonitrile S54a. The reaction mixture was diluted with EtOAc,

ﬁltered through Celite, and concentrated under reduced pressure. The

crude material was puriﬁed by ﬂash chromatography (10% EtOAc/

Hex) to aﬀord the title compound as a light yellow oil (96 mg, 61%).

was dried with sodium sulfate and concentrated under reduced

pressure. The product was puriﬁed by ﬂash chromatography (0−20%

EtOAc/Hex) to aﬀord the title compound as a light orange solid (573

mg, 79%). LCMS [M + H]⁺490.85 m/z (⁷⁹Br), 492.86 m/z (⁸¹Br);

¹H NMR (500 MHz, CHLOROFORM-d): δ ppm 8.47 (s, 1H), 8.05

(d, J = 8.3 Hz, 2H), 7.88 (s, 1H), 7.30 (d, J = 7.8 Hz, 2H), 2.86 (s,

3H), 2.39 (s, 3H).

1

LCMS [M + H]⁺477.0 m/z; H NMR (500 MHz, chloroform-d): δ

3-(5-Bromo-4-methyl-1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-

benzonitrile (S54b). 5-Bromo-3-iodo-1-tosyl-1H-pyrrolo[2,3-b]-

pyridine S53b (573 mg, 1.20 mmol), (3-cyanophenyl)boronic acid

(206 mg, 1.40 mmol), and PdCl₂(dppf)·CH₂Cl₂(95 mg, 0116 mmol)

were combined in a microwave vial that was purged with nitrogen and

evacuated three times. Dioxane (6.0 mL, 0.20 M) and 2 M K₂CO₃

(1.8 mL, 3.60 mmol) were added, and the reaction mixture was

degassed for ∼10 min. The reaction was run in the microwave (120

°C) for 5 min. The reaction mixture was diluted with EtOAc, ﬁltered

through Celite, and concentrated. The product was puriﬁed by ﬂash

chromatography (0−50% EtOAc/Hex) to aﬀord the title compound

as a dull yellow solid (335 mg, 62%). LCMS [M + H]⁺465.96 m/z

ppm −0.05 (s, 9H), 0.97 (t, J = 8.3 Hz, 2H), 1.41 (s, 12H), 3.71 (t, J

= 8.3 Hz, 2H), 5.95 (s, 2H), 7.66 (t, J = 7.8 Hz), 7.72 (d, J = 7.8 Hz,

1H), 8.29 (d, J = 7.8 Hz, 1H), 8.34 (s, 1H), 8.73 (s, 1H), 8.97 (s,

1H).

3-(5-(1-(Tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-((2-

(trimethylsilyl)ethoxy)methyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)-

benzonitrile (S56a). 3-(5-(4,4,5,5-Tetramethyl-1,3,2-dioxaborolan-2-

yl)-1-((2-(trimethylsilyl)ethoxy)methyl)-1H-pyrazolo[3,4-b]pyridin-

3-yl)benzonitrile S55a (96 mg, 0.201 mmol), 4-bromo-1-(tetrahydro-

2H-pyran-4-yl)-1H-pyrazole S41a (58 mg, 0.251 mmol), and

PdCl₂(dppf)·CH₂Cl₂(19 mg, 0.023 mmol) were combined in a

reaction vial that was ﬁlled with nitrogen and evacuated three times.

Dioxane (2.0 mL, 0.10 M) was added to the reaction mixture,

followed by the addition of 2 M K₂CO₃(0.3 mL, 0.600 mmol). The

reaction mixture was degassed and run in the microwave (145 °C, H

abs) for 10 min. The reaction mixture was diluted with EtOAc,

ﬁltered through Celite, and concentrated. The crude material was

puriﬁed by ﬂash chromatography (20−60% EtOAc/Hex) to aﬀord the

title compound as an orange oil (37 mg, 36%). LCMS [M + H]⁺

1

(⁷⁹Br), 467.96 m/z (⁸¹Br); H NMR (500 MHz, chloroform-d): δ

ppm 8.52 (s, 1H), 8.12 (d, J = 8.3 Hz, 2H), 7.72 (d, J = 7.8 Hz, 1H),

7.68 (s, 2H), 7.63 (d, J = 7.8 Hz, 1H), 7.57 (t, J = 8.3 Hz, 1H), 7.33

(d, J = 8.3 Hz, 2H), 2.41 (s, 3H), 2.23 (s, 3H).

3-(4-Methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-

tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (S55b). The title

compound was prepared according to General Procedure E on a

335 mg scale using 3-(5-bromo-4-methyl-1-tosyl-1H-pyrrolo[2,3-

b]pyridin-3-yl)benzonitrile 54b. The crude material was puriﬁed by

ﬂash chromatography (20% EtOAc/Hex) to aﬀord the title

compound as a white solid (175 mg, 47%). LCMS [M + H]⁺

1

501.1 m/z; H NMR (500 MHz, chloroform-d): δ ppm −0.04 (s,

9H), 0.98 (t, J = 8.3 Hz, 2H), 2.16−2.25 (m, 4H), 3.60 (td, J = 8.3,

3.9 Hz, 2H), 3.74 (t, J = 8.8 Hz, 2H), 4.17 (d, J = 11.2 Hz, 2H),

4.39−4.50 (m, 1H), 5.95 (s, 2H), 7.66 (t, J = 7.8 Hz, 1H), 7.73 (d, J =

7.8 Hz, 1H), 7.82 (s, 1H), 7.89 (s, 1H), 8.27 (d, J = 7.8 Hz, 1H), 8.30

(s, 1H), 8.30 (s, 1H), 8.79 (d, J = 2.0 Hz, 1H).

1

514.12 m/z; H NMR (500 MHz, chloroform-d): δ ppm 8.76 (s,

1H), 8.14 (d, J = 8.3 Hz, 2H), 7.69 (m, J = 3.9, 2.0 Hz, 2H), 7.61−

7.66 (m, 2H), 7.53 (t, J = 7.8 Hz, 1H), 7.29 (d, J = 8.3 Hz, 2H), 2.39

(s, 3H), 2.37 (s, 3H), 1.33 (s, 12H).

3-(5-(1-(Tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1H-

pyrazolo[3,4-b]pyridin-3-yl)benzonitrile (32). To 3-(5-(1-(tetrahy-

dro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-((2-(trimethylsilyl)ethoxy)-

methyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)benzonitrile S56a (37 mg,

0.074 mmol) was added 4 M HCl in dioxane (0.600 mL, 2.40 mmol).

The reaction mixture was stirred at room temperature for 3 days, then

at 50 °C overnight. The reaction was stopped and cooled to room

temperature. The solvent was evaporated and the resulting yellow

residue was redissolved in MeOH. Si-carbonate was added and the

mixture was stirred overnight at room temperature. The Si-carbonate

was ﬁltered oﬀ and the ﬁltrate was puriﬁed by ﬂash chromatography

(2−5% MeOH/DCM) to aﬀord the title compound as a white solid

(10 mg, 38%). LCMS [M + H]⁺371.06 m/z 64; ¹H NMR (500 MHz,

DMSO-d₆): δ ppm 14.02 (br s, 1H), 8.91 (d, J = 1.6 Hz, 1H), 8.75 (d,

J = 1.6 Hz, 1H), 8.50 (s, 1H), 8.46 (s, 1H), 8.44 (d, J = 8.2 Hz), 8.15

(s, 1H), 7.90 (d, J = 7.7 Hz, 1H), 7.76 (t, J = 7.7 Hz, 1H), 4.45 (tquin,

J = 6.6, 6.6, 4.9, 4.9, 4.9, 4.9 Hz, 1H), 4.00 (d, J = 13.7 Hz, 2H), 3.51

(td, J = 11.7, 1.9 Hz, 2H), 1.94−2.09 (m, 4H).

3-(4-Methyl-5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-1-

tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (S56b). 4-Bromo-1-

(tetrahydro-2H-pyran-4-yl)-1H-pyrazole S41a (87 mg, 0.376 mmol)

and PdCl₂(dppf)·CH₂Cl₂(28 mg, 0.034 mmol) were combined in a

reaction vial that was ﬁlled with nitrogen and evacuated three times.

3-(4-Methyl-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-1-tosyl-

1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile S55b (175 mg, 0.341

mmol) was dissolved in dioxane (2.0 mL, 0.17 M) and added to

the reaction mixture, followed by the addition of 2 M K₂CO₃(0.70

mL, 01.40 mmol). The reaction mixture was degassed and run in the

microwave (145 °C) for 5 min. The reaction mixture was diluted with

EtOAc, ﬁltered through Celite, and concentrated. The crude material

was puriﬁed by ﬂash chromatography (50−70% EtOAc/Hex, step

gradient) to aﬀord the title compound as a tan solid (69 mg, 38%).

1

LCMS [M + H]⁺538.05 m/z; H NMR (500 MHz, DMSO-d₆): δ

5-Bromo-3-iodo-4-methyl-1H-pyrrolo[2,3-b]pyridine (S52b). 5-

Bromo-4-methyl-1H-pyrrolo[2,3-b]pyridine S51b (412 mg, 1.95

mmol) was dissolved in acetonitrile (12 mL, 0.17 M) and N-

iodosuccinimide (690 mg, 3.07 mmol) was added. The reaction

mixture was stirred at 50 °C for 2 h. The reaction was stopped and

cooled to room temperature. Upon cooling, a tan precipitate was

observed and collected by vacuum ﬁltration (washed with hexanes) to

aﬀord the title compound as a dull orange solid (495 mg, 75%).

ppm 8.38 (s, 1H), 8.03−8.11 (m, 4H), 7.98 (s, 1H), 7.89 (d, J = 7.3

Hz, 2H), 7.70 (s, 1H), 7.68 (t, J = 7.8 Hz, 1H), 7.44 (d, J = 8.3 Hz,

2H), 4.43 (spt, J = 5.9 Hz, 1H), 3.96 (d, J = 10.2 Hz, 2H), 3.43−3.51

(m, 2H), 2.36 (s, 3H), 2.19 (s, 3H), 1.91−2.04 (m, 4H).

3-(4-Methyl-5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-

1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile (33). The title compound

was prepared according to General Procedure D on a 69 mg scale

using 3-(4-methyl-5-(1-(tetrahydro-2H-pyran-4-yl)-1H-pyrazol-4-yl)-

1-tosyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzonitrile S56b. The reac-

tion was run for 5 min and the crude material was puriﬁed directly by

ﬂash chromatography (5% MeOH/DCM) to aﬀord the title

compound as an oﬀ-white solid (29 mg, 60%). LCMS [M + H]⁺

1

LCMS [M + H]⁺336.85 m/z (⁷⁹Br), 338.86 m/z (⁸¹Br); H NMR

(500 MHz, chloroform-d): δ ppm 9.09 (br s, 1H), 8.38 (s, 1H), 7.41

(d, J = 2.0 Hz, 1H), 2.95 (s, 3H).

5-Bromo-3-iodo-4-methyl-1-tosyl-1H-pyrrolo[2,3-b]pyridine

(S53b). 5-Bromo-3-iodo-4-methyl-1H-pyrrolo[2,3-b]pyridine 52b

(495 mg,1.47 mmol) was suspended in DCM (7.4 mL, 0.19 M),

and TEA (0.60 mL, 4.30 mmol), DMAP (215 mg, 1.76 mmol), and 4-

methylbenzenesulfonyl chloride (700 mg, 3.67 mmol) were added in

that order. The reaction mixture was stirred overnight at room

temperature. The reaction mixture was washed once with 1 M HCl,

once with sat. aq. NaHCO₃, and once with brine. The organic layer

1

384.14 m/z; H NMR (500 MHz, DMSO-d₆): δ ppm 11.94 (br s,

1H), 8.24 (s, 1H), 8.04 (s, 1H), 7.92 (s, 1H), 7.82 (d, J = 7.8 Hz,

1H), 7.78 (d, J = 7.8 Hz), 7.68 (s, 1H), 7.62 (t, J = 7.8 Hz, 1H), 7.58

(s, 1H), 4.44 (spt, J = 6.3 Hz, 1H), 3.98 (d, J = 11.7 Hz, 2H), 3.48 (t,

J = 11.0 Hz, 2H), 2.31 (s, 3H), 1.95−2.07 (m, 4H).

9428

https://doi.org/10.1021/acs.jmedchem.1c00674

J. Med. Chem. 2021, 64, 9404−9430

Journal of Medicinal Chemistry

pubs.acs.org/jmc

Article

Ali Syed − Center for Discovery and Innovation in Parasitic

Diseases, Skaggs School of Pharmacy and Pharmaceutical

Sciences, University of California, San Diego, California

92093, United States

Nelly El-Sakkary − Center for Discovery and Innovation in

Parasitic Diseases, Skaggs School of Pharmacy and

Pharmaceutical Sciences, University of California, San Diego,

California 92093, United States

ASSOCIATED CONTENT

* Supporting Information

The Supporting Information is available free of charge at

https://pubs.acs.org/doi/10.1021/acs.jmedchem.1c00674.

■

sı

Additional biological and ADME data, experimental

procedures, and characterization (PDF)

Molecular formula strings (CSV)

Conor R. Caﬀrey − Center for Discovery and Innovation in

Parasitic Diseases, Skaggs School of Pharmacy and

Pharmaceutical Sciences, University of California, San Diego,

California 92093, United States

Francisco Gamarro − Instituto de Parasitología y Biomedicina

“López-Neyra” Consejo Superior de Investigaciones

Cientíﬁcas (CSIC), Granada 18016, Spain

Luis Miguel Ruiz-Perez − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

Dolores Gonzalez Pacanowska − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain;

orcid.org/0000-0002-4303-5209

Miguel Navarro − Instituto de Parasitología y Biomedicina

“López-Neyra” Consejo Superior de Investigaciones

Cientíﬁcas (CSIC), Granada 18016, Spain

AUTHOR INFORMATION

Corresponding Author

Lori Ferrins − Department of Chemistry & Chemical Biology,

Northeastern University, Boston, Massachusetts 02115,

United States; orcid.org/0000-0001-8992-0919;

Phone: 617-373-3715; Email: l.ferrins@northeastern.edu

■

Authors

Dana M. Klug − Department of Chemistry & Chemical

Biology, Northeastern University, Boston, Massachusetts

02115, United States; orcid.org/0000-0002-8982-0640

Eftychia M. Mavrogiannaki − Department of Chemistry &

Chemical Biology, Northeastern University, Boston,

Massachusetts 02115, United States

Katherine C. Forbes − Department of Chemistry & Chemical

Biology, Northeastern University, Boston, Massachusetts

02115, United States

Michael P. Pollastri − Department of Chemistry & Chemical

Biology, Northeastern University, Boston, Massachusetts

02115, United States; orcid.org/0000-0001-9943-7197

Lisseth Silva − Department of Chemistry & Chemical Biology,

Northeastern University, Boston, Massachusetts 02115,

United States

Complete contact information is available at:

Rosario Diaz-Gonzalez − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

Guiomar Pérez-Moreno − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

Gloria Ceballos-Pérez − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

Raquel Garcia-Hernández − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

Cristina Bosch-Navarrete − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

Carlos Cordón-Obras − Instituto de Parasitología y

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

https://pubs.acs.org/10.1021/acs.jmedchem.1c00674

Notes

The authors declare no competing ﬁnancial interest.

ACKNOWLEDGMENTS

■

The authors acknowledge funding from the National Institute

of Allergy and Infectious Diseases (M.P.P. and M.N.,

R01AI114685; M.P.P., 1R21AI127594, R01AI124046;

C.R.C., R21AI126296; https://www.niaid.nih.gov/), the Span-

ish Ministerio de Economí a, Industria y Competitividad

(M.N., SAF2015-71444-P; D.G.-P., SAF2016-79957-R;

http://www.mineco.gob.es), Subdireccion General de Redes

y Centros de Investigacion Cooperativa (RICET, https://

www.ricet.es/) (M.N., RD16/0027/0019; D.G.P., RD16/

0027/0014), and RTI2018-097210-B-I00 (MINCIU-FEDER)

to F.G. An ACS MEDI Predoctoral Fellowship for D.M.K. is

gratefully acknowledged, as is support from the National

Science Foundation for K.F. (CHE-1262734). We thank

AstraZeneca, Charles River Laboratories, and GlaxoSmithKline

for the provision of the in vitro ADME and physicochemical

properties data. The use of JChem/ChemAxon software is

acknowledged.

́

Claudia Gómez-Linán − Instituto de Parasitología y

̃

Biomedicina “López-Neyra” Consejo Superior de

Investigaciones Cientíﬁcas (CSIC), Granada 18016, Spain

Andreu Saura − Instituto de Parasitología y Biomedicina

“López-Neyra” Consejo Superior de Investigaciones

Cientíﬁcas (CSIC), Granada 18016, Spain

Jeremiah D. Momper − Center for Discovery and Innovation

in Parasitic Diseases, Skaggs School of Pharmacy and

Pharmaceutical Sciences, University of California, San Diego,

California 92093, United States

Maria Santos Martinez-Martinez − Diseases of the Developing

World (DDW), Tres Cantos Medicines Development

Campus, GlaxoSmithKline, Tres Cantos 28760, Spain

Pilar Manzano − Diseases of the Developing World (DDW),

Tres Cantos Medicines Development Campus,

ABBREVIATIONS

■

ADME, absorption distribution metabolism excretion; Clint,

intrinsic clearance; Cmax, maximum concentration; CNS-

MPO, central nervous system-multiparameter optimization;

GSK, GlaxoSmithKline; HAT, human African trypanosomiasis;

HLM, human liver microsomes; HTS, high-throughput screen;

ip, intraperitoneal; LLE, lipophilic ligand eﬃciency; NECT,

nifurtimox−eﬂornithine combination therapy; NTD, neglected

tropical disease; PK, pharmacokinetic; PPB, plasma protein

GlaxoSmithKline, Tres Cantos 28760, Spain

9429

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J. Med. Chem. 2021, 64, 9404−9430

Journal of Medicinal Chemistry

pubs.acs.org/jmc

Article

Roncal, N. E.; Penn, E. C.; Erath, J.; Rodriguez, A.; Sciotti, R. J.;

Campbell, R. F.; McKerrow, J. H.; Siqueira-Neto, J.; Ferrins, L.;

Pollastri, M. P. Scaffold and parasite hopping: discovery of new

protozoal proliferation inhibitors. ACS Med. Chem. Lett. 2020, 11,

249−257.

binding; SD, standard error of the mean; T.b.b., Trypanosoma

brucei brucei; TEA, triethylamine; t_max, time at which maximum

concentration is achieved; TPSA, topological polar surface

area; WHO, World Health Organization

(19) Probst, A.; Nguyen, T. N.; El-Sakkary, N.; Skinner, D.; Suzuki,

B. M.; Buckner, F. S.; Gelb, M. H.; Caffrey, C. R.; Debnath, A.

Bioactivity of Farnesyltransferase Inhibitors Against Entamoeba

histolytica and Schistosoma mansoni . Frront. Cell. Infect. Microbiol.

2019, 9, No. e478.

(20) Long, T.; Rojo-Arreola, L.; Shi, D.; El-Sakkary, N.; Jarnagin, K.;

Rock, F.; Meewan, M.; Rascón, A. A., Jr.; Lin, L.; Cunningham, K. A.;

Lemieux, G. A.; Podust, L.; Abagyan, R.; Ashrafi, K.; McKerrow, J. H.;

Caffrey, C. R. Phenotypic, chemical and functional characterization of

cyclic nucleotide phosphodiesterase 4 (PDE4) as a potential

anthelmintic drug target. PLoS Neglected Trop. Dis. 2017, 11,

No. e0005680.

(21) Long, T.; Neitz, R. J.; Beasley, R.; Kalyanaraman, C.; Suzuki, B.

M.; Jacobson, M. P.; Dissous, C.; McKerrow, J. H.; Drewry, D. H.;

Zuercher, W. J.; Singh, R.; Caffrey, C. R. Structure-Bioactivity

Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like

Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni .

PLoS Neglected Trop. Dis. 2016, 10, No. e0004356.

(22) Kyere-Davies, G.; Agyare, C.; Boakye, Y. D.; Suzuki, B. M.;

Caffrey, C. R. Effect of Phenotypic Screening of Extracts and

Fractions of Erythrophleum ivorense Leaf and Stem Bark on Immature

and Adult Stages of Schistosoma mansoni . J. Parasitol. Res. 2018, 2018,

No. 9431467.

REFERENCES

■

(1) World Health Organization. Neglected Tropical Diseases.

http://www.who.int/neglected_diseases/diseases/en/ (accessed

Sept 13, 2016).

(2) Buscher, P.; Cecchi, G.; Jamonneau, V.; Priotto, G. Human

̈

African Trypanosomiasis. Lancet 2017, 390, 2397−2409.

(3) Becker, B.; Mehlhorn, H.; Andrews, P.; Thomas, H.; Eckert, J.

Light and electron microscopic studies on the effect of praziquantel

on Schistosoma mansoni , Dicrocoelium dendriticum , and Fasciola

hepatica (Trematoda) in vitro. Z Parasitenkd. 1980, 63, 113−128.

(4) Fetterer, R. H.; Pax, R. A.; Bennett, J. L. Praziquantel, potassium

and 2,4-dinitrophenol: analysis of their action on the musculature of

Schistosoma mansoni . Eur. J. Pharmacol. 1980, 64, 31−38.

(5) Renganathan, E.; Cioli, D. An international initiative on

praziquantel use. Parasitol. Today 1998, 14, 390−391.

(6) Drugs for Neglected Diseases Initiative. Acoziborole. https://

dndi.org/research-development/portfolio/acoziborole/ (accessed

April 10, 2021)

(7) Klug, D. M.; Gelb, M. H.; Pollastri, M. P. Repurposing Strategies

for Neglected Diseases. Bioorg. Med. Chem. Lett. 2016, 26, 2569−

2575.

(8) Merritt, C.; Silva, L. E.; Tanner, A. L.; Stuart, K.; Pollastri, M. P.

Kinases as Druggable Targets in Trypanosomatid Protozoan Parasites.

Chem. Rev. 2014, 114, 11280−11304.

(9) Naula, C.; Parsons, M.; Mottram, J. C. Protein kinases as drug

targets in trypanosomes and Leishmania . Biochim. Biophys. Acta 2005,

1754, 151−159.

(23) Abdulla, M.-H.; Lim, K.-C.; Sajid, M.; McKerrow, J. H.;

Caffrey, C. R. Schistosomiasis Mansoni : Novel Chemotherapy Using a

Cysteine Protease Inhibitor. PLoS Med. 2007, 4, No. e14.

(10) Hammarton, T. C.; Kramer, S.; Tetley, L.; Boshart, M.;

Mottram, J. C. Trypanosoma brucei Polo-like Kinase is Essential for

Basal Body Duplication, kDNA Segregation and Cytokinesis. Mol.

Microbiol. 2007, 65, 1229−1249.

(11) Diaz, R.; Luengo-Arratta, S.; Seixas, J. D.; Amata, E.; Devine,

W.; Cordon-Obras, C.; Rojas-Barros, D. I.; Jimenez, E.; Ortega, F.;

Crouch, S.; Colmenarejo, G.; Fiandor, J. M.; Martin, J. J.; Berlanga,

M.; Gonzalez, S.; Manzano, P.; Navarro, M.; Pollastri, M. P.

Identification and Characterization of Hundreds of Potent and

Selective Inhibitors of Trypanosoma brucei Growth from a Kinase-

Targeted Library Screening Campaign. PLoS Neglected Trop. Dis.

2014, 8, No. e3253.

(12) Shultz, M. D. The thermodynamic basis for the use of lipophilic

efficiency (LipE) in enthalpic optimizations. Bioorg. Med. Chem. Lett.

2013, 23, 5992−6000.

(13) Wager, T.; Hou, X.; Verhoest, P. R.; Villalobos, A. Moving

beyond rules: The development of a central nervous system

multiparameter optimization (CNS MPO) approach to enable

alignment of druglike properties. ACS Chem. Neurosci. 2010, 1,

435−449.

(14) Cruciani, G.; Carosati, E.; De Boeck, B.; Ethirajulu, K.; Mackie,

C.; Howe, T.; Vianello, R. MetaSite: Understanding metabolism in

human cytochromes from the perspective of the chemist. J. Med.

Chem. 2005, 48, 6970−6979.

(15) Lovering, F.; Bikker, J.; Humblet, C. Escape from flatland:

Increasing saturation as an approach to improving clinical success. J.

Med. Chem. 2009, 52, 6752−6756.

(16) Ishikawa, M.; Hashimoto, Y. Improvement in aqueous

solubility in small molecule drug discovery programs by disruption

of molecular planarity and symmetry. J. Med. Chem. 2011, 54, 1539−

1554.

(17) Gupta, M.; Lee, H. J.; Barden, C. J.; Weaver, D. F. The blood-

brain barrier (BBB) score. J. Med. Chem. 2019, 62, 9824−9836.

(18) Singh, B.; Bernatchez, J. A.; McCall, L.-I.; Calvet, C. M.;

Ackermann, J.; Souza, J. M.; Thomas, D.; Silva, E. M.; Bachovchin, K.

A.; Klug, D. M.; Jalani, H. B.; Bag, S.; Buskes, M. J.; Leed, S. E.;

9430

https://doi.org/10.1021/acs.jmedchem.1c00674

J. Med. Chem. 2021, 64, 9404−9430

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Lead Optimization of 3,5-Disubstituted-7-Azaindoles for the Treatment of Human African Trypanosomiasis

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