Diversity-oriented synthesis of bicyclic fragments containing privileged azines

Article abstract of DOI:10.1016/j.bmcl.2018.11.046

An innovative and efficient reagent- and scaffold-based diversity oriented synthesis (DOS) of a fragment set was developed for fragment-based drug discovery (FBDD) programs. Twelve diverse, functionalized and bicyclic scaffolds were rapidly accessed by adopting a convenient synthetic toolkit around three privileged azine cores in order to effectively modulate biomolecules. These structures are characterized by both key motifs for interacting with diverse biological targets via hydrogen bonds and useful points of growth for subsequent fragment optimization.

Full text of DOI:10.1016/j.bmcl.2018.11.046

Bioorganic & Medicinal Chemistry Letters xxx (xxxx) xxx–xxx
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Diversity-oriented synthesis of bicyclic fragments containing privileged
azines
Nicola Luise, Paul G. Wyatt
Drug Discovery Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK
A R T I C L E I N F O
A B S T R A C T
Keywords:
An innovative and efficient reagent- and scaffold-based diversity oriented synthesis (DOS) of a fragment set was
developed for fragment-based drug discovery (FBDD) programs. Twelve diverse, functionalized and bicyclic
scaffolds were rapidly accessed by adopting a convenient synthetic toolkit around three privileged azine cores in
order to effectively modulate biomolecules. These structures are characterized by both key motifs for interacting
with diverse biological targets via hydrogen bonds and useful points of growth for subsequent fragment opti-
mization.
Drug discovery
Heterocycles
Fused-ring system
Diversity-oriented synthesis
Synthetic methods
Since the seminal paper in 2000 by Shreiber, diversity-oriented
synthesis (DOS) has gained considerable popularity within the field of
chemical biology, medicinal chemistry and drug discovery due to its
ability to deliver reliable solutions to the complexity and diversity is-
(CeH HBD) adjacent to the ring nitrogens (Scheme 1).7 This ability is
particularly highlighted in the field of kinase inhibitors where diverse
heteroaromatic scaffolds interact with the amides of the backbone of the
8
kinase hinge region, through this hydrogen bonding pattern. Although
1
sues encountered by combinatorial chemistry.
the strength of binding delivered by CeH HBDs is possibly not as strong
as that provided by an amide NeH or hydroxyl OeH, these interactions
are important because of their ability to modulate ADME properties,
especially at the late lead optimization stage within drug discovery
More recently, attention has been focused on the ability to produce
relevant biological active molecules via incorporation of essential pri-
vileged structures (privileged-substructure-based DOS (pDOS)). Indeed,
as stated by Kim et al., privileged structures (e.g. indole, pyridine,
purine, etc.) are recurring motifs within bioactive molecules that can be
exploited as “chemical navigators” to access novel chemical and bio-
9
programs. An increased number of heteroatom-H bond donor func-
tionalities in a compound has been shown to be detrimental for multiple
ADME parameters, including solubility (intermolecular H-bonding),
membrane penetration, and CNS penetration (ability to cross membrane
and PgP substrate susceptibility). Therefore replacing amides and ureas
with heteroaromatics can alleviate these issues. These bicyclic fragments
were synthesized based on their compliance with the Drug Discovery
Unit, University of Dundee, UK’s (DDU) fragment criteria (MW ≤ 300;
log P = −2 to 2; log D = −2 to 2; tPSA = ≤90; HBA ≤ 6; HBD ≤ 3;
2
logical space.
Despite the tangible benefit of this approach to furnish complex
3
drug-like molecules able to modulate biological targets, its application
4
to fragment-based drug-discovery (FBDD) has been infrequent and
only a few publications highlight the preparation of low-molecular
5
weight (≤250 Da) fragments.
10
In view of this, we describe both optimized and new convenient
synthetic routes (one- or two-step reactions) to access bicyclic frag-
ments with an embedded privileged motif that are either novel or have
limited commercial availability. In particular, both reagent- and scaf-
fold-based DOS was applied to three privileged structures that are
commonly present in drugs and bioactive natural products: pyridine,
NROT ≤ 3), which conforms to the “rule-of-three” (Ro3). The rules
were adopted to control complexity to increase hit rates and physico-
chemical properties to ensure compounds were soluble at the high con-
centration needed for fragment screening, and minimize aggregation in
solution and non-specific interactions with proteins.
The described chemistry emphasizes how medicinal chemists can
readily access interesting small molecules, from readily available
starting material, in order to enrich fragment libraries. Moreover, this
approach can be widely applied to diverse privileged scaffolds to con-
struct unprecedented heterocyclic systems.
6
pyrimidine and pyrazine (Fig. 1).
The application of such synthetic approach delivered twelve scaffolds
with optimal fragment properties for subsequent optimization and for
binding to biomolecules, for example by exploiting the ability of the
pyridine, pyrazine and pyrimidine motifs to not only accept hydrogen
bonds but to act as hydrogen bond donators through aromatic CeH
Our strategy for the construction of bicyclic fragments (6–14 and
17–30) (Scheme 1) was based on the presence of two adjacent
E-mail address: p.g.wyatt@dundee.ac.uk (P.G. Wyatt).
https://doi.org/10.1016/j.bmcl.2018.11.046
Received 27 September 2018; Received in revised form 19 November 2018; Accepted 22 November 2018
0960-894X/ © 2018 Published by Elsevier Ltd.
Please cite this article as: Luise, N., Bioorganic & Medicinal Chemistry Letters, https://doi.org/10.1016/j.bmcl.2018.11.046

N. Luise, P.G. Wyatt
Bioorganic & Medicinal Chemistry Letters xxx (xxxx) xxx–xxx
Scheme 2. Synthetic approach for 2 and 3.
optimized reaction conditions were successfully applied to 2 and 3 to
afford the novel thieno-pyrimidine 7 and -pyrazine 8, respectively
(
entries 6 and 7).
Similarly, the synthesis of the unprecedented functionalized fur-
oazines 9, 10 and 11 was attempted (Scheme 1(B)) (Table 1). The
electrophilic species was in this case an isocyanate, which is rarely used
in organic synthesis. Gratifyingly, the abovementioned reaction con-
ditions gave similar results when employed for the pyrimidine and
pyrazine core (10 and 11) (entries 8 and 9). However, a decrease in
yield was observed for the synthesis of 9 (entry 10), probably due to a
combination of the lower reactivity of both oxygen and pyridine com-
pared to sulfur and diazines, respectively. After chromatographic pur-
ification, intermediate 9′ was recovered along with the desired final
fragment 9. Unfortunately, neither an enhanced reaction time nor a
higher temperature were beneficial for improving the reaction outcome
Fig. 1. Bioactive molecules containing privileged structures.
functionalities on the azine cores to develop key reactions. In this re-
gard, compounds 1–3 were initially chosen, bearing a methylene-ester
and a halide as exploitable functional groups. Because of the high cost
of 2 and 3, it was decided to synthesize them by following literature
(
entry 13). An extra 0.5 equivalent of base, potentially due to depro-
tonation of the alpha carbon next to the carbonyls of the forming 9′,
augmented the final yield (entry 11). In contrast, an increase in the
isocyanate amount or a change of base did not enable any significant
improvements (entries 12 and 14). With these six bicyclic systems in
hand (6–11), the conversion of the ester group into more polar func-
tionalities was attempted. NaOH promoted the hydrolysis of 6–8 to
afford 12–14 in excellent yield, conversely 9–11 were not stable under
the same reaction conditions and the side products 15 (trace) and 16
were mainly obtained (Scheme 3).
methods. Pyrimidinone 4 was treated with POCl at high temperature
3
1
1
to access 2, whereas dichloropyrazine 5 yielded 3 after treatment
1
2
with the enolate of EtOAc (Scheme 2).
The first set of fragments were the bicyclic thienoazines 6–8
(
Scheme1(A)), bearing two handles (ester and amine) either for further
functionalization and elaboration or to make interesting interactions
(
e.g. hydrogen bonds) (Scheme 1(A)). The idea was to exploit the nu-
cleophilicity of an activated methylene and the high electrophilicity of
1
3
methyl isothiocyanate, inspired by Bremner et al.’s strategy. The
synthetic route was rapidly tested on 1 (Table 1), considering its lower
propensity for SnAr compared to 2 and 3. In this regard, higher tem-
perature and shorter reaction time, under microwave irradiation (entry
Concurrently, generation of secondary amides was attempted.
Reaction of 12–14 with diverse coupling reagents did not deliver the
required results, so the Weinreb’s procedure was tried to access 17–22
via ester aminolysis of 6–11. Pleasingly, the use of AlMe and methy-
3
3
2
), led to a better yield compared to conventional heating (entry 1 and
), whereas no substantial increase in yield was observed when DMSO
lamine, in a sealed microwave vial under conventional heating, led to
1
7–22 in > 50% yields (Table 2).14
and NMP were used instead of DMF (entries 4 and 5). Then, the
Scheme 1. Reagent- and scaffold-based diversity-oriented synthesis of pyrido-, pyrimido- and -pyrazo-containing heterobicyclic fragments.
2

N. Luise, P.G. Wyatt
Bioorganic & Medicinal Chemistry Letters xxx (xxxx) xxx–xxx
Table 1
Optimization of reaction conditions for the synthesis of thieno- and furo-azines.
Entry (substrate)
Reagent
Solvent
Base
Temperature/heating conditions
Time (h)
Product
Yield %
1
2
3
4
5
6
7
8
9
1
1
1
1
1
(1)
(1)
Isothiocyanate (1.1 equiv.)
DMF
NaH (1.2 equiv.)
70 °C (conventional)
24
2
2
2
2
2
2
2
2
2
2
2
5
2
6
59
”
”
”
120 °C (conventional)
6
67
(1)
”
“
”
120 °C (microwave, 250 W)
6
72
(1)
”
DMSO
”
”
6
69
(1)
”
NMP
”
”
6
68
(2)
”
DMF
”
”
7
75
(3)
”
”
”
”
”
”
”
”
”
”
”
8
73
(2)
Isocyanate (1.1 equiv.)
”
”
10
11
9
68
(3)
”
”
”
71
0 (1)
1 (1)
2 (1)
3 (1)
4 (1)
”
”
”
28
”
NaH (1.7 equiv.)
”
9
40
Isocyanate (1.5 equiv.)
NaH (1.2 equiv.)
”
9
29
Isocyanate (1.1 equiv.)
”
”
120–150 °C (microwave, 250 W)
”
9
29
KHMDS/LiHMDS/t-BuOK (1.2 equiv.)
9
22–26
Scheme 4. Synthesis of aza-oxo-indoles fragments.
Scheme 5. Synthesis of fluorinated fragment 29.
Scheme 3. Ester hydrolysis of fragments 6–11.
Table 2
Ester aminolysis of 6–11.
Entry (substrate)
Product
Yield %
1
2
3
4
5
6
(1)
(2)
(3)
(1)
(2)
(3)
17 (X, Y = CH; Z = S; R = CH
3
)
57
60
59
51
53
55
18 (X = N; Y = CH; Z = S; R = CH
19 (X = CH; Y = N; Z = S; R = CH
3
3
)
)
20 (X, Y = CH; Z = O; R = CH(CH
3
)
2
)
21 (X = N; Y = CH; Z = O; R = CH(CH
22 (X = CH; Y = N; Z = O; R = CH(CH
3
3
)
2
2
)
)
)
Scheme 6. Synthesis of dihydropyridazinone-containing fragments.
Generation of the bicyclic aza-oxo-indole moieties was then in-
vestigated (Scheme 1(C)). 2-Chloropyridines and 2/4-chlorodiazines
readily undergo SnAr reactions and the preparation of 23–25 was based
around the concept of promoting nucleophilic aromatic displacement
and amide formation, preferably, in a single step. However, 1–3 showed
low reactivity towards amines. This result was in line with a recent
work published by Simig et al.,15 which described a two-step synthesis
of pyrimido-pyrrolidinones, starting from 2 and other derivatives, by
employing harsh conditions (T = 260 °C). In order to identify a shorter
and milder route, it was decided to try an AlMe -mediated amide
3
3

N. Luise, P.G. Wyatt
Bioorganic & Medicinal Chemistry Letters xxx (xxxx) xxx–xxx
building blocks (1–3) or their subsequent intermediates (e.g. 28 and 33/
3
4), once binding information is acquired (Fig. 2b). In summary, structu-
rally diverse fragments (6–14 and 17–30), compliant with the DDU
fragment library’s rules that conform to the Ro3, were rapidly generated
by harnessing the concept of reagent- and scaffold-based DOS. A limited
set of optimized reaction conditions was applied to three privileged azines
(
1–3), sharing two functionalities to build aromatic and non-aromatic
counterparts. This approach permitted the access of twelve diverse and
functionalized scaffolds that were either novel or had limited commercial
availability, providing potential ligands for diverse biological targets
during FBDD campaigns. Moreover, these small molecules are character-
ized by distinct point of growths that can be exploited for further opti-
mization during a hit-to-lead phase.
Acknowledgments
Fig. 2. (a) Examples of exploitable vectors for fragment optimization. (b)
Potential fragment elaboration upon acquisition of ligand-target binding
knowledge, by varying the commercial available reactants.
We thank the School of Life Sciences, University of Dundee and
Nicholl-Lindsay Studentship for supporting our research.
formation and cyclisation in one step. Pleasingly, when 2 was reacted at
Appendix A. Supplementary data
1
10 °C for 2 h with a mixture of AlMe
3
and MeNH , ester aminolysis and
2
successive intramolecular lactam generation was achieved in one step
to give 24 (Scheme 4a). By contrast, no cyclisation took place on the
pyridine and pyrazine scaffold probably due to their lower reactivity
towards SnAr. However, the desired fragments 23 and 24 were suc-
cessfully accessed when intermediate 26 and 27 were irradiated in
Supplementary data to this article can be found online at https://
doi.org/10.1016/j.bmcl.2018.11.046.
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