A novel protocol for the one-pot borylation/Suzuki reaction provides easy access to hinge-binding groups for kinase inhibitors

Article abstract of DOI:10.1039/c5ob01915j

The one-pot borylation/Suzuki reaction is a very efficient means of accessing cross-coupling products of two aryl-halide partners that generally requires the use of specific catalysts or ligands and/or relatively long reaction times. This new microwave-assisted method provides a quick one-pot borylation/Suzuki reaction protocol that we applied to the synthesis of various bi- or poly-aryl scaffolds, including a variety of aryl and heteroaryl ring systems and the core frameworks of kinase inhibitors vemurafenib and GDC-0879.

Full text of DOI:10.1039/c5ob01915j

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A novel protocol for the one-pot borylation/Suzuki reaction
provides easy access to hinge-binding groups for kinase inhibitors
A. Hooper,a A. Zambona+ and C. J. Springera+*
Received 00th January 20xx,
Accepted 00th January 20xx
The one-pot borylation/Suzuki reaction is a very efficient means of accessing cross-coupling products of two aryl-halide
partners that generally requires the use of specific catalysts or ligands and/or relatively long reaction times. This new
microwave-assisted method provides a quick one-pot borylation/Suzuki reaction protocol that we applied to the synthesis
of various bi- or poly- aryl scaffolds, including a variety of aryl and heteroaryl ring systems and the core frameworks of
kinase inhibitors vemurafenib and GDC-0879.
DOI: 10.1039/x0xx00000x
www.rsc.org/
high expense and instability of certain boronic species. In order
to circumvent these issues, Miyaura explored the use of
bis(pinocolato)diboron as the boronic acid equivalent in a one-
Introduction
Kinases are key functional proteins that regulate signal
transduction pathways in cells by catalyzing phosphorylation
of serine, threonine, or tyrosine residues. Deregulation of
protein kinases is implicated in many diseases including
cancer, diabetes, and inflammation: as a consequence kinases
have been major targets for recent small molecule drug
development.1-3
pot borylation/Suzuki reaction, which eliminates the need to
isolate the boronic intermediate. Despite subsequent
improvements to the methodology,11-15 current one-pot
borylation/Suzuki protocols require double loading of specific
catalysts, use of additional ligands or relatively long reaction
times, and their scope is generally limited to one specific
scaffold.16-18
A common feature of most kinase inhibitors is the presence of
a hinge-binding moiety,4 a group that is able to form hydrogen
bonds to the cleft between N- and C- lobes of the kinase
Our aim was to develop a robust one-pot borylation/Suzuki
protocol that employs one single loading of catalyst with no
need for additional ligands and to use it to access a small panel
of putative hinge binding fragments, which were then profiled
for kinase selectivity.
known as the hinge region.4 Typically,
a hinge-binding
structure consists of a hetero-aromatic group containing
hydrogen bond donors and/or acceptors in either a mono- or
bi-dentate fashion. This mode of binding mimics that of the
adenosine ring of the natural kinase ligand, ATP.
Results and discussion
As a model reaction for the optimisation of the one-pot
protocol, we selected the coupling of 5-bromoindanone 1a and
3-bromopyridine 3a to give 3-pyridinylindenone 4a, mediated
by the formation of pinacolate boronic ester 2a. We reasoned
that the structure of 4a could act as a basic scaffold for a
kinase inhibitor, with the pyridine group acting as hinge binder
and the indanone elaborating into the ATP binding pocket.
Variation of this basic structure would then allow us to access
a panel of compounds with potential kinase activity.
The palladium-catalysed Suzuki-Miyaura reaction, which
couples aryl halide and aryl boronic species for the formation
5-8
of new C-C bonds,
is particularly suited to access hinge
binding fragments thanks to its tolerance of functional groups
and mild reaction conditions. Furthermore, extensive
literature describes a wide range of experimental procedures.9,
10
Despite its wide scope, the Suzuki-Miyaura cross-coupling
reaction has a number of limitations such as lack of availability,
The original borylation conditions, developed by Miyaura11
were assessed utilising Pd(dppf)Cl2 as the catalytic species and
KOAc as the base. Although this yields the boronic ester 2a
with 100% conversion, addition of 3-bromopyridine 3a, along
with catalyst and base did not yield 4a (Table 1, entry 1).
Pd(PPh3)4 as catalyst was assessed for the Suzuki step but again
4a was not formed (entry 2). However, the borylation reaction
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time could be shortened to 1 hour at 120 °C under microwave Table 1 Optimisation of the reaction conditionsa
irradiation resulting in the formation of intermediate 2a. This is
ii)
Br
i)
B (pin)
2 2
O
a significant time reduction from 18 h needed at 80 °C using
both catalytic species (entries 3 and 4). From this point, only
tetrakis(triphenylphosphine)palladium(0) as catalyst was
utilized to avoid a mixture of catalytic species as this was
deemed most suitable due to its wide use and cheaper cost.
O
Cat1
Base1
O
N
3a
Cat2
Base2
dioxane
O
B
o
T, t1
120 C, t2
Br
O
N
1a
2a
4a
Entry
Cat1/
Base1
t2 (h) T (°C)
2a
Cat2/
t2
4a
To identify the best reaction conditions to access 4a for a one
(%)b
Base2
(h)
(%)b
pot reaction, we postulated a bicyclic mechanism merging the
Pd(dppf)Cl2/
KOAc
Pd(dppf)Cl2/
KOAc
1
2
3
4
5
6
7
18
18
1
80
80
100
1
0
catalytic cycles
the borylation and coupling steps respectively,11, 19 as outlined
in Figure 1. Cycle is a typical borylation cycle with oxidative-
1 and 2 elucidated by Miyaura and Suzuki for
Pd(dppf)Cl2/
KOAc
Pd(PPh3)4/
KOAc
100
100
1
1
1
1
-
0
0
1
addition of the first halide to the catalytic species, oxidising the
palladium species from the neutral state of the Pd(PPh3)4 to
the Pd(II) species. Base1 then displaces the halide within the
catalytic complex, activating it for the subsequent
transmetallation step with bis(pinocolato)diboron.11, 19 A final
reductive-elimination step recovers the Pd(0) catalytic species
Pd(dppf)Cl2/
KOAc
Pd(PPh3)4/
KOAc
120c
Pd(PPh3)4/
KOAc
Pd(PPh3)4/
KOAc
1
120c,d 100
0
Pd(PPh3)4/
KOAc
Pd(PPh3)4/
Na2CO3(aq)
1
120c
120c
120c
100
0e
100
-
Pd(PPh3)4/
Na2CO3(aq)
Pd(PPh3)4/
KOAc
and completes cycle
1, releasing the aryl-boronic species; at
1
-
this stage the reactions carried out in entries 1-4 stalled.
45
- /
30
100
100
min
Na2CO3(aq)
min
Similarly, catalytic cycle
2 is initiated by oxidative addition of
aReaction conditions: 1a (1 equiv.), B2(pin)2 (1.2 equiv.), catalyst (10 mol%) and
base (3 equiv.) in dioxane (0.5 M) followed by 3a (1 equiv.), catalyst (10 mol%)
the second halide to the catalyst and the displacement of the
halide by Base2 followed by addition of the aryl boronate to
form the biaryl-substituted palladium species. Complexation of
a base to the aryl boronate is essential at this stage in order to
accelerate the transmetallation step20 by forming a more
reactive boronate to interact with the palladium species21 and
facilitate an intramolecular transmetallation.22 We postulated
and base (2 equiv.).bConversion by LCMS.cReactions performed in
a
microwave.dInitially heated to 80 °C over 18 h but after no product 2a formation
was observed, it was heated to 120 °C in a microwave for 1 h.eOnly indanone
dimer observed.
We then applied a change of base to our model system,
introducing sodium carbonate as second base after the
that a stronger base is required at this step in cycle
2 than the
formation of intermediate 2a
,
and pleasingly the
one needed in cycle 1, which only has the role to displace the
pyridinylindenone product 4a is formed with 100% conversion
(entry 5). As a further confirmation of the reaction mechanism,
the introduction of sodium carbonate in the borylation step
affords only the homocoupling product (entry 6).
halide from the first palladium species.
Once the optimal base/catalyst system was identified, we
worked to eliminate the second catalyst loading and decrease
the reaction times. In these optimised conditions, 100%
conversion to product 4a was obtained (entry 7) using a single
initial loading of Pd(PPh3)4, with 45 minutes at 120 °C under
microwave irradiation for the borylation step, followed by
addition of 3a and Na2CO3 with further heating to 120 °C for 30
min in the Suzuki step.
Next, we applied this optimised protocol to the synthesis of a
small panel of putative kinase inhibitors. To explore the scope
of the reaction and provide a set of hinge-binding fragments,
we included in the reaction panel keto, boc-protected aniline,
halo, aryl, indanone, pyridyl, pyrazole, azaindole and quinoline
functional groups. To this end,
commercially available, relatively undecorated halides was
chosen: four heteroaromatic rings containing either
hydrogen bond acceptor, a hydrogen bond donor or both (3a-
and four phenyl moieties 1a-d), to be coupled in
a selection of eight
Fig. 1 Proposed catalytic cycle.
a
d
)
(
combination to obtain 16 products (4a-p). Within this set is
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compound 4j, which is a precursor of the BRAF-selective Pleasingly, regioselectivity in the coupling reaction was
inhibitor, vemurafenib. The isolated yields obtained were good obtained for 1c (entries 9 to 12) and 3d (entries 4, 8, 12 and 6),
to excellent with the single exception of 4b (Table 2). which only reacted at the bromine and not at the chlorine.
Table 2 Scope of reaction to perform basic scaffoldsa
Entry
1
First Halide
Second Halide
Product
Yield (%)b
70
1a
4a
3a
2
3
4
1a
1a
1a
12
3b
4b
67
3c
4c
100
3d
3a
4d
4e
BocHN
5
6
52
53
Br
1b
1b
3b
4f
7
8
1b
1b
3c
46
40
4g
3d
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4h
9
3a
3b
3c
42
1c
1c
4i
10
11
32
62
4j
1c
1c
4k
4l
12
13
14
3d
3a
3b
49
81
45
1d
1d
4m
4n
4o
4p
15
16
1d
1d
3c
87
68
3d
aReaction conditions: First halide (1 equiv.), B2(pin)2 (1.2 equiv.), Pd(PPh3)4 (10 mol%) and KOAc (3 equiv.) in dioxane (0.5 M) followed by second halide (1 equiv.) and
2M Na2CO3 (aq) (2 equiv.).bIsolated yield.
The new protocol was then evaluated for the synthesis of GDC-087923 analogues 5a-d in moderate to good yields (Table
more complex scaffolds; coupling of halides 1a-d with the 3) with a slightly modified protocol allowing for longer reaction
trityl-protected 4-(4-bromopyrazolyl)pyridine 3e provided times.
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Table 3 Scope of reaction to form complex scaffoldsa
Entry
First Halide
Second Halide
Product
Yield (%)b
1
1a
57
3e
3e
5a
2
1b
33
5b
3
3e
1c
49
5c
4
3e
1d
65
5d
aReaction conditions: First halide (1 equiv.), B2(pin)2 (1.2 equiv.), Pd(PPh3)4 (10 mol%) and KOAc (3 equiv.) in dioxane (0.4 M) followed by second halide (1 equiv.) and
2M Na2CO3 (aq) (2 equiv.).bIsolated yield.
The 20 compounds synthesised were assessed on a small panel these, 4o and 4p have a selective profile, inhibiting just ABL
of kinases using the ProfilerPro® Selectivity Assay Kits (Caliper (entry 10, 4o) or both ABL and CK1 (entry 11, 4p) at the
Life Sciences, Inc.). The inhibition of 24 kinases was concentrations used. There is one commercially available ABL
determined at a compound concentration of 300 μM; of the 20 inhibitor which contains a quinoline moiety, Rebastinib (DCC-
compounds, 11 showed greater than 50% inhibition of at least 2036), but this has a binding mode in which the quinolone
one kinase (Table 4) with compounds 4j, 4n,
4o and 4p does not interact with the hinge region.24
showing greater than 90% inhibition for at least one kinase. Of
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Table 4 Results of kinase screen using a small panel of kinase inhibitor-like scaffolds.
O
O
BocHN
N
N
N
H
N
N
H
4a
4b
4f
Cl
Cl
Cl
Cl
Cl
N
N
N
N
N
H
4i
4j
4k
4l
Cl
N
N
N
N
N
H
4m
4n
4o
4p
Kinase %Inhibition
AurA RSK1 PRAK Erk1 PKD2 CK1δ CHK1 ABL FYN LYNα CHK2 MET LCK SRC GSK3β Erk2 PKACα INSR MSK1
Entry Compound
1
2
4a
4b
4f
51
76
60
61
89
45
7
41
-2
19
3
14
16
8
38
6
38
46
50
34
73
70
68
58
94
44
92
10
15
13
0
41
37
23
68
87
65
36
43
85
95
94
-2
1
33
20
24
63
30
29
-7
35
41
35
25
43
18
3
16
16
9
31
16
29
61
16
43
11
18
63
54
67
25
20
8
56
26
8
14
19
-7
10
53
1
6
24
61
46
24
58
21
12
26
93
44
49
28
4
-14
37
52
46
22
29
56
61
37
59
3
20
52
91
31
3
40
26
86
22
-1
18
32
87
34
-35
13
92
16
18
-25
54
79
-1
19
42
69
13
13
26
43
15
24
4
4i
7
17
47
29
16
28
52
35
35
43
79
19
3
30
45
26
60
14
57
26
50
5
4j
55
6
6
6
4k
4l
-9
-7
-12
80
1
7
0
18
27
53
30
48
3
8
4m
4n
4o
4p
51
99
45
66
30
70
34
48
27
47
12
14
8
46
76
49
64
37
91
18
37
25
62
23
36
4
9
62
7
66
1
10
11
6
-1
-7
In order to validate hits 4o and 4p, ABL IC50s were determined
(Invitrogen) at a starting compound concentration of 100 μM.
Compound 4o inhibits ABL with an IC50 of 8 μM, corresponding
to a high ligand efficiency of 0.45, as shown in Table 5 and,
although it has a higher IC50, a similar ligand efficiency is
observed for 4p with ABL. Conversely, the IC50 of 4p for CK1δ
was > 300 μM, further highlighting the selectivity of the
scaffold.
Conclusions
In conclusion, a novel, quick and robust microwave-assisted
protocol for the one-pot borylation/Suzuki reaction has been
developed to access a small panel of putative kinase inhibitors
containing a variety of aryl and heteroaryl ring systems. These
scaffolds have been assessed for inhibition of a panel of
kinases, and a ligand efficiency of 0.45 is observed with the
Table 5 Determination of IC50 and ligand efficiency with ABL
for 4o and 4p at compound concentration of 100 µM
kinase ABL for compound 4o
.
Entry
Compound
ABL IC50 (µM)
8.11
Ligand Efficiency
Acknowledgements
1
2
4o
4p
0.45
0.39
19.2
We thank Wellcome Trust (grant WEL081X) for funding. We
also thank Dr Jonathan Macdonald for assistance with the
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ProfilerPro Assay as well as Dr Maggie Liu, Dr Amin Mirza and
Mr Meirion Richards for assistance with NMR and LCMS
analysis.
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