Discovery of a Covalent Inhibitor of KRASG12C (AMG 510) for the Treatment of Solid Tumors

Article abstract of DOI:10.1021/acs.jmedchem.9b01180

KRAS^G12C has emerged as a promising target in the treatment of solid tumors. Covalent inhibitors targeting the mutant cysteine-12 residue have been shown to disrupt signaling by this long-"undruggable" target; however clinically viable inhibitors have yet to be identified. Here, we report efforts to exploit a cryptic pocket (H95/Y96/Q99) we identified in KRAS^G12C to identify inhibitors suitable for clinical development. Structure-based design efforts leading to the identification of a novel quinazolinone scaffold are described, along with optimization efforts that overcame a configurational stability issue arising from restricted rotation about an axially chiral biaryl bond. Biopharmaceutical optimization of the resulting leads culminated in the identification of AMG 510, a highly potent, selective, and well-tolerated KRAS^G12C inhibitor currently in phase I clinical trials (NCT03600883).

Full text of DOI:10.1021/acs.jmedchem.9b01180

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Drug Annotation
Discovery of a covalent inhibitor of KRASG12C
(AMG 510) for the treatment of solid tumors
Brian A Lanman, Jennifer R. Allen, John G. Allen, Albert K Amegadzie, Kate S. Ashton, Shon K. Booker, Jian
Jeffrey Chen, Ning Chen, Michael J Frohn, Guy Goodman, David J Kopecky, Longbin Liu, Patricia Lopez,
Jonathan D Low, Vu Ma, Ana Elena Minatti, Thomas T Nguyen, Nobuko Nishimura, Alexander J. Pickrell,
Anthony B. Reed, Youngsook Shin, Aaron Siegmund, Nuria A. Tamayo, Christopher M Tegley, Mary C Walton,
Hui-Ling Wang, Ryan P. Wurz, May Xue, Kevin C Yang, Pragathi Achanta, Michael D. Bartberger, Jude
Canon, L Steven Hollis, John D McCarter, Christopher Mohr, Karen Rex, Anne Y Saiki, Tisha San Miguel,
Laurie Volak, Kevin H Wang, Douglas A. Whittington, Stephan G Zech, J. Russell Lipford, and Victor J. Cee
J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.9b01180 • Publication Date (Web): 10 Dec 2019
Downloaded from pubs.acs.org on December 10, 2019
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Lipford, J. Russell; Amgen Inc
Cee, Victor; Amgen Inc, Medicinal Chemistry
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Discovery of a covalent inhibitor of KRASG12C (AMG 510) for the
treatment of solid tumors
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Brian A. Lanman,*,† Jennifer R. Allen,† John G. Allen,† Albert K. Amegadzie,† Kate S. Ashton,† Shon
K. Booker,† Jian Jeffrey Chen,† Ning Chen,† Michael J. Frohn,† Guy Goodman,† David J. Kopecky,†
Longbin Liu,† Patricia Lopez,† Jonathan D. Low,† Vu Ma,† Ana E. Minatti,† Thomas T. Nguyen,†
Nobuko Nishimura,† Alexander J. Pickrell,† Anthony B. Reed,† Youngsook Shin,† Aaron C. Siegmund,†
Nuria A. Tamayo,† Christopher M. Tegley,† Mary C. Walton,† Hui-Ling Wang,† Ryan P. Wurz,† May
Xue,† Kevin C. Yang,† Pragathi Achanta,‡ Michael D. Bartberger,§ Jude Canon,‡ L. Steven Hollis,‖ John
D. McCarter,¶ Christopher Mohr,§ Karen Rex,‡ Anne Y. Saiki,‡ Tisha San Miguel,¶ Laurie P. Volak,#
Kevin H. Wang,┴ Douglas A. Whittington,┴ Stephan G. Zech,‖ J. Russell Lipford,‡ Victor J. Cee†
Departments of †Medicinal Chemistry, ‡Oncology Research, §Molecular Engineering, ¶Discovery Technologies, and
#Pharmacokinetics and Drug Metabolism, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320,
United States
Departments of ‖Discovery Attribute Sciences and ┴Molecular Engineering, Amgen Research, 360 Binney Street,
Cambridge, Massachusetts 02142, United States
Keywords: RAS pathway; GDP-KRAS; switch II pocket; structure-based design; cryptic pocket; cysteine alkylation;
atropisomerism
ABSTRACT: KRASG12C has emerged as a promising target in the treatment of solid tumors. Covalent inhibitors targeting the mutant
cysteine-12 residue have been shown to disrupt signaling by this long-“undruggable” target, however clinically viable inhibitors have
yet to be identified. Here, we report efforts to exploit a cryptic pocket (H95/Y96/Q99) we identified in KRASG12C to identify inhibitors
suitable for clinical development. Structure-based design efforts leading to the identification of a novel quinazolinone scaffold are
described, along with optimization efforts that overcame a configurational stability issue arising from restricted rotation about an
axially chiral biaryl bond. Biopharmaceutical optimization of the resulting leads culminated in the identification of AMG 510, a
highly potent, selective, and well-tolerated KRASG12C inhibitor currently in Phase I clinical trials (NCT03600883).
Despite being one of the first oncogenes identified, three
INTRODUCTION
decades of effort has failed to identify clinically useful
inhibitors of the KRAS protein.4 Two features of KRAS
confound its tractability as a drug target: (1) KRAS binds to
GDP and GTP with picomolar affinity, severely hindering
efforts to develop nucleotide-competitive inhibitors, and (2) the
KRAS protein lacks other deep surface hydrophobic pockets,
thwarting efforts to identify high-affinity allosteric inhibitors.1
Mutations in the RAS oncogene are the most common
activating mutation in human cancer, occurring in 30% of
human tumors.1 Although the RAS gene family comprises three
isoforms (KRAS, HRAS, and NRAS), 85% of RAS-driven
cancers are caused by mutations in the KRAS isoform,2 with
mutations occurring most frequently in solid tumors such as
lung adenocarcinoma, pancreatic ductal carcinoma, and
colorectal carcinoma.1 Amongst KRAS-mutant tumors, 80% of
all oncogenic mutations occur within codon 12, with the most
common mutations being p.G12D (41%), p.G12V (28%), and
p.G12C (14%).3
In 2013, Shokat and coworkers reported a novel strategy
aimed at overcoming these challenges that used a covalent
inhibitor to target the reactive cysteine-12 of KRASG12C.5 They
envisioned that covalent modification of Cys12 would allow for
persistent disruption of KRASG12C-driven pro-proliferative
signaling by allowing relatively low-affinity, non-covalent
interactions to selectively template the formation of a covalent
bond between the inhibitor and KRAS, resulting in the
permanent inactivation of the adducted protein. In addition to
providing a means of overcoming the poor “druggability” of
KRAS, it was hoped that this strategy might also allow for the
selective growth inhibition of KRAS-mutant cells (i.e., tumors)
while sparing non-mutant cells (i.e., normal tissue), potentially
overcoming the anticipated toxicological challenges posed by
non-selective inhibition of KRAS-driven cell growth.
In growth factor signaling pathways, the KRAS protein
functions as a molecular switch, regulating proliferation by
alternating between a guanosine diphosphate (GDP)-bound
inactive form and a guanosine triphosphate (GTP)-bound active
form capable of engaging downstream effector proteins to elicit
a pro-proliferative response. Codon 12 mutations impair the
regulated cycling between these two forms by disrupting the
association of GTPase-activating proteins (GAPs), impairing
the inactivation of KRAS and leading to the accumulation of
the pro-proliferative form.
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Figure 1. Comparison of the GDP-KRASG12C binding modes of ARS-1620 (blue, PDB: 5V9U)6 and the internally identified indole lead 1
(pink, PDB: 6P8Z).7 The tetrahydroisoquinoline portion of indole 1 engages a “cryptic pocket” (magenta) not exploited by prior inhibitors,
which is induced by sidechain rotation of H95 and comprises the residues Y96, H95, and Q99. Inhibitor activity on downstream ERK
phosphorylation (p-ERK IC50, 2 h incubation) is indicated.
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After significant optimization efforts, early hits identified by
the Shokat group were modified to provide a tool compound
suitable for in vivo applications, ARS-1620 (Figure 1).8,9 A co-
crystal structure of ARS-1620 with KRASG12C confirmed that
ARS-1620 covalently bound to cysteine-12 of the GDP-bound
form of KRAS, with the quinazoline core of the molecule
occupying an allosteric pocket (the “switch II pocket” (S-IIP))
located beneath the effector protein-engaging switch II loop
region of the protein. While this adduct demonstrated
promising anti-proliferative activity against KRAS p.G12C-
mutant tumors both in vitro and in vivo,9 further improvements
Such a strategy was expected to face some challenges: our prior
efforts to modify the quinazoline core of ARS-1620 had shown
us that perturbation of the hydrogen bond between N1 and the
H95 sidechain of KRAS typically led to significant losses in
functional activity. Nevertheless, as this strategy promised to
identify new alternatives to the metabolically labile 1, we
pursued this approach, anticipating that a successful hybrid
molecule would not only deliver enhanced potency (via
effective engagement of the cryptic pocket)12 but also improved
ADME properties.
in cellular potency appeared necessary to deliver
a
therapeutically useful molecule. Here, we describe efforts at
Amgen to discover and develop a targeted covalent inhibitor of
KRASG12C suitable for clinical application.
F
O
Cl
Y
N
N
A
R
OH
RESULTS AND DISCUSSION
Z
Prior to the Shokat lab’s initial disclosure of their efforts
X
targeting KRASG12C, we had independently initiated our own
research program to identify covalent inhibitors of KRASG12C
,
Figure 2.
Overlay of the GDP-KRASG12C-bound
driven by the same strategic considerations. To support our
initial screening efforts and provide access to focused libraries
of cysteine-reactive compounds, we entered into a collaboration
with Carmot Therapeutics. Using Carmot’s Chemotype
Evolution platform,10 we identified a series of selective covalent
inhibitors of KRASG12C that were optimized—via structure-
based design and additional rounds of targeted library
synthesis—to provide advanced lead 1, which potently
inactivated KRASG12C in biochemical and cellular assays.7
Co-crystallization of 1 with GDP-KRASG12C revealed
compound 1 to adopt a novel binding mode relative to ARS-
1620, with the tetrahydroisoquinoline ring of 1 occupying a
previously unexploited cryptic pocket on the surface of KRAS
unveiled by rotation of the histidine-95 sidechain and
comprising portions of H95, Y96, and Q99 (Figure 1).11
Although engagement of this cryptic pocket led to a multi-fold
enhancement in cellular potency relative to ARS-1620,
compound 1 suffered from very high clearance and low oral
bioavailability in rodent model systems, making it unsuitable
for in vivo use. We therefore sought alternative means of
exploiting the H95/Y96/Q99 cryptic pocket that might deliver
leads with improved pharmaceutical properties.
conformations of ARS-1620 (blue) and indole lead 1 (pink),
suggesting potential access to the Y96/H95/Q99 cryptic pocket
by substitution of the N1 position of the ARS-1620 scaffold.
Conceptual hybrid structure shown at right.
To test this hypothesis, we prepared a series of phthalazine
analogues, wherein the C4 position (Y) of the phthalazine core
(X = N, Y = C) was substituted with a range of aryl substituents
(Table 1). We used a pair of assays to gauge the ability of the
resulting analogs to disrupt KRAS-mediated signaling: (1) a
cell-free AlphaScreenTM assay,13 which measured inhibition of
SOS1-catalyzed GDP/GTP exchange by monitoring the
disruption of the interaction between GTP-KRASG12C and the
Ras binding domain (RBD) of c-RAF, and (2) a cell-based
phospho-ERK1/2 immunoassay (MSD),14 which detected
decreased ERK phosphorylation resulting from disrupted
upstream KRAS signaling. Phenyl substitution of C4 (2) led to
an analogue ~10-fold less potent than ARS-1620 in our
exchange assay (IC50 = 20.1 µM) and 20-fold less potent in our
p-ERK cellular assay (IC50 = 58 µM).
Co-crystallization of compound 2 with GDP-KRASG12C
confirmed that compound 2 adopted a similar binding mode to
ARS-1620, but with the newly introduced C4 phenyl
substituent occupying the H95/Y96/Q99 cryptic pocket, as
designed (Figure 3a). The C4 phenyl group, however, failed to
make many non-covalent contacts with the cryptic pocket
residues (e.g., Y96), prompting us to examine whether further
substitution of the phenyl ring could produce additional
Superposition of the binding modes of indole lead 1 and
ARS-1620 (Figure 2) suggested that substitution of the
quinazolinone nitrogen (N1) of ARS-1620 might provide an
alternative means of accessing the H95 cryptic pocket, and thus
of generating new, enhanced-potency inhibitors of KRASG12C
.
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contacts with the cryptic pocket residues that would lead to
enhanced potency.
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O
Cl
N
N
OH
(Y = N1 / C4)
N
Y
6
X
R
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9
Table 1. Biochemical and cellular activity of hybrid scaffolds
designed to access the Y96/H95/Q99 cryptic pocket
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p-ERK
Exchange
Cmpd
X
Y
R
--
IC50
IC50 (µM)a
(µM)b
ARS-
1620
CH
N
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0.939
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Cl
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3.52
0.903
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Figure 3. X-ray crystallography confirms hybrid scaffolds 2
(a; tan, PDB: 6PGO) and 9 (b; violet, PDB: 6PGP) access the
cryptic pocket. Additional van der Waals contacts between the
isopropyl moiety of 9 and H95, Y96, and Q99 account for the
increased biochemical and cellular potency of 9.
N
Et
N
Co-crystallization of compound 9 with GDP-KRASG12C
(Figure 3b) confirmed 9 to adopt a binding mode in which the
isopropylphenyl substituent was positioned in close contact
with the Y96, H95, and Q99 residues of the cryptic pocket and
one in which the isopropylphenyl and phthalazine rings were
nearly orthogonally oriented. Although compound 9 consisted
of a mixture of atropisomers about the biaryl C–N bond (due to
restricted rotation about the bis-ortho-substituted biaryl
linkage), only the R-atropisomer18 showed significant
occupancy of the switch II pocket crystallographically.
Separation of the R- and S-atropisomers by chiral
chromatography confirmed (R)-9 to be significantly more
potent than the corresponding S-atropisomer.19 Accordingly,
subsequent studies were performed with the atropisomer which
oriented its larger ortho substituent toward the Y96/H95/Q99
cryptic pocket (typically the R-atropisomer) (Table 2).
MeO
c-Pr
i-Pr
i-Pr
N
1.55
N
0.683
0.101
CO
SOS1-catalyzed GDP/GTP exchange (AlphaScreenTM
,
a
KRASG12C / c-RAF Ras binding domain), 5 min incubation.15 b p-
ERK1/2 immunoassay (MSD), EGF-stimulated MIA PaCa-2 cells,
2 h incubation.16 All data represent n ≥ 2.
To test this hypothesis, a series of increasingly large ortho-
substituents were added to the phenyl ring of 2 (see compounds
3–8, Table 1) with the aim of enhancing contacts with Y96.
Encouragingly, methyl substitution (3) provided a 4-fold
increase in biochemical potency and 16-fold increase in cellular
activity, and ethyl substitution (5) led to further gains in potency
(exchange IC50 = 0.903 µM, p-ERK IC50 = 2.6 µM). Isopropyl
substitution (8) proved optimal, however, demonstrating
biochemical and cellular IC50 values on a par with ARS-1620.
Although (R)-9 proved an exceptionally potent inhibitor of
KRASG12C signaling (p-ERK IC50 = 0.130 µM), the GDP-
KRASG12C co-crystal structure suggested several prospects for
further optimization: (1) substitution of the piperazine C2
position appeared to offer an opportunity to enhance activity
through additional contacts with C12, E62, and Y96, and (2)
replacement of the fluorophenol “tail” of (R)-9 appeared to offer
an opportunity to form more extensive contacts with lipophilic
residues (e.g., V9 and I100) and to modulate polar interactions
with R68 or D69. Additionally, despite the promising potency
profile of (R)-9, PK studies revealed no measurable oral
bioavailability in BALB/c mice. Low membrane permeability
(2 µcm/s in a Madin–Darby Canine Kidney (MDCK) cell trans-
well permeability assay) and relatively poor aqueous solubility
(Table 2) were viewed as likely contributing factors. Therefore,
C2 and C7 modifications were also viewed as potential
opportunities to modulate the biopharmaceutical properties of
(R)-9 to enhance the bioavailability of future analogues.
In an effort to further enhance the potency of these initial
leads, we also examined the effect of changing the phthalazine
core of 8. Notably, quinazolinone 9 (X = CO, Y = N; Table 1)
was found to offer a significant improvement in biochemical
and cellular potency relative to 8, with the resulting compound
proving ~3–9 times more potent than ARS-1620 in in vitro
assays.17
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Cl
N
O
R1
X 8
7
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N
R2
N
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i-Pr
Table 2. Optimization of the piperazine substituent (R2) and lipophilic “tail” (R1) regions of (R)-9 enhances potency & bioavailability
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HT
p-ERK
IC50 MIA
PaCa-2
(μM)b
Viability
IC50 MIA
PaCa-2 |
Mu | H hep
CLint
MDCK
Permeabili
ty A–B
Solubility
(μM, PBS |
FaSSIF |
Mouse CL (L/h/kg)
| Vss (L/kg) | t1/2
(h) | %Fd
Cmpd
(R)-9
10
R1a
R2
H
X
(μL/min/106
cells)
A549 (μM)c
(μcm/s)
0.01 N HCl)
F
CH
CH
0.130
--
0.033 | 10.3
0.017 | 2.7
195 | 56
2
0 | 191 | 0
0 | 71 | 0
0.3 | 0.8 | 3.4 | <0.5
HO
H
|
--
| | |
e
OH
(R)-11
H
H
CH
CH
0.008
0.004 | 1.7
180 | 121
4
0 | 218 | 0
4.2 | 5.3 | 2.8 | <0.5
NH
f
N
(R)-12
(R)-13
(R)-14
15
0.080
0.047
0.220
0.442
0.022 | 6.4
0.006 | 5.8
0.018 | 7.4
0.040 | 7.4
415 | 197
356 | 166
397 | 317
270 | 148
7
10
6
0 | 344 | 0
0 | 260 | 0
0 | 255 | 0
0 | 218 | 0
| | |
1.6 | 1.4 | 0.9 | 12
| | |
F
F
Me CH
Me CH
Me CH
Cl
3
| | |
F3C
g
F
F
F
(R)-16
(R)-17
(R)-18
Me CH
0.028
0.069
0.044
0.014 | 15.3
0.011 | 11.5
0.005 | 14.2
263 | 113
109 | 32
119 | 38
1
6
9
0 | 226 | 0
14 | 204 | 14
9 | 184 | 7
| | |
HO
HO
H
N
N
0.8 | 0.5 | 1.5 | 1.3
0.4 | 0.4 | 1.3 | 33
Me
HO
F
(R)-19
(R)-20
(R)-21
Me
Me
Me
N
N
N
0.066
0.056
0.146
0.005 | 7.9
0.016 | 7.1
0.013 | 12.2
236 | 135
319 | 205
288 | 82
20
12
18
11 | 224 | 0
0 | 175 | 0
3.6 | 2.3 | 0.6 | 9
5.4 | 4.8 | 0.6 | 12
1.7 | 0.8 | 0.5 | 10
Cl
88 | 299 | 57
HO
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a Unless noted, separable C7 biaryl bond atropisomers were not observed. b p-ERK1/2 immunoassay (MSD), 2 h incubation. c Viability
assessed at 72 h by CellTiter-Glo® luminescence assay (Promega) in MIA PaCa-2 (p.G12C) and A549 (p.G12S) cell lines. All data represent
n ≥ 2. d IV/PO dosing in BALB/c mice (vehicle, IV: 1 mg/kg, DMSO; PO: 10 mg/kg, 1% Tween 80, 2% HPMC, 97% water). e Mixture of
four atropisomers (isopropylphenyl and naphthol biaryl bonds). Single indazole biaryl bond atropisomer. Mixture of isopropylphenyl
atropisomers.
1
2
3
4
f
g
5
6
7
8
We began our SAR efforts around (R)-9 by replacing its C7
fluorophenol moiety with larger groups designed to make
additional contacts with residues in the “tail” sub-pocket.
While we continued to employ an ERK phosphorylation assay
as our primary screen for KRAS-based cell activity, we also
profiled new compounds in CellTiter-Glo®-based proliferation
assays20 using KRAS p.G12C (MIA PaCa-2) and KRAS p.G12S
(A549) cells to confirm that growth-inhibitory activity was
specific to p.G12C-mutant cells and sparing of those in which
Gly12 was instead mutated to serine (G12S). Naphthol (10) and
indazole (11) substituents did indeed show enhanced activity in
ERK phosphorylation and viability assays (Table 2), however
these analogues continued to demonstrate poor aqueous
solubility, low MDCK permeability, and, in the case of indazole
11, no improvement in oral bioavailability.
stability, and oral bioavailability. Thus, due to its unique
balance of promising pharmacokinetic profile and excellent
potency, azaquinazolinone 18 became our new lead for
subsequent optimization.
Disappointingly, we soon discovered a new challenge with
compound 18, originating in the axial chirality of its
isopropylphenyl–quinazolinone biaryl bond. Although the
sterically congested environment about this bond dramatically
restricted rotation, giving rise to separable atropisomers, it
unfortunately did not completely restrict rotation about this
bond. Slow interconversion of the R- and S-atropisomers
occurred at 25 °C with a half-life of 8 days and an
interconversion free energy barrier (ΔG‡) of 26 kcal/mol,22
behavior which promised to greatly complicate the
development of (R)-18 as a pure substance (Figure 4).
F
9
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In an effort to enhance MDCK permeability, we examined
the effect of removing the phenolic moiety from (R)-9 to
provide fluorophenyl 12. Interestingly, this modification led to
no loss in activity in either the p-ERK or viability assays, and a
more than 3-fold increase in MDCK permeability. Good
MDCK permeability was also retained in a related analog
wherein a piperazine C2-methyl substituent was introduced
(13). Notably, methylpiperazine 13 not only demonstrated
further improvements in cellular activity (p-ERK IC50 = 47 nM)
but also measurable mouse oral bioavailability (12%).
Attempts to replace the fluorophenyl tail of 13 with larger
lipophilic substituents (e.g., o-chlorophenyl (14) or o-
trifluorotolyl (15)) proved detrimental, however, and led to
reduced cellular activity and MDCK permeability. Likewise,
while re-introduction of the phenolic moiety into 13 (to provide
fluorophenol 16) again had minimal impact on cellular activity,
membrane permeability was dramatically reduced (PAB = 1
µcm/s).
O
Cl
5
N
18
(R)-
N
Me
N
OH
p-ERK 2 h IC50 = 0.044 M
MIA PaCa-2 Viability IC50 = 0.005 M
N
N
O
Me
Me
G‡ = 26 kcal/mol
t1/2 = 8 days

F
O
Cl
5
N
18
(S)-
p-ERK 2 h IC50 = 0.500 M
MIA PaCa-2 Viability IC50 = 0.045 M
N
Me
N
Me
OH
Me
N
N
O
Figure 4. Compound 18 atropisomers are not configurationally
stable at 25 °C.
With the phenolic functionality of (R)-9 and (R)-16 emerging
as a key contributor to the reduced MDCK permeability of these
analogues, we also decided to examine an alternative strategy
to mitigate the adverse effect of this group. As de-solvation of
the phenol during membrane diffusion was hypothesized to add
to the energetic cost of membrane permeation, we investigated
whether nitrogen incorporation at the C8 position of the
quinazolinone ring could enhance MDCK permeability by
providing an internal hydrogen-bond acceptor to satisfy the
adjacent phenolic donor during membrane permeation.21
Gratifyingly, azaquinazolinones 17 and 18 both demonstrated
not only significantly enhanced MDCK permeability relative to
their non-aza congeners (9 and 16), but also significantly
improved aqueous solubility. While the oral bioavailability of
Strategies for addressing atropisomerism in drug discovery
have previously been reviewed,23 however, and drawing upon
this guidance, we initiated a trio of strategies to identify a lead
molecule with atropisomer configurational properties suitable
for drug development needs. These strategies included (1)
raising the energetic barrier to atropisomer interconversion
(ΔG‡ > 30 kcal/mol) to allow for the development of a single,
pure atropisomer, (2) lowering the interconversion barrier (ΔG‡
< 20 kcal/mol) to allow for the development of a freely
interconverting mixture of atropisomers, or (3) symmetrizing
the cryptic pocket substituent to avoid the generation of an axis
of chirality.
compound
17
remained
disappointing
(1.3%),
We used two methods to assess the atropisomer
interconversion free-energy barriers of our lead molecules:
slowly interconverting atropisomers were assessed using time-
course 1H NMR experiments, fitting atropisomer ratio
information with the Eyring equation to determine ΔG‡; rapidly
interconverting atropisomers, in contrast, were assessed using
the VT NMR method described in Figure 5.24
azaquinazolinone 18 demonstrated significantly enhanced oral
bioavailability (33%) and excellent cellular activity (p-ERK
IC50 = 44 nM; MIA PaCa-2 viability IC50 = 5 nM).
While further improvements in MDCK permeability could be
achieved by removing the phenolic functionality from
compound 18 (see compounds 19 & 20), the resulting
compounds suffered from reduced bioavailability and increased
in vivo clearance relative to 18. Similarly, although removal of
the fluorine substituent from 18 (to provide phenol 21)
enhanced both MDCK permeability and aqueous solubility,
such benefits came at the cost of reduced potency, metabolic
We first explored methods to further restrict rotation about
the isopropylphenyl–quinazolinone biaryl bond, probing the
effect of ortho-substituent steric demand on the rotational free-
energy barrier. While replacement of isopropyl substituent with
a cyclopropyl ring (22) did little to alter the atropisomer
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Journal of Medicinal Chemistry
interconversion barrier (and led to some loss in activity, see restored biochemical and cellular activity. Interestingly,
1
2
3
4
5
6
7
8
Table 3), introduction of a tert-butyl group (23) led to
significantly increased configurational stability, with minimal
loss in activity. Bis-ortho substitution (24) proved optimal,
however, both locking of rotation about the biaryl bond (ΔG‡ >
30 kcal/mol) and leading to enhanced biochemical and cellular
activity (p-ERK IC50 = 28 nM). The isopropyl group in 24
proved crucial to this effect, as its replacement with a non-
branched ethyl substituent (25) led to a dramatic reduction in
the biaryl rotational barrier (ΔG‡ = 24 kcal/mol), as well as
some loss in biochemical potency.
attempts to fully restrict biaryl bond rotation by bis-ortho-
substitution of five-membered ring cryptic pocket substituents
(c.f., 29) were unsuccessful, contrasting with this strategy’s
success in the context of six-membered rings substituents (c.f.,
(R)-24). These studies hence reveal biaryl bond rotation to be
influenced by a complex interplay of factors including
substituent size, substitution pattern, and ring size.
F
O
Cl
9
N
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
N
N
R
OH
Me
N
N
O
Table 3. Atropisomer stability and KRASG12C activity as a
function of cryptic pocket arene identity and substitution pattern
Interconve
Exchange
IC50
p-ERK
IC50
rsion
barrier
Cmpd
Ra
(µM)b
(µM)c
(ΔG‡,
kcal/mol)d
(R)-18
22
0.051
0.225
0.117
0.044
0.109
0.051
26.01
25.01
>302
i-Pr
c-Pr
t-Bu
(R)-23
Me
Me
N
(R)-24
0.025
0.127
0.028
0.025
>302
>242
i-Pr
25
Et
Figure 5. VT NMR method for determining atropisomer
interconversion free energy barriers (ΔG‡). Coalescence of the
H5 1H NMR resonance was monitored at elevated temperature,
and the coalescences temperature (Tc) and chemical shift
difference (Δν; slow exchange limit) were used for calculation
of G‡. (Compensation applied for minor temperature
dependence in the H5 chemical shift.) 1H spectra (DMSO-d6)
for compound 27 are depicted. At 298 K, methylpiperazine
conformational exchange causes H5 line broadening, which is
averaged out at T > 320 K.
26
27
28
0.083
0.164
0.081
0.053
0.218
0.063
23.52
21.52
17.52
i-Pr
i-Pr
N
N
S
N
i-Pr
i-Pr
Me
Et
Me
We next examined whether replacement of the
isopropylphenyl ring of (R)-18 with less sterically demanding
groups could lower the rotational barrier sufficiently to restore
(R)-29
30
0.053
0.306
0.068
0.127
0.199
0.036
25.81
NA
N
N
Me
free rotation about the biaryl bond.
Replacing the
isopropylphenyl group with an analogous isopropylpyridine
(c.f., compound 26) meaningfully reduced the rotational barrier
(ΔG‡ = 23.5 kcal/mol), however the resulting atropisomers
remained metastable (t1/2 ~ 5 h at 25 °C) and unsuitable for
further development. Contraction of the pendant six-membered
ring to a five-membered ring (c.f., pyrazole 27) further reduced
the rotational barrier (ΔG‡ = 21.5 kcal/mol) but failed to fully
free rotation about the biaryl bond and led to moderate losses in
biochemical and cellular potency. Introducing a sulfur atom at
the open ortho-position of the five-membered ring (c.f., 28),
however both restored free rotation about the biaryl bond and
Et
31
NA
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c-Pr
subcutaneously implanted with MIA PaCa-2 T2 human tumor
1
2
3
4
5
6
7
8
cells (homozygous KRAS p.G12C). Serum and tumor samples
were collected two hours post-dosing, revealing dose-
proportional exposure of (R)-24 across administered doses (10–
100 mg/kg), with maximal suppression of downstream ERK
phosphorylation achieved at doses as low as 30 mg/kg (Figure
6a).26 Significantly, at this timepoint, the 30 mg/kg dose group
showed unbound plasma and total tumor exposures (3 and 11
nM, respectively) considerably lower than the in vitro p-ERK
IC50 (28 nM; determined after a 2 h incubation), providing an
initial indication that covalent inactivation of KRASG12C could
have durable downstream effects, even in the absence of
circulating drug.
32
33
N
0.034
0.021
0.036
0.025
NA
NA
c-Pr
i-Pr
N
i-Pr
N
N
a Atropisomer configuration assigned by co-crystallization with
GDP-KRASG12C, except for compound 29 (configuration assigned
by analogy: more potent isomer assigned R-configuration). b SOS1-
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
catalyzed GDP/GTP exchange (AlphaScreenTM, KRASG12C / c-
c
RAF Ras binding domain), 5 min incubation.
immunoassay (MSD), 2 h incubation. All data represent n ≥ 2. For
separable atropisomers, data is reported for the more potent R-
p-ERK1/2
Table 4. Mouse PK profilesa of compounds with atropisomer
configurational properties suitable for development
d
atropisomer, as depicted. Atropisomer interconversion barrier
(ΔG‡) as determined by time-course NMR experiment or VT
1
2
10 mg/kg
CL
(L/h/kg)
PPB
(fu)b
Cmax,uc / p-
ERK IC50
NMR.
Cmpd
t1/2 (h)
%F
As a final strategy to avoid configurationally unstable biaryl
bond atropisomers, we examined the properties of
symmetrically bis-ortho-substituted cryptic pocket substituents.
Although bis-methyl substitution (30) failed to afford a potent
lead, bis-ethyl (31), cyclopropyl (32), and isopropyl (33)
substitution all afforded compounds with good biochemical and
cellular activity and no potential to generate rotational
atropisomers.
(R)-24
28
2.7
2.2
3.3
3.3
2.3
0.03
0.02
0.03
0.08
0.03
0.5
1.1
0.5
0.5
0.8
21
22
8
4.5
1.5
0.8
0.6
0.8
31
32
7
33
13
a IV/PO dosing in BALB/c mice (vehicle, IV: 1 mg/kg, DMSO;
PO: 10 mg/kg, 1% Tween 80, 2% HPMC, 97% water). b PPB by
Although all three strategies to address the axial
chirality/configurational stability issue were ultimately
successful in identifying potent KRASG12C inhibitors suitable
for subsequent development, the resulting leads demonstrated
quite distinct pharmacological profiles when dosed orally (10
mg/kg) in BALB/c mice (Table 4). Whereas (R)-24 showed
moderate oral bioavailability (21%) and good in vivo target
coverage (4.5× coverage of the p-ERK IC50 at Cmax),25
compound 28 demonstrated much more modest in vivo target
coverage, and compounds 31–33 failed to show appreciable in
vivo target coverage, even at Cmax, possibly due in part to the
reduced oral bioavailability of these analogues. (R)-24 thus
became our lead candidate for subsequent pharmacodynamic
and efficacy testing in xenograft models.
c
ultracentrifugation. Maximum unbound plasma concentration
(Cmax • fu)
Greatly encouraged by this result, we subsequently profiled
(R)-24 in a nude mouse xenograft efficacy study using the same
MIA PaCa-2 T2 cell line employed in the prior study. Dosed
orally once daily (10–100 mg/kg) over two weeks following
tumor establishment, (R)-24 fully suppressed tumor growth at a
dose of 30 mg/kg and elicited tumor regression at doses of ≥60
mg/kg (Figure 6b).27 A time-course PK study of (R)-24 in nude
mice (30 mg/kg, PO) again confirmed results from our earlier
PK/PD study, showing that in vivo coverage of the in vitro 2 h
p-ERK IC50 for <2–3 h was sufficient to achieve tumor growth
stasis (Figure 6c).
To test the effect of (R)-24 on KRAS signaling in vivo, (R)-
24 was dosed orally in athymic nude mice that had been
Figure 6. (R)-24 inhibits ERK1/2 phosphorylation in KRAS p.G12C tumors (MIA PaCa-2 T2) and causes tumor regression at QD
PO doses of ≥60 mg/kg. a. Mice bearing MIA PaCa-2 T2 tumors were given a single oral dose of vehicle (black bar), (R)-24 (blue
bars), or ARS-1620 (red bar); tumors were harvested two hours later and assessed for p-ERK levels. Plasma and tumor concentrations
of (R)-24 are indicated by red triangles and blue open circles, respectively. Data presented as percent of control versus vehicle ±
SEM (n = 3/group). ****p < 0.0001; *p < 0.05 by one-way Anova followed Dunnett’s post-hoc analysis. b. Effect of (R)-24 on MIA
PaCa-2 T2 tumor growth in nude mice (QD PO dosing). Data represent mean tumor volume ± SEM (n = 10/group). ****p < 0.0001
#
by RMANOVA followed by Dunnett’s post-hoc analysis, p < 0.0001 regression by paired T-test. c. Mean unbound plasma
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Journal of Medicinal Chemistry
concentrations + SEM (n = 3) following 30 mg/kg PO dosing in nude mice. p-ERK IC50,u = in vitro cellular IC50 • fu,media (fraction
unbound in cell culture media).
1
2
3
4
5
6
7
8
F
R
O
6
N
N
OH
Me
N
N
Me
N
Y
9
O
i-Pr
X
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Table 5. Biopharmaceutical optimization of (R)-24 significantly enhances bioavailability
p-ERK
IC50
MIA
Viability
IC50 MIA
PaCa-2 |
A549
Mu | H
hep CLint Permea
(μL/min/
106
cells)
MDCK
HT Solubility
(μM, PBS |
FaSSIF | 0.01
N HCl)
Mouse CL (L/h/kg) |
Vss (L/kg) | t1/2 (h)
| %Fd
logD (pH 7.4)
| PSA (Å2)a
Cmpd
R
X
Y
bility
A–B
(μcm/s)
PaCa-2
(μM)b
(μM)c
(R)-24 Cl CH CH
3.6 | 89
2.4 | 102
2.4 | 102
1.7 | 115
3.0 | 89
0.028
0.011
0.065
0.038
0.090
0.068
0.142
0.128
0.002 | 11.9 102 | 30
15
1
12 | 204 | 9
46 | 381 | 500
335 | 435 | 534
499 | 500 | 421
41 | 164 | 24
1.4 | 0.8 | 0.9 | 4–12e
3.9 | 1.4 | 0.4 | <0.5
1.4 | 0.4 | 0.4 | <0.5
3.5 | 1.1 | 0.3 | <0.5
2.0 | 1.0 | 0.5 | <0.5
(R)-34 Cl
(S)-35f Cl CH
(R)-36 Cl
N
CH
N
0.001 | 34.1
0.003 | 32.4
0.003 | >50
75 | 11
96 | 5
2
N
N
139 | 5
1
(R)-37
(R)-38
(S)-39f
(R)-40
F
F
F
F
CH CH
0.011 | 11.6 111 | 37
22
6
N
CH
N
CH
N
2.0 | 102
2.0 | 102
1.2 | 115
0.005 | 36.5
0.016 | 49.1
0.009 | >50
36 | 9
100 | 9
65 | 5
423 | 492 | 499 1.6 | 0.7 | 0.5 | 22–40
1
426 | 477 | 484
495 | 500 | 500
3.7 | 1.1 | 0.3 | 15
4.7 | 1.7 | 0.3 | 10
N
<1
a logD (pH 7.4) and PSA (polar surface area) calculated using ACD/Percepta (ACD/Labs, Toronto, Canada) b p-ERK1/2 immunoassay
(MSD), 2 h incubation. c Viability assessed at 72 h by CellTiter-Glo® luminescence assay (Promega) in MIA PaCa-2 (p.G12C) and A549
(p.G12S) cell lines. All data represent n ≥ 2. d IV/PO dosing in BALB/c mice (vehicle, IV: 1 mg/kg, DMSO; PO: 10 mg/kg, 1% Tween 80,
e
f
2% HPMC, 97% water). Crystalline polymorphs. Presence of the pyridyl nitrogen changes IUPAC substituent priority for naming
purposes; the isopropyl substituent remains oriented toward the cryptic pocket, as in other analogues.
It came as a great disappointment to us, then, when we
subsequently found crystalline polymorphic forms of (R)-24 to
have significantly reduced oral bioavailability (4–12%) relative
to that of the amorphous form used in our earlier studies (Table
5), impairing our ability to achieve suitable plasma exposures
in future studies. As reduced bioavailability coincided with
dramatically reduced solubility in biorelevant media (<0.004
mg/mL (crystalline forms) vs. >0.108 mg/mL (amorphous
form) in FaSSGF, FaSSIF, PBS), we subsequently prioritized
efforts to identify (R)-24 analogues that demonstrated superior
aqueous solubility. Two strategies dominated these efforts: (1)
reducing the lipophilicity of (R)-24 by changing the
quinazolinone C6 halogen substituent, and (2) increasing the
polar surface area of (R)-24 by introducing an additional
nitrogen atom into the cryptic pocket ring (Table 5).
the C6 chloro substituent of (R)-24 with a fluoro substituent
(compound 37) led to a modest loss of activity in cellular assays
(e.g., p-ERK IC50 = 90 nM), the change also resulted in a modest
increase in aqueous solubility (~3-fold) and no adverse impact
on membrane permeability (PAB = 22 µcm/s). Unfortunately,
(R)-37 failed to show any measurable oral bioavailability (%F
<0.5). Combining C6 fluoro substitution with nitrogen
incorporation in the cryptic pocket arene ring (compounds 38–
40), however, overcame the consistently low bioavailabilities
seen with prior analogues.
Although nitrogen atom
incorporation again led to significantly reduced MDCK
permeabilities for all three compounds, this combination of
features led to dramatically enhanced aqueous solubilities
(>423 µM in all biorelevant media). From these studies, (R)-38
emerged as the standout molecule, showing good activity in
cellular assays (p-ERK IC50 = 68 nM), moderate permeability
(PAB = 6 µcm/s), and exceptional oral bioavailability (22–40%
as crystalline form).
Initial efforts focused on nitrogen atom incorporation into the
cryptic pocket ring. Replacement of the carbon atoms adjacent
to the isopropyl or methyl substituents with nitrogen atoms (cf.,
compounds 34 and 35, respectively) significantly enhanced
aqueous solubility without appreciably altering KRAS activity.
Such substitution also substantially reduced MDCK
permeability, however, affording molecules with no measurable
oral bioavailability (BALB/c mice). Although bis-nitrogen
substitution (36) likewise further enhanced aqueous solubility,
the resulting pyrimidine analogue similarly suffered from low
permeability and no measurable oral bioavailability.
Gratifyingly, (R)-38 demonstrated dose-proportional plasma
exposure when dosed orally (0.3–100 mg/kg) in our nude
mouse MIA PaCa-2 xenograft model, and significantly
suppressed ERK phosphorylation at doses ≥10 mg/kg (Figure
7a).26 To further interrogate the PK/PD relationship for (R)-38,
we also conducted a time-course pharmacodynamic study in
this xenograft model (Figure 7b). This study supported earlier
results with (R)-24 and (R)-38, showing that, while maximal
suppression of ERK phosphorylation was achieved 60–120 min
post-dosing, peak (R)-38 plasma and tumor exposures were
achieved 30 min post-dosing, and by the 120 min timepoint,
only low concentrations of (R)-38 remained in circulation.
We next investigated whether reducing the lipophilicity of
the quinazolinone C6 substituent could enhance aqueous
solubility while preserving cellular activity. While replacing
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A time-course study of KRASG12C ligand occupancy in the
phosphorylation to closely mirror the extent of covalent
modification of KRASG12C 26
.
Covalent modification of
1
2
3
4
MIA PaCa-2 xenograft model shed further light on this PK/PD
relationship (Figure 7c). Using protein immunocapture, trypsin
digestion, and mass spectrometry, KRASG12C covalent
modification in tumor cells recovered from treated mice was
monitored over time, revealing suppression of ERK
KRASG12C was nearly complete 120 min post-dosing, at which
point minimal (R)-38 remained in circulation.
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Figure 7.28 p-ERK (a) dose-response and (b) time-course (MSD) data with plasma and tumor exposures for compound (R)-38. Mice
bearing MIA PaCa-2 T2 tumors were given a single oral dose of either vehicle (black bars) or (R)-38 (blue bars) and harvested at the
indicated time. Data represent percent of control versus vehicle ± SEM (n = 3/group). Plasma and tumor concentrations of (R)-24
are indicated by red triangles and blue open circles, respectively. ****p < 0.0001; ***p < 0.001; *p < 0.05 by one-way Anova followed
Dunnett’s post-hoc analysis. c. p-ERK POC (MSD) and percent KRASG12C covalent modification (MS) time-course in MIA PaCa-2
T2 mouse xenografts. Markers represent mean p-ERK1/2 levels (percent of basal ERK1/2) ± SEM and mean %covalent modification
± SEM (n = 3/group).
Encouraged by these promising pharmacodynamic effects,
(R)-38 was profiled in a mouse xenograft efficacy study
employing MIA PaCa-2 T2 (p.G12C) tumor cells. Once-daily
oral dosing (10–100 mg/kg) achieved 86% tumor growth
inhibition (TGI) at 10 mg/kg and produced significant tumor
regression at doses of ≥30 mg/kg (Figure 8a). Unbound plasma
exposures from this study (Figure 8b) again illustrated that
durable growth responses could be achieved in the absence of
continuous drug exposure given the covalent inhibitor
mechanism of action. At a dose of 10 mg/kg, plasma coverage
of the in vitro p-ERK IC50 was only sustained for ~1 h, and
circulating, unbound concentrations of (R)-38 had dropped
below 1 nM 8 hours post dosing. Nonetheless, 1 h coverage of
the in vitro p-ERK IC50 proved sufficient to achieve near-stasis
in tumor growth, and in vitro IC50 coverage for as little as 2 h
(30 mg/kg dose) was sufficient to cause tumor regression.
Figure 8.28 Compound (R)-38 dosed orally once daily results in regression of KRAS p.G12C tumor xenografts. a. Effect of compound
(R)-38 on MIA PaCa-2 T2 xenograft growth in nude mice (QD PO dosing). Data represent mean tumor volume ± SEM (n = 10/group).
****p < 0.0001 by Dunnett’s post-hoc analysis; #p < 0.05 regression by paired T-test. b. Mean unbound plasma concentrations ± SEM
(n = 2/group). p-ERK IC50,u = in vitro cellular IC50 • fu,media (fraction unbound in cell culture media).
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lives for (R)-38 were relatively short in all species, this was not
1
2
3
4
5
6
7
8
viewed as a liability, given our findings from prior
pharmacodynamic studies that durable covalent inhibition of
KRASG12C could be achieved without continuous drug
exposure. Such persistent PD effects are in line with those
expected for covalent inhibitors, where duration of target
inhibition is determined not by the duration of target IC50
coverage but rather by the resynthesis rate of the covalently
inactivated target protein.29 Given KRAS’s long protein half-
life (~22 h),30 rapid covalent inactivation allows for durable
pharmacodynamic effects even in the face of relatively short
inhibitor plasma half-lives.
Although mass spectrometric studies31 established (R)-38 to
have a second-order rate constant for covalent inactivation of
KRASG12C (kinact/KI) of 9,900 M-1s-1, rapid inactivation of KRAS
was not indicative of promiscuous cysteine reactivity.
Incubation of (R)-38 under conditions mimicking intracellular
glutathione levels (5 mM GSH, 37 °C, pH 7.4)32 revealed (R)-
38 to have a GSH conjugation half-life of 200 min. Cysteine-
proteome profiling (MS) further revealed (R)-38 to be highly
selective for covalent modification of KRASG12C: of 6451
cysteine-containing peptides profiled, only the KRASG12C C12
peptide was found to be modified.28
9
10
11
12
13
14
Figure 9. X-ray crystal structure of compound (R)-38 bound to
GDP-KRASG12C (cyan, PDB: 6OIM)
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Delighted by the promising pharmacodynamic effect of (R)-
38 in our mouse models, we undertook further characterization
of (R)-38 to assess its potential as a possible development
candidate. Co-crystallization with KRASG12C revealed (R)-38
to adopt a similar binding mode to prior quinazolinone leads,
with the quinazolinone core of (R)-38 occupying the KRAS
switch II pocket and the acrylamide moiety making a covalent
bond with C12 (Figure 9). The (S)-methyl piperazine ring of
(R)-38 adopted a twist-boat conformation, with the C2 methyl
substituent making close contacts with C12 and Y96.
Critically, the isopropyl substituent of the pyridyl ring again
made close contacts with Y96, H95, and Q99, largely filling the
cryptic pocket revealed by sidechain rotation of the H95 residue
and contributing to the exceptional potency of this molecule.
Nitrogen substitution of the cryptic pocket arene ring was not
found to adversely impact the configurational stability of the
potent R-atropisomer, which was calculated to have a
Based on the compelling pharmacological profile of (R)-38
and its marked ability to regress KRAS p.G12C-mutant tumors
in vivo, promising biopharmaceutical properties, and excellent
tolerability in preclinical toxicological models,33 we nominated
(R)-38 for clinical development as AMG 510. AMG 510
entered human clinical trials in August 2018, and a phase I/II
trial evaluating its safety, tolerability, pharmacokinetic
properties, and efficacy in KRAS p.G12C mutant tumors is
currently ongoing (NCT0360088334). Early results from this
study have confirmed AMG 510 to demonstrate excellent
tolerability and promising antitumor activity when administered
as a monotherapy to patients with advanced KRAS p.G12C-
mutant solid tumors.35 Dose-expansion efforts are currently
ongoing.
racemization t1/2 of >180 years at 25 °C (ΔG‡
kcal/mol; Table 6).
> 31
rotation
Table 6. Additional in vitro and PK characterization of
compound (R)-38
CONCLUSIONS
In conclusion, by exploiting a previously unrecognized
H95/Y96/Q99 cryptic pocket in GDP-KRASG12C, we were able
to create highly potent and selective covalent inhibitors of
KRASG12C. A collaboration with Carmot Therapeutics7 enabled
us to rapidly screen cysteine-reactive libraries and investigate
the potential of this cryptic pocket. Structure-based design
efforts facilitated our discovery of a quinazolinone-based
scaffold, which exploited this pocket for enhanced potency and
provided ADME properties for suitable further optimization.
Optimally leveraging the H95/Y96/Q99 cryptic pocket required
us to address axial chirality and configurational stability issues,
which were overcome by optimization of the cryptic pocket-
engaging arene moiety. Further refinement of the resulting
leads to address permeability, solubility, and oral
bioavailability challenges then led to our discovery of AMG
510. AMG 510 has shown great promise in the treatment of
KRAS p.G12C-mutant tumors both pre-clinically and clinically.
Efforts to further demonstrate the clinical potential of AMG
510 are currently underway.
Atropisomer interconversion
>31
barrier (ΔG‡, kcal/mol)a
Rat CL (L/h/kg) | Vss (L/kg) |
3.4 | 2.0 | 0.5 | 28
t1/2 (h) | %Fb
Dog CL (L/h/kg) | Vss (L/kg)
2.2 | 0.73 | 0.4 | 34
| t1/2 (h) | %Fc
PPB Mu | R | D | Hu (0.25
0.06 | 0.05 | 0.17 | 0.09
μM, UC, fu)
KRASG12C kinact/KI (M-1s-1)d
5 mM GSH t1/2 (min)e
9,900 ± 1,800
200 min
a Determined by NMR kinetic data. b IV/PO dosing in Sprague-
Dawley rat (vehicle, IV: 1 mg/kg, DMSO; PO: 10 mg/kg, 1%
Tween 80, 2% HPMC, 97% water). c IV/PO dosing in Beagle dog
(vehicle, IV: 1 mg/kg, 10% DMAC, 10% EtOH, 30% propylene
glycol, 50% water; PO: 10 mg/kg, 1% Tween 80, 2% HPMC, 97%
d
water).
kinact/KI was determined from time-course relative
%bound data at varied inhibitor concentrations, as assessed by
e
mass spectrometry.28,31 t1/2 determined by parent depletion (MS
EXPERIMENTAL SECTION
detection) in 5 mM GSH, 37 °C, pH 7.4 aqueous phosphate
buffer.32
General synthetic procedures. All materials were obtained
from commercial suppliers and used without further
purification unless otherwise noted. Anhydrous solvents were
obtained from Sigma-Aldrich and used directly. Reactions
Rat and dog pharmacokinetic parameters for (R)-38 were in
line with those observed in mouse, with reasonable oral
bioavailability observed in all species. Although terminal half-
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Journal of Medicinal Chemistry
Page 12 of 15
involving air- or moisture-sensitive reagents were performed
under nitrogen or argon atmosphere. Silica gel
was allowed to cool to ambient temperature. Water (10 mL)
and 1 N NaOH solution (20 mL) were sequentially added, and
1
a
2
3
4
5
6
7
8
9
chromatography was performed using pre-packed silica gel
cartridges (RediSep® Rf, Teledyne ISCO). Reverse-phase
HPLC purification was performed using Gilson (Middleton,
WI) workstations. NMR spectra were acquired on Bruker
Avance 400, 500, or 600 MHz spectrometers equipped with 5
mm BBFO probes. All final compounds were purified to >95%
purity as determined by LC-MS using an Agilent 1100 or 1260
multi-wavelength detector (215 nm detection) and an Advanced
Materials Technology HALO C18 column (50 × 3.0 mm, 2.7
μm) at 40 °C with a 2.0 mL/min flow rate using a 5−95%
gradient of acetonitrile/water with 0.1% trifluoracetic acid over
1.5 min. Low-resolution MS data were obtained concurrently
with UV chromatography using an Agilent G1956B MSD SL,
6120B, 6130B, or 6140A quadrupole MS in positive
electrospray ionization mode. Resolved atropisomers were
purified to >95% ee (or de) using a Thar 80, 200, or 350
preparative SFC. Enantiomeric, and diastereomeric excesses
were determined by SFC (Waters Acquity UPC2 or Agilent
1260 Infinity analytical systems).
the resulting mixture was extracted with EtOAc (2×). The
combined organic extracts were dried over anhydrous sodium
sulfate and concentrated in vacuo.
Chromatographic
purification of the residue (silica gel; 0–15% MeOH/DCM)
provided 2-isopropyl-4-methylpyridin-3-amine (284 mg, 98%
1
yield) as a brown solid. H NMR (400 MHz, DMSO-d6) δ ppm
7.66 (d, J = 4.6 Hz, 1 H), 6.78 (d, J = 4.8 Hz, 1 H), 4.72 (br s, 2
H), 3.14-3.25 (m, 1 H), 2.08 (s, 3 H), 1.14 (d, J = 6.8 Hz, 6 H).
m/z (ESI, +ve ion): 151.1 (M+H)+.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Step
3.
7-Chloro-6-fluoro-1-(2-isopropyl-4-
methylpyridin-3-yl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-
dione. To an ice-cooled solution of 2,6-dichloro-5-fluoro-N-
((2-isopropyl-4-methylpyridin-3-yl)carbamoyl)nicotinamide
(9.2 g, 24.0 mmol) in THF (40 mL) was slowly added KHMDS
(1 M solution in THF, 50.2 mL, 50.2 mmol). The ice bath was
removed, and the resulting mixture was stirred for 40 min at
ambient temperature. Saturated aqueous ammonium chloride
solution was added, and the resulting mixture was extracted
with EtOAc (3×). The combined organic extracts were dried
over anhydrous sodium sulfate and concentrated in vacuo.
Chromatographic purification of the residue (silica gel; 0–50%
3:1 EtOAc-EtOH/heptane) provided 7-chloro-6-fluoro-1-(2-
isopropyl-4-methylpyridin-3-yl)pyrido[2,3-d]pyrimidine-
2,4(1H,3H)-dione (9.24 g, quantitative yield). 1H NMR (400
MHz, DMSO-d6) δ 12.27 (br s, 1 H), 8.48–8.55 (m, 2 H), 7.29
(d, J = 4.8 Hz, 1 H), 2.87 (quin, J = 6.6 Hz, 1 H), 1.99–2.06 (m,
3 H), 1.09 (d, J = 6.6 Hz, 3 H), 1.01 (d, J = 6.6 Hz, 3 H). 19F
NMR (376 MHz, DMSO-d6) δ –126.90 (s, 1 F). m/z (ESI, +ve
ion): 349.1 (M+H)+.
Synthesis of AMG 510 [(R)-38]. Step 1. 2,6-Dichloro-5-
fluoronicotinamide. Oxalyl chloride (2 M solution in DCM,
11.9 mL, 23.8 mmol) and DMF (0.05 mL) were sequentially
added to 2,6-dichloro-5-fluoro-nicotinic acid (4.0 g, 19.1 mmol,
AstaTech, Inc.) in DCM (48 mL), and the resulting mixture was
stirred at ambient temperature for 16 h. The reaction mixture
was then concentrated in vacuo, and the residue was dissolved
in 1,4-dioxane (48 mL) and cooled to 0 °C. Ammonium
hydroxide solution (28–30% NH3 basis, 3.6 mL, 28.6 mmol)
was slowly added, and the resulting mixture was stirred at 0 °C
for 30 min. The mixture was then concentrated in vacuo, and
the residue diluted with 1:1 EtOAc/heptane, agitated for 5 min,
and filtered. The filtrate was concentrated to half-volume and
re-filtered. The combined collected solids were washed with
heptane and dried overnight in a reduced-pressure oven (45 °C)
to provide 2,6-dichloro-5-fluoronicotinamide (2.0 g, 50%
Step
4.
4,7-Dichloro-6-fluoro-1-(2-isopropyl-4-
methylpyridin-3-yl)pyrido[2,3-d]pyrimidin-2(1H)-one.
Phosphorus oxychloride (1.63 mL, 17.5 mmol) was added,
dropwise, to a solution of 7-chloro-6-fluoro-1-(2-isopropyl-4-
methylpyridin-3-yl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione
(4.7 g, 13.5 mmol) and DIPEA (3.5 mL, 20 mmol) in
acetonitrile (20 mL), and the resulting mixture was stirred at 80
°C for 1 h, then cooled to ambient temperature and concentrated
in vacuo to provide 4,7-dichloro-6-fluoro-1-(2-isopropyl-4-
methylpyridin-3-yl)pyrido[2,3-d]pyrimidin-2(1H)-one, which
was used without further purification. m/z (ESI, +ve ion): 367.1
(M+H)+.
1
yield). H NMR (400 MHz, DMSO-d6) δ 8.23 (d, J = 7.9 Hz, 1
H) 8.09 (br s, 1 H) 7.93 (br s, 1 H). 19F NMR (376 MHz, DMSO-
d6) δ: –122.39 (s, 1 F). m/z (ESI, +ve ion): 208.9 (M+H)+.
Step 2.
2,6-Dichloro-5-fluoro-N-((2-isopropyl-4-
methylpyridin-3-yl)carbamoyl)nicotinamide. To an ice-
cooled slurry of 2,6-dichloro-5-fluoronicotinamide (5.0 g, 23.9
mmol) in THF (20 mL) was slowly added oxalyl chloride (2 M
solution in DCM, 14.4 mL, 28.8 mmol). The resulting mixture
was stirred at 75 °C for 1 h, then allowed to cool and
concentrated in vacuo to half volume. The concentrate was
cooled to 0 °C and diluted with THF (20 mL). A solution of 2-
isopropyl-4-methylpyridin-3-amine (3.59 g, 23.9 mmol) in
THF (10 mL) was added dropwise via cannula. The resulting
mixture was stirred at 0 °C for 1 h, diluted with a 1:1 mixture
of brine and saturated aqueous ammonium chloride, and
extracted with EtOAc (3×). The combined organic extracts
were dried over anhydrous sodium sulfate and concentrated in
vacuo to provide 2,6-dichloro-5-fluoro-N-((2-isopropyl-4-
methylpyridin-3-yl)carbamoyl)nicotinamide, which was used
without further purification. m/z (ESI, +ve ion): 385.1 (M+H)+.
Step 5. (S)-tert-Butyl 4-(7-chloro-6-fluoro-1-(2-isopropyl-
4-methylpyridin-3-yl)-2-oxo-1,2-dihydropyrido[2,3-
d]pyrimidin-4-yl)-3-methylpiperazine-1-carboxylate. To an
ice-cooled solution of 4,7-dichloro-6-fluoro-1-(2-isopropyl-4-
methylpyridin-3-yl)pyrido[2,3-d]pyrimidin-2(1H)-one (13.5
mmol) in acetonitrile (20 mL) was added DIPEA (7.1 mL, 40.3
mmol) followed by (S)-4-Boc-2-methyl piperazine (3.23 g, 16.1
mmol, Combi-Blocks, Inc.). The resulting mixture was warmed
to ambient temperature and stirred for 1 h, then diluted with
cold saturated aqueous sodium bicarbonate solution (200 mL)
and EtOAc (300 mL). The mixture was stirred for an additional
5 min, and the organic layer was collected. The aqueous layer
was extracted with additional EtOAc (1×), and the combined
organic extracts were dried over anhydrous sodium sulfate and
concentrated in vacuo. Chromatographic purification of the
residue (silica gel; 0–50% EtOAc/heptane) gave (S)-tert-butyl
4-(7-chloro-6-fluoro-1-(2-isopropyl-4-methylpyridin-3-yl)-2-
oxo-1,2-dihydropyrido[2,3-d]pyrimidin-4-yl)-3-
Intermediate, Step 2. 2-Isopropyl-4-methylpyridin-3-
amine: To a slurry of 3-amino-2-bromo-4-picoline (360 mg,
1.9 mmol; Combi-Blocks, Inc.) in THF (4 mL) was added [1,1′-
bis(diphenylphosphino)ferrocene]dichloropalladium(II),
1
complex with DCM (79 mg, 0.10 mmol). The resulting slurry
was deoxygenated with argon, then 2-propylzinc bromide (0.5
M solution in THF, 5.4 mL, 2.7 mmol) was added. The
resulting solution was stirred at 60 °C for 17 h, then the reaction
methylpiperazine-1-carboxylate (5.71 g, 80% yield). H NMR
(400 MHz, DMSO-d6) δ 8.45–8.51 (1 H, m), 8.31–8.41 (1 H,
m), 7.23–7.29 (1 H, m), 4.67–5.01 (1 H, m), 4.09–4.25 (1 H,
m), 3.88–4.07 (1 H, m), 3.78–3.87 (1 H, m), 3.59–3.74 (1 H,
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Journal of Medicinal Chemistry
m), 3.04–3.21 (2 H, m), 2.59–2.66 (1 H, m), 1.88–1.98 (3 H, (2-isopropyl-4-methylpyridin-3-yl)-2-oxo-1,2-
1
2
3
4
5
6
7
8
m), 1.43–1.50 (9 H, m), 1.27–1.35 (3 H, m), 1.03–1.10 (3 H,
dihydropyrido[2,3-d]pyrimidin-4-yl)-3-methylpiperazine-1-
carboxylate (6.3 g, 10 mmol) in DCM (30 mL), and the
resulting mixture was stirred at ambient temperature for 1 h.
The mixture was then concentrated in vacuo, and the residue
was taken up in DCM (30 mL), cooled to 0 °C, and sequentially
treated with DIPEA (7.3 mL, 42 mmol) and a solution of
acryloyl chloride (0.849 mL, 10.4 mmol) in DCM (3 mL; added
dropwise). The resulting mixture was stirred at 0 °C for 10 min,
then diluted with half-saturated aqueous sodium bicarbonate
and extracted with DCM (2×). The combined extracts were
dried over anhydrous sodium sulfate and concentrated in vacuo.
Chromatographic purification of the residue (silica gel; 0–100%
3:1 EtOAc-EtOH/heptane) followed by chiral supercritical fluid
chromatography (Chiralpak IC, 30  250 mm, 5 µm, 55%
MeOH/CO2, 120 mL/min, 102 bar) provided (1R)-6-Fluoro-7-
(2-fluoro-6-hydroxyphenyl)-1-[4-methyl-2-(1-methylethyl)-3-
pyridinyl]-4-[(2S)-2-methyl-4-(1-oxo-2-propen-1-yl)-1-
piperazinyl]-pyrido[2,3-d]pyrimidin-2(1H)-one (AMG 510;
(R)-38; 2.25 g, 43% yield) as the first-eluting peak. 1H NMR
(600 MHz, DMSO-d6) δ ppm 10.20 (s, 1H), 8.39 (d, J = 4.9 Hz,
1H), 8.30 (d, J = 8.9 Hz, 0.5H), 8.27 (d, J = 8.7 Hz, 0.5H), 7.27
(q, J = 8.4 Hz, 1H), 7.18 (d, J = 4.9 Hz, 1H), 6.87 (dd, J = 16.2,
10.8 Hz, 0.5H), 6.84 (dd, J = 16.2, 10.7 Hz, 0.5H), 6.74 (d, J =
8.4 Hz, 1H), 6.68 (t, J = 8.4 Hz, 1H), 6.21 (d, J = 16.2 Hz, 0.5H),
6.20 (d, J = 16.2 Hz, 0.5H), 5.76 (d, J = 10.8 Hz, 0.5H), 5.76
(d, J = 10.7 Hz, 0.5H), 4.91 (m, 1H), 4.41 (d, J = 12.2 Hz, 0.5H),
4.33 (d, J = 12.2 Hz, 1H), 4.28 (d, J = 12.2 Hz, 0.5H), 4.14 (d,
J = 12.2 Hz, 0.5H), 4.02 (d, J = 13.6 Hz, 0.5H), 3.69 (m, 1H),
3.65 (d, J = 13.6 Hz, 0.5H), 3.52 (t, J = 12.2 Hz, 0.5H), 3.27 (d,
J = 12.2 Hz, 0.5H), 3.15 (t, J = 12.2 Hz, 0.5H), 2.72 (m, 1H),
1.90 (s, 3H), 1.35 (d, J = 6.7 Hz, 3H), 1.08 (d, J = 6.7 Hz, 3H),
0.94 (d, J = 6.7 Hz, 3H). 19F NMR (376 MHz, DMSO-d6) δ –
115.6 (d, J = 5.2 Hz, 1 F), –128.6 (br. s., 1 F). 13C NMR (151
MHz, DMSO-d6) δ ppm 165.0 (1C), 163.4 (1C), 162.5 (1C),
160.1 (1C), 156.8 (1C), 153.7 (1C), 151.9 (1C), 149.5 (1C),
148.3 (1C), 145.2 (1C), 144.3 (1C), 131.6 (1C), 130.8 (1C),
127.9 (0.5C), 127.9 (0.5C), 127.8 (0.5C), 127.7 (0.5C), 123.2
(1C), 122.8 (1C), 111.7 (1C), 109.7 (1C), 105.7 (1C), 105.3
(1C), 51.4 (0.5C), 51.0 (0.5C), 48.9 (0.5C), 45.4 (0.5C), 44.6
(0.5C), 43.7 (0.5C), 43.5 (0.5C), 41.6 (0.5C), 29.8 (1C), 21.9
(1C), 21.7 (1C), 17.0 (1C), 15.5 (0.5C), 14.8 (0.5C). FTMS
(ESI) m/z: [M+H]+ Calcd for C30H30F2N6O3 561.24202; Found
561.24150.
m), 0.94–1.03 (3 H, m). m/z (ESI, +ve ion): 531.2 (M+H)+.
Step 6.
(3S)-tert-Butyl 4-(6-fluoro-7-(2-fluoro-6-
hydroxyphenyl)-1-(2-isopropyl-4-methylpyridin-3-yl)-2-
oxo-1,2-dihydropyrido[2,3-d]pyrimidin-4-yl)-3-
methylpiperazine-1-carboxylate. A mixture of (S)-tert-butyl
4-(7-chloro-6-fluoro-1-(2-isopropyl-4-methylpyridin-3-yl)-2-
oxo-1,2-dihydropyrido[2,3-d]pyrimidin-4-yl)-3-
methylpiperazine-1-carboxylate (4.3 g, 8.1 mmol), (2-fluoro-6-
hydroxyphenyl)potassium trifluoroborate (2.9 g, 10.5 mmol),
potassium acetate (3.2 g, 32.4 mmol) and [1,1′-
bis(diphenylphosphino)ferrocene]dichloropalladium(II),
complex with dichloromethane (661 mg, 0.81 mmol) in 1,4-
dioxane (80 mL) was sparged with nitrogen for 1 min. De-
oxygenated water (14 mL) was added, and the resulting mixture
was heated at 90 °C for 1 h, then cooled to ambient temperature,
diluted with half-saturated aqueous sodium bicarbonate, and
sequentially extracted with EtOAc (2×) and DCM (1×). The
combined organic extracts were dried over anhydrous sodium
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
sulfate and concentrated in vacuo.
Chromatographic
purification of the residue (silica gel; 0–60% 3:1 EtOAc-
EtOH/heptane) furnished (3S)-tert-butyl 4-(6-fluoro-7-(2-
fluoro-6-hydroxyphenyl)-1-(2-isopropyl-4-methylpyridin-3-
yl)-2-oxo-1,2-dihydropyrido[2,3-d]pyrimidin-4-yl)-3-
1
methylpiperazine-1-carboxylate (4.52 g, 92% yield). H NMR
(400 MHz, DMSO-d6) δ 10.19 (br s, 1 H), 8.38 (d, J = 5.0 Hz,
1 H), 8.26 (dd, J = 12.5, 9.2 Hz, 1 H), 7.23–7.28 (m, 1 H), 7.18
(d, J = 5.0 Hz, 1 H), 6.72 (d, J = 8.0 Hz, 1 H), 6.68 (t, J = 8.9
Hz, 1 H), 4.77–4.98 (m, 1 H), 4.24 (br t, J = 14.2 Hz, 1 H), 3.93–
4.08 (m, 1 H), 3.84 (br d, J = 12.9 Hz, 1 H), 3.52–3.75 (m, 1
H), 3.07–3.28 (m, 1 H), 2.62–2.74 (m, 1 H), 1.86–1.93 (m, 3
H), 1.43–1.48 (m, 9 H), 1.35 (dd, J = 10.8, 6.8 Hz, 3 H), 1.26–
1.32 (m, 1 H), 1.07 (dd, J = 6.6, 1.7 Hz, 3 H), 0.93 (dd, J = 6.6,
2.1 Hz, 3 H). 19F NMR (376 MHz, DMSO-d6) δ –115.6 (s, 1 F),
–128.6 (s, 1 F). m/z (ESI, +ve ion): 607.3 (M+H)+.
Intermediate,
Step
6.
(2-Fluoro-6-
hydroxyphenyl)potassium trifluoroborate: A solution of
potassium fluoride (44.7 g, 770 mmol) in water (75 mL) was
added to a suspension of (2-fluoro-6-hydroxyphenyl)boronic
acid (30 g, 192 mmol, Combi-Blocks, Inc.) in acetonitrile (750
mL). After 2 min of stirring, a solution of L-(+)-tartaric acid
(72.2 g, 481 mmol) in THF (375 mL) was added over 10 min.
The resulting mixture was mechanically stirred for 1 h.
Suspended solids were removed by filtration and washed with
a small amount of THF. The combined filtrate was then
partially concentrated in vacuo until solids began to precipitate.
ASSOCIATED CONTENT
Experimental details for in vitro and in vivo studies, additional
crystallographic data for compounds 2 and 9, and synthetic
procedures for compounds 2–40 can be found in the Supporting
Information, available free of charge via the Internet at
http://pubs.acs.org.
°
The filtrate was cooled to –20 C and stirred for 16 h, then
slowly warmed to ambient temperature. 2-Propanol (20 mL)
was added, and the precipitated solid was collected by filtration
and washed with 2-propanol to provide 27.5 g of solid. The
filtrate was again partially concentrated (until precipitation was
observed), cooled to –20 °C, and stirred for 20 min. Additional
2-propanol was added, and the precipitated solid was collected
by filtration and washed with 2-propanol. The two batches of
ACCESSION CODES
Atomic coordinates for the X-ray structures of compound 2 (PDB
6PGO) and 9 (PDB 6PGP) bound to GDP-KRASG12C are available
from the RCSB Protein Data Bank (www.rcsb.org).
solid
were
combined
to
provide
2-fluoro-6-
hydroxyphenyl)potassium trifluoroborate (34.6 g, 82% yield).
1H NMR (400 MHz, DMSO-d6) δ 8.07 (q, J = 14.7 Hz, 1 H)
6.93 (q, J = 7.5 Hz, 1 H) 6.30–6.38 (m, 2 H).
AUTHOR INFORMATION
Corresponding Author
* Phone: (805) 313-5777. E-mail: blanman@amgen.com
AMG 510 [(R)-38].
(1R)-6-Fluoro-7-(2-fluoro-6-
hydroxyphenyl)-1-[4-methyl-2-(1-methylethyl)-3-
pyridinyl]-4-[(2S)-2-methyl-4-(1-oxo-2-propen-1-yl)-1-
piperazinyl]-pyrido[2,3-d]pyrimidin-2(1H)-one:
Author Contributions
Manuscript prepared by B.L. with contributions from all authors.
Trifluoroacetic acid (25 mL, 320 mmol) was added to a solution
of (3S)-tert-butyl 4-(6-fluoro-7-(2-fluoro-6-hydroxyphenyl)-1-
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Journal of Medicinal Chemistry
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(7) Shin, Y.; Jeong, J.W.; Wurz, R.P.; Achanta, P.; Arvedson, T.;
ACKNOWLEDGMENT
Bartberger, M.D.; Campuzano, I.D.G.; Fucini, R.; Hansen, S.K.; Iwig,
J.; Lipford, J.R.; Ma, V.; Kopecky, D.J.; McCarter, J.; San Miguel, T.;
Mohr, C.; Sabet, S.; Saiki, A.Y.; Sawayama, A.; Sethofer, S.; Tegley,
C.M.; Volak, L.P.; Yang, K.; Lanman, B.A.; Erlanson, D.A.; Cee, V.J.
1
2
3
4
5
6
7
8
These discovery efforts were critically enabled by the support of a
diverse set of talented teams, functional leaders, and highly
motivated scientists, without whom this work would not have been
possible. Special thanks to Larry Miller, Wes Barnhart, Heather
Eastwood, and Shannon Rumfelt for their crucial assistance with
the chiral and achiral purification of project leads and
intermediates. Thanks to David Bauer, Jim Brown, Rob Rzasa, and
Ted Judd for their efforts in the initial synthetic scale-up of AMG
510 and to Rajiv Kapoor and the Syngene Amgen Research
Collaboration (SARC) for their support in supplying key
intermediates. Our thanks to Roman Shimanovich, Prashant
Agarwal, and Melanie Cooke for their pharmaceutics and
formulation support. We also thank Crystallographic Consulting,
LLC and the Advanced Light Source staff at beamline 5.0.2 for data
collection and their support. The Berkeley Center for Structural
Biology is supported in part by the National Institutes of Health,
National Institute of General Medical Sciences, and the Howard
Hughes Medical Institute. The Advanced Light Source is supported
by the Director, Office of Science, Office of Basic Energy
Sciences, of the U.S. Department of Energy under Contract No.
DE-AC02-05CH11231. We also acknowledge the Southeast
Regional Collaborative Access Team (SER-CAT) 22-ID beamline
at the Advanced Photon Source, Argonne National Laboratory for
data collection and support. SER-CAT is supported by its member
institutions, and equipment grants (S10_RR25528 and
S10_RR028976) from the National Institutes of Health. Use of the
Advanced Photon Source was supported by the U. S. Department
of Energy, Office of Science, Office of Basic Energy Sciences,
under Contract No. W-31-109-Eng-38. Figures were generated
using The PyMOL Molecular Graphics System, Version 2.2.0
Schrödinger, LLC.
Discovery
of
N-(1-Acryloylazetidin-3-yl)-2-(1H-Indol-1-
yl)Acetamides as a Covalent Inhibitor of KRASG12C. ACS Med. Chem.
Lett. 2019, 10, 1302–1308.
(8) Patricelli, M. P.; Janes, M. R.; Li, L.-S.; Hansen, R.; Peters, U.;
Kessler, L. V.; Chen, Y.; Kucharski, J. M.; Feng, J.; Ely, T.; Chen, J.
H.; Firdaus, S. J.; Babbar, A.; Ren, P.; Liu, Y. Selective Inhibition of
Oncogenic KRAS Output with Small Molecules Targeting the Inactive
State. Cancer Discov. 2016, 6, 316–329.
(9) Janes, M. R.; Zhang, J.; Li, L.-S.; Hansen, R.; Peters, U.; Guo,
X.; Chen, Y.; Babbar, A.; Firdaus, S. J.; Darjania, L.; Feng, J.; Chen, J.
H.; Li, S.; Li, S.; Long, Y. O.; Thach, C.; Liu, Y.; Zarieh, A.; Ely, T.;
Kucharski, J. M.; Kessler, L. V.; Wu, T.; Yu, K.; Wang, Y.; Yao, Y.;
Deng, X.; Zarrinkar, P. P.; Brehmer, D.; Dhanak, D.; Lorenzi, M. V.;
Hu-Lowe, D.; Patricelli, M. P.; Ren, P.; Liu, Y. Targeting KRAS
Mutant Cancers with a Covalent G12C-Specific Inhibitor. Cell 2018,
172, 578–589.
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(10) Hansen, S.; Erlanson, D.; Cancilla, M. Methods of Chemotype
Evolution. U.S. Patent 10,107,798, October 23, 2018.
(11) For independent identification of the H95/Y96/Q99 groove
from a KRAS M72C screen, see Gentile, D. R.; Rathinaswamy, M. K.;
Jenkins, M. L.; Moss, S. M.; Siempelkamp, B. D.; Renslo, A. R.;
Burke, J. E.; Shokat, K. M. Ras Binder Induces a Modified Switch-II
Pocket in GTP and GDP States. Cell Chem. Biol. 2017, 24, 1455–1466.
(12) It should be noted that covalent inhibitors derive their potency
not only from non-covalent protein binding affinity (which facilitates
protein–ligand pre-association), but also from features of the protein–
ligand complex which accelerate covalent bond formation. Improved
ligand “potencies” as described in this manuscript should be
understood as arising from varying contributions of these two factors.
(13)
For
details,
see
https://www.perkinelmer.com/Content/RelatedMaterials/Brochure
s/BRO_AlphaScreen2004.pdf (accessed Sep 7, 2019)
ABBREVIATIONS
(14)
For
details,
see
KRAS, Kirsten Rat Sarcoma virus oncogene; GDP, guanosine
diphosphate; GTP, guanosine triphosphate; S-IIP, switch II pocket;
SOS1, son of sevenless homolog 1 protein; c-RAF, rapidly
accelerated fibrosarcoma kinase (cellular homolog); p-ERK,
phosphorylated extracellular signal-regulated kinase; MSD, Meso
Scale Diagnostics; EGF, epidermal growth factor; PK,
pharmacokinetic; MDCK, Madin-Darby Canine Kidney cell; IV,
intravenous; PO, per os (oral); SAR, structure–activity relationship;
QD, quaque die (once daily); TGI, tumor growth inhibition;
FaSSGF, fasted-state simulated gastric fluid; FaSSIF, fasted-state
simulated intestinal fluid; PBS, phosphate-buffered saline; MS,
mass spectrometry; GSH, glutathione
https://www.mesoscale.com/en/products/phospho-total-erk1-2-
whole-cell-lysate-kit-k15107d/ (accessed Sep 7, 2019)
(15) 5-min incubation represented the shortest incubation time that
could be practically executed.
(16) 2-h incubation was estimated to be the minimum time required
to achieve “complete” (~95%) covalent modification of KRASG12C
based on the GTP hydrolysis rate reported in ref. 8.
(17) Possible reasons for the increased activity of compound 8
include more optimal orientation of the isopropylphenyl substituent in
the cryptic pocket (a B3LYP/6-31G* quantum mechanical model
predicts compound 8 to adopt a ground-state biaryl torsion angle of 65°,
whereas the quinazolinone and phenyl rings are nearly perpendicular in
compound 9, enhancing contacts with the cryptic pocket residues) and
enhanced contacts between the quinazolinone carbonyl group and
proximal protein residues and water molecules.
(18) For IUPAC naming conventions, see Moss, G. P. Basic
Terminology of Stereochemistry (IUPAC Recommendations 1996).
Pure Appl. Chem. 1996, 68, 2193–2222.
(19) (R)-9 was ~20-fold more potent than (S)-9 in the ERK
phosphorylation assay (MSD, 4 h incubation).
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X.; Chen, Y.; Babbar, A.; Firdaus, S. J.; Darjania, L.; Feng, J.; Chen, J.
H.; Li, S.; Li, S.; Long, Y. O.; Thach, C.; Liu, Y.; Zarieh, A.; Ely, T.;
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172, 578–589.
(20) For details, see https://www.promega.com/products/cell-
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luminescent-cell-viability-assay/?catNum=G7570 (accessed Sep 7,
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(21) Intramolecular hydrogen bonding has previously been
demonstrated to enhance passive membrane permeability: Rezai, T.;
Bock, J. E.; Zhou, M. V.; Kalyanaraman, C.; Lokey, R. S.; Jacobson,
M. P. Conformational Flexibility, Internal Hydrogen Bonding, and
Passive Membrane Permeability: Successful In Silico Prediction of the
Relative Permeabilities of Cyclic Peptides. J. Am. Chem. Soc. 2006,
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(22) Atropisomer interconversion was monitored by 1H NMR.
Exchange rates were calculated from line-shape analysis, coalescence
temperatures, or half-lives. Free energy barriers (ΔG‡) were calculated
from exchange rates using Eyring’s equation. For details, see Claridge,
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Cyclophanes. Org. Biomol. Chem. 2013, 11, 110–118.
(25) In vitro p-ERK IC50 values were derived from EGF-stimulated
MIA PaCa-2 cells.
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1
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(30) As determined by stable-isotope labelling (SILAC)
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Irreversible Inhibitors: A Complete Workflow. J. Biomol. Screen.
2016, 21, 136–144.
9
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C.; Arvedson, T.; McCarter, J.; Tasker, A. S.; Fotsch, C. Systematic
Study of the Glutathione (GSH) Reactivity of N-Arylacrylamides: 1.
Effects of Aryl Substitution. J. Med. Chem. 2015, 58, 9171–9178
(33) Data to be reported separately.
(34) Details of this trial can be found at https://clinicaltrials.gov/
(accessed Sep 7, 2019)
(35) Fakih, M.; O'Neil, B.; Price, T. J.; Falchook, G. S.; Desai, J.;
Kuo, J.; Govindan, R.; Rasmussen, E.; Morrow, P. K. H.; Ngang, J.;
Henary, H. A.; Hong, D. S. J. Clin. Oncol. 2019, 37 (suppl; abstr 3003).
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(26) Residual ERK phosphorylation (~30%) is attributable to non-
mutant KRAS activity resulting from stromal contamination of the
clonal KRAS p.G12C tumors (confirmed by RNAseq) and is observed
both at later timepoints and at higher doses.
(27) No significant body weight loss was observed at any dose level
in this study.
(28) Data initially published in Canon, J.; Rex, K.; Saiki, A. Y.;
Mohr, C.; Cooke, K.; Bagal, D.; Gaida, K.; Holt, T.; Knutson, C. G.;
Koppada, N.; Lanman, B. A.; San Miguel, T.; O’Neil, B. H.; Ortiz, R.;
Osgood, T.; Sun, J.-R.; Zhu, S.; McCarter, J. D.; Volak, L. P.; Henary,
H.; Arvedson, T.; Cee, V. J.; Lipford, J. R. The First Clinical KRASG12C
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