Asymmetric Synthesis of Akt Kinase Inhibitor Ipatasertib

Article abstract of DOI:10.1021/acs.orglett.7b02228

A highly efficient asymmetric synthesis of the Akt kinase inhibitor ipatasertib (1) is reported. The bicyclic pyrimidine 2 starting material was prepared via a nitrilase biocatalytic resolution, halogen-metal exchange/anionic cyclization, and a highly dia

Full text of DOI:10.1021/acs.orglett.7b02228

Letter
pubs.acs.org/OrgLett
Asymmetric Synthesis of Akt Kinase Inhibitor Ipatasertib
Chong Han,† Scott Savage,† Mohammad Al-Sayah,‡ Herbert Yajima,† Travis Remarchuk,†
Reinhard Reents,§ Beat Wirz,§ Hans Iding,§ Stephan Bachmann,§ Serena M. Fantasia,§
Michelangelo Scalone,§ Andre Hell,§ Pirmin Hidber,§ and Francis Gosselin*,†
́
‡
†Department of Small Molecule Process Chemistry, Department of Small Molecule Analytical Chemistry and Quality Control,
Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
§Department of Pharma Technical Development Small Molecules, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070
Basel, Switzerland
S
* Supporting Information
ABSTRACT: A highly efficient asymmetric synthesis of the
Akt kinase inhibitor ipatasertib (1) is reported. The bicyclic
pyrimidine 2 starting material was prepared via a nitrilase
biocatalytic resolution, halogen−metal exchange/anionic cyc-
lization, and a highly diastereoselective biocatalytic ketone
reduction as key steps. The route also features a halide
activated, Ru-catalyzed asymmetric hydrogenation of a vinyl-
ogous carbamic acid to produce α-aryl-β-amino acid 3 in high
yield and enantioselectivity. The API was assembled in a
convergent manner through a late-stage amidation/depro-
tection/monohydrochloride salt formation sequence.
he serine-threonine protein kinase Akt (protein kinase B)
functions as a pivotal junction in the PI3K/Akt/mTOR
signaling cascade and regulates cell growth, proliferation,
survival, and apoptosis.1 Drug discovery efforts in our
laboratories identified GDC-0068 (1, ipatasertib) as a novel
and potent inhibitor that targets the ATP-binding cleft of all
three isoforms of Akt kinase (Figure 1).2 Ipatasertib is currently
long-term manufacturing synthesis based on the efficient
construction of 2 and 3 and their final assembly into ipatasertib
(1).
T
Our second-generation route to the unexpectedly challenging
ketone 4 was designed to overcome issues associated with
racemization of the C-5-methyl center in the carbonylation−
Dieckmann approach we reported previously.3b As depicted in
Scheme 1, we started from (R)-triester 5, obtained in two steps
from conjugate addition of dimethyl malonate with methyl
crotonate followed by lipase resolution.3b Condensation of 5
with formamidine acetate and chlorination using POCl3 gave
4,6-dichloropyrimidine methyl ester 6. Attempted aromatic
Finkelstein bromination proved fruitless, since the solubility
difference between chloride and bromide salts in organic
solvents does not favor the equilibrium toward the 4,6-
dibromopyrimidine product. More forcing conditions led to
halide-mediated SN2 dealkylation and concurrent lactonization
to 8 as determined by HPLC-MS analysis.4
Reaction using NaI in acetone at reflux gave the
corresponding 4-iodo-6-chloropyrimidine. Attempted iodina-
tion using hydroiodic acid led to only formation of ring-opened
product derived from lactone 8. We found that reaction with
excess NaI in CH3CN in the presence of Me3SiCl as a
promoter, or preferably with MeSO3H as a Brønsted acid,
allowed full and clean conversion to the desired 4,6-
diiodopyrimidine 7. Subsequent nucleophilic aromatic sub-
stitution with N-Boc-piperazine followed by ester hydrolysis
Figure 1. Structure and retrosynthesis of ipatasertib.
in Phase III clinical trials for the treatment of metastatic
castration-resistant prostate cancer and triple negative meta-
static breast cancer. The active pharmaceutical ingredient (API)
is a complex 6,7-dihydro-5H-cyclopenta[d]pyrimidine piper-
azine amide compound containing three chiral centers from the
assembly of chiral bicyclic pyrimidine 2 and chiral α-aryl-β-
amino acid 3 (Figure 1). As a further challenge to process
chemistry, the highly hygroscopic and deliquescent API
monohydrochloride salt form was selected for development.3
This letters highlights our efforts to develop a highly efficient
Received: July 21, 2017
© XXXX American Chemical Society
A
DOI: 10.1021/acs.orglett.7b02228
Org. Lett. XXXX, XXX, XXX−XXX

Organic Letters
Letter
Scheme 1. Asymmetric Synthesis of Ketone 4
Scheme 2. Improved Asymmetric Synthesis of Ketone 4
gave 9a. Functional group interconversion, halogen−metal
exchange on Weinreb amide 9b using i-PrMgCl in THF at −10
°C, and inverse quench into aqueous NH4Cl allowed smooth
formation of the desired (R)-ketone 4 in 82% isolated yield
after crystallization from MTBE/heptane.5 Although this
approach was used to synthesize multihundred kilogram
amounts of 4, we identified a number of drawbacks that
limited the long-term sustainability of the route: The
biocatalytic resolution to obtain triester (R)-5 required an
extended reaction time (>5 d, 20−30% yield) and thus proved
unsuitable for late-stage development, and the aromatic
Finkelstein halogen exchange required a large excess of NaI
to drive reaction equilibrium to 7. Besides cost considerations
and poor atom economy, the aromatic Finkelstein conditions
created a significant waste disposal issue, since iodide is toxic to
freshwater aquatic life at low concentration.6
We surmised that introduction of a nitrile functional group
would provide a more robust handle for the overall process,
especially under the Finkelstein reaction and the cyclization
reaction conditions (Scheme 2). Furthermore, the nitrile would
avoid unproductive functional group interconversions including
protection−deprotection steps. We found that conjugate
addition of dimethyl malonate to crotononitrile 10 proceeded
smoothly when mediated by sodium tert-amylate in THF at
60−70 °C and provided rac-11. Gratifyingly, we identified a
nitrilase enzyme that afforded the desired (R)-nitrile 11 in 38−
45% yield and >99.8:0.2 er. Interestingly, we found that enzyme
activity was enhanced by high concentrations of sulfate, citrate,
and phosphate ions. In contrast, addition of polar organic
cosolvents impaired enzyme activity. The resolution was thus
performed in aqueous 0.5 M K2SO4/50 mM KH2PO4 buffer at
pH 7.2 and 20% substrate concentrations without organic
cosolvents. Cyclocondensation of (R)-11 with formamidine
acetate in MeOH gave (R)-4,6-dihydroxypyrimidine 12 in 84%
yield. A three-step through-process started with chlorination of
12 with POCl3 in toluene and 2,6-lutidine as the base gave (R)-
4,6-dichloropyrimidine 13, and then bromination with
Me3SiBr7 in CH3CN gave (R)-4,6-dibromopyrimidine 14 that
was treated directly with N-Boc-piperazine and Et3N to afford
(R)-bromo-piperazine-pyrimidine 15 in 93% yield. Halogen−
metal exchange required slow addition of i-PrMgCl over 4 h in
2-MeTHF/toluene at 0−10 °C and concomitant cyclization
afforded a persistent primary (R)-enamine 16. Primary enamine
16 proved persistent under a variety of conditions and could be
isolated in crude form by quenching with aqueous NH4Cl. We
observed a strong pH dependence on the rate of hydrolysis of
the metallo-enamine intermediate, since a pH 6 aqueous
quench gave preferentially enamine 16, whereas a pH 5
aqueous quench afforded complete hydrolysis to ketone 4.
Ultimately, we found that quenching and hydrolysis of 16 with
aqueous NaHSO4 gave (R)-ketone 4 in 74% yield without
detectable racemization as determined by HPLC analysis of the
crude reaction mixture.8 This quench procedure provided a
clean phase separation and stable mixture with ≤2% 4 loss to
the aqueous layer. The product (R)-ketone 4 was then directly
crystallized after a solvent switch to MTBE/heptane in 84%
yield without any detectable racemization at the C-5-methyl
center as ascertained by chiral HPLC analysis.
Preliminary experiments toward the reduction of ketone 4
showed that substrate selectivity provided the undesired
(5R,7S)-diastereomer 17 preferentially under a number of
conditions (Table 1, entry 1).3b We identified a Ru-catalyzed
asymmetric transfer hydrogenation (ATH) that provided a
viable solution to the intrinsic diastereoselectivity problem
(entry 2). After optimization, the ATH using RuCl(p-
cymene)[(1R,2R)-Ts-DACH] as the catalyst coupled with an
efficient crystallization procedure afforded the desired alcohol 2
in 79% yield with 99.4:0.6 dr after recrystallization.9 In parallel,
we identified a ketoreductase enzyme (KRED1) that in
conjunction with glucose dehydrogenase (GDH) as a
coenzyme, NADP as a cofactor, and D-glucose as a terminal
reductant provided excellent diastereoselectivities up to 99:1 for
the desired (5R,7R)-2 in 79% isolated yield (entry 3). We then
developed a simple solution using a single enzyme KRED2 in
B
DOI: 10.1021/acs.orglett.7b02228
Org. Lett. XXXX, XXX, XXX−XXX

Organic Letters
Letter
crystallization upgraded the chiral purity of amino acid 3 to
99.5:0.5 er in a reproducible fashion. Removal of residual Ru
from the process stream proved cumbersome and required use
of an expensive and insoluble metal scavenger. Thus, over 50
different chiral diphosphines were evaluated as ligands for Ru in
the asymmetric hydrogenation of 18. We found that the
complex prepared by combination of ruthenium dimer complex
[Ru(COD)(TFA)2]2 with atropisomeric diphosphines such as
(S)-BINAP (L1)11 or (S)-MeOBIPHEP (L2)12 provided the
highest catalytic activity and best enantioselectivities (entries
2−3).13 We opted for the BINAP catalyst system based on
slightly higher enantioselectivity observed, ligand availability
and cost considerations. During this optimization effort, we
found that some batches of vinylogous carbamic acid 18
performed well in the asymmetric hydrogenation while others
led to almost no conversion to 3. We determined that a small
amount of residual NaCl in the bulk 18 led to catalyst
activation under hydrogenation conditions. Using halide-free 18,
[Ru(TFA)2(S)-BINAP] allowed for S/C = 10 000 with catalyst
activation using NaBr as an additive (entry 3).14−16 The optimal
ratio to ensure reaction robustness was selected as Ru/NaBr =
1:20 and thus afforded >99% conversion and 98.8:1.2 er. It is
noteworthy that when addition of NaBr was omitted we
observed only 29% conversion after 12 h with 90:10 er (entry
4).17 Using such low catalyst loadings (10 ppm relative to 18)
allowed complete elimination of the scavenging step and
resulted in a greatly simplified isolation process where α-aryl-β-
amino acid 3 was readily crystallized from EtOH/MTBE in
92% yield as the corresponding nonhygroscopic and
enantiomerically pure sodium salt 3a.
Table 1. Diastereoselective Ketone Reduction
a
entry
catalyst
reductant
yield (%)
dr
1
2
3
4
5% Pd/C
HCO2H
63
79
79
86
6.0:94.0
95.8:4.2
>99.0:1.0
b
Ru
HCO2Na
D-glucose
2-propanol
c
KRED1
d
KRED2
>99.5:0.5
a
b
Determined by HPLC analysis of the crude reaction mixture. 0.2
c
mol % RuCl(p-cymene)[(1R,2R)-Ts-DACH] in MeTHF. [4] = 4.0
wt %, KRED1 (1.0 wt %), GDH (2.7 wt %), NADP (2.8 wt %),
d
DMSO/H2O/pH 7 phosphate buffer. [4] = 20 wt %, KRED2 (3.0 wt
%), NADP (0.1 wt %), pH 7 phosphate buffer.
conjunction with 2-propanol as the terminal reductant, and
further optimization afforded alcohol 2 in 86% yield and
essentially perfect diastereoselectivity (entry 4). The sensitivity
of ketone 4 in solution was apparent by generation of ppm
levels of highly colored impurities but was overcome by
performing the KRED step in a slurry-to-slurry reaction mode
at room temperature to maintain robust performance. For long-
term purposes, we preferred the biocatalytic asymmetric
reduction of ketone 4 since it provided levels of diaster-
eoselectivity that avoided downstream dr upgrades and
eliminated operations associated with purging of Ru.
Scheme 3. End-Game Chemistry to Ipatasertib (1)
Table 2. Ru Catalyzed Asymmetric Hydrogenation
a
b
c
entry
catalyst
additive
conv (%)
er
d
1
[RuCl2((S)-L1)]
LiBF4
NaBr
NaBr
−
99 (87)
93.0:7.0
98.0:2.0
98.8:1.2
90:10
e
2
[Ru(TFA)2((S)-L2)]
[Ru(TFA)2((S)-L1)]
>99 (95)
>99.5 (92)
f
3
4
[Ru(TFA)2((S)-L1)]
29
a
b
c
Additive/Ru = 20:1. Isolated yield in parentheses. Determined by
chiral HPLC analysis of the crude reaction mixture. S/C = 1500,
EtOH, 30 atm of H2, 60 °C. S/C = 5000, NaBr/Ru = 20:1, EtOH (12
mL/g), 18 atm of H2, 60 °C. S/C = 10 000, NaBr/Ru = 20:1, EtOH
d
e
f
(12 mL/g), 18 atm of H2, 60 °C.
The original conditions for the amidation step used HBTU/
DIEA in CH2Cl2.18,19 Based on the undesirable properties of
HBTU and its byproducts, we sought to substitute it for a more
innocuous reagent. Deprotection of 2 with HCl in n-PrOH
gave 18, and a series of experiments identified propane-
phosphonic anhydride (T3P) as a superior amidation reagent
that provided 19 in 97% assay yield without detectable
epimerization of the sensitive β-amino acid 3 chiral center
(Scheme 3). Simple aqueous washes were required to remove
The first generation asymmetric hydrogenation of 18 using
[RuCl2(S)-BINAP] (S/C = 1500) required the use of LiBF4 to
abstract chloride ion from ruthenium and 30 atm of H2 at 60
°C.10 We observed fluctuations in performance of the
asymmetric hydrogenation with enantioselectivities ranging
from er 99.5:0.5 to 93.0:7.0 (Table 2, entry 1), but the final
C
DOI: 10.1021/acs.orglett.7b02228
Org. Lett. XXXX, XXX, XXX−XXX

Organic Letters
Letter
(4) McMurry, J. Org. React. 1976, 24, 187.
residual 3 and phosphonate byproducts from T3P, and
piperazine amide 19 was crystallized from toluene/heptane in
82% isolated yield. Removal of the Boc group in 19 with HCl in
n-PrOH gave dihydrochloride 20 that was treated with
Amberlite FPA51 polymer or titrated with aqueous NaOH to
afford, after a solvent switch to EtOAc, the crystalline
monohydrochloride 21 as the corresponding EtOAc solvate.
Myriad attempts to crystallize ipatasertib were met with
failure and afforded variable mixtures of amorphous and
crystalline materials. We identified a simple solution to this
problem by dissolving 21 in water, spray-drying the resulting
solution, and obtained amorphous ipatasertib API (1) in high
yield, with unusually high bulk density (0.45 g/cm3) and
excellent material properties for downstream pharmaceutical
processing.
In summary, by leveraging a combination of careful synthesis
design and efficient use of chemo- and biocatalysis, we have
identified and developed a sustainable and highly efficient
asymmetric synthesis of ipatasertib that has been demonstrated
on the multihundred kilogram scale and exhibits the desired
attributes of a good pharmaceutical manufacturing process.
(5) In our hands, 4,6-dichloropyrimidine 6 and its derivatives proved
unreactive in halogen−metal exchange reactions to afford the desired
ketone 4. Forcing conditions led to decomposition.
(6) An ion-exchange iodide recovery procedure was developed as
part of the manufacturing process for the HIV protease inhibitor
indinavir sulfate (crixivan); see: Venkat, E.; Magliette, R. J.; McKinney,
D.; Michaels, A. S. U.S. patent 6,379,556, Apr 30, 2002.
(7) Schlosser, M.; Cottet, F. Eur. J. Org. Chem. 2002, 2002, 4181.
(8) Racemization of the C-5-methyl chiral center, presumably
through a pentadienyl anion intermediate, has been observed in
earlier routes to ketone 4; see ref 3b. For a related indanone
dialkylation, see: Trost, B. M.; Latimer, L. J. Org. Chem. 1977, 42,
3212.
(9) (a) Canivet, J.; Labat, G.; Stoeckli-Evans, H.; Suss-Fink, G. Eur. J.
̈
Inorg. Chem. 2005, 2005, 4493. (b) Ohkuma, T.; Noyori, R. In
Comprehensive Asymmetric Catalysis, 1st ed.; Jacobsen, E. N., Pfaltz, A.,
Yamamoto, H., Eds.; Springer Verlag: Berlin, 1999; Chapter 6.1.
(c) Ohkuma, T.; Noyori, R. In Comprehensive Asymmetric Catalysis
Supplement 1: Jacobsen, E. N., Pfaltz, A., Yamamoto, H., Eds.; Springer
Verlag: Berlin, 2004; Supplement to Chapter 6.1.
(10) Remarchuk, T.; Babu, S.; Stults, J.; Zanotti-Gerosa, A.;
Roseblade, S.; Yang, S.; Huang, P.; Sha, C.; Wang, Y. Org. Process
Res. Dev. 2014, 18, 135.
(11) Miyashita, A.; Yasuda, A.; Takaya, H.; Toriumi, K.; Ito, T.;
Souchi, T.; Noyori, R. J. Am. Chem. Soc. 1980, 102, 7932.
ASSOCIATED CONTENT
* Supporting Information
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/acs.or-
glett.7b02228.
■
S
(12) (a) Schmid, R.; Cereghetti, M.; Heiser, B.; Schonholzer, P.;
̈
Hansen, H. J. Helv. Chim. Acta 1988, 71, 897. (b) Schmid, R.;
Foricher, J.; Cereghetti, M.; Schonholzer, P. Helv. Chim. Acta 1991, 74,
̈
370.
(13) [Ru(TFA)2(S)-BINAP] was first reported in: Heiser, B.; Broger,
E. A.; Crameri, Y. Tetrahedron: Asymmetry 1991, 2, 51.
Experimental procedures and characterization (PDF)
(14) Chloride content was determined by elemental analysis or
titration with aqueous AgNO3 with a limit of detection of 0.05%.
(15) While a higher performance could be achieved using either HBr
or HCl as additives, we selected NaBr in order to avoid formation of
potential genotoxic impurities due to reactivity with EtOH.
(16) Although the corresponding ethyl ester performed well in the
asymmetric hydrogenation (94% conversion in 12 h at S/C = 4000, er
= 98.7:1.3), the downstream ester hydrolysis proved problematic due
to competing racemization of the sensitive chiral center.
(17) Trace amounts of NH4Cl have been shown to improve Rh-
catalyzed asymmetric hydrogenation of unprotected β-enamine amide;
see: Clausen, A. M.; Dziadul, B.; Cappuccio, K. L.; Kaba, M.; Starbuck,
C.; Hsiao, Y.; Dowling, T. M. Org. Process Res. Dev. 2006, 10, 723.
(18) Carpino, L. A.; Imazumi, H.; El-Faham, A.; Ferrer, F. J.; Zhang,
AUTHOR INFORMATION
■
Corresponding Author
*E-mail: gosselin.francis@gene.com.
ORCID
Chong Han: 0000-0002-2863-3921
Francis Gosselin: 0000-0001-9812-4180
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
We thank Dr. Anne Kraft, Kathrin Schneider, Gino Semadeni,
Jannik Martin, Patrick Stocker, Patrick Meier, and colleagues in
the analytical laboratories of Genentech and F. Hoffmann-La
Roche AG for technical contributions and support.
C.; Lee, Y.; Foxman, B. M.; Henklein, P.; Hanay, C.; Mugge, C.;
̈
Wenschuh, H.; Klose, J.; Beyermann, M.; Bienert, M. Angew. Chem.,
Int. Ed. 2002, 41, 441.
(19) Safety concerns associated with handling of triazole-based
reagents including HBTU and its reaction byproducts have been noted
in: Dunn, P. J.; Hoffmann, W.; Kang, Y.; Mitchell, J. C.; Snowden, M.
J. Org. Process Res. Dev. 2005, 9, 956. (b) Patterson, D. E.; Powers, J.
D.; LeBlanc, M.; Sharkey, T.; Boehler, E.; Irdam, E.; Osterhout, M. H.
Org. Process Res. Dev. 2009, 13, 900.
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DOI: 10.1021/acs.orglett.7b02228
Org. Lett. XXXX, XXX, XXX−XXX