Enantioselective synthesis of GNE-6688, a potent and selective inhibitor of interleukin-2 inducible T-cell kinase (ITK)

Article abstract of DOI:10.1016/j.tetlet.2019.02.014

An enantioselective synthesis of the previously-disclosed ITK inhibitor GNE-6688 is described. Synthesis of the nitropyrazole fragment is highlighted by a Ru-catalyzed transfer hydrogenation using the Wills tethered ligand system. Synthesis of the pyrazole carboxylic acid fragment features an allylboration catalyzed by a chiral diol-SnCl₄ complex, followed by a highly diastereoselective directed cyclopropanation.

Full text of DOI:10.1016/j.tetlet.2019.02.014

Accepted Manuscript
Enantioselective synthesis of GNE-6688, a potent and selective inhibitor of in-
terleukin-2 inducible T-cell kinase (ITK)
Jared Moore, Kevin Lau, Xiaofeng Xu, Yamin Zhang, Jason D. Burch
PII:
S0040-4039(19)30135-2
https://doi.org/10.1016/j.tetlet.2019.02.014
TETL 50608
DOI:
Reference:
Tetrahedron Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
30 July 2018
6 February 2019
7 February 2019
Please cite this article as: Moore, J., Lau, K., Xu, X., Zhang, Y., Burch, J.D., Enantioselective synthesis of GNE-6688,
a potent and selective inhibitor of interleukin-2 inducible T-cell kinase (ITK), Tetrahedron Letters (2019), doi:
https://doi.org/10.1016/j.tetlet.2019.02.014
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Enantioselective synthesis of GNE-6688, a
potent and selective inhibitor of interleukin-2
inducible T-cell kinase (ITK)
Jared Moore, Kevin Lau, Xiaofeng Xu, Yamin Zhang, and Jason Burch*

1
Tetrahedron Letters
Enantioselective synthesis of GNE-6688, a potent and selective inhibitor of
interleukin-2 inducible T-cell kinase (ITK)
Jared Moorea, Kevin Laua, Xiaofeng Xub, Yamin Zhangb and Jason D. Burcha,c*
aDiscovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
bPharmaron Beijing Ltd. Co., No. 6 TaiHe Rd. BDA, Beijing 100176, China
cPresent address: Inception Sciences Canada, 7150 Frederick-Banting, Montreal, QC, H4S 2A1, Canada; jburch@inceptionsci.ca
ARTICLE INFO
ABSTRACT
Article history:
Received
Received in revised form
Accepted
An enantioselective synthesis of the previously-disclosed ITK inhibitor GNE-6688 is described.
Synthesis of the nitropyrazole fragment is highlighted by a Ru-catalyzed transfer hydrogenation
using the Wills tethered ligand system. Synthesis of the pyrazole carboxylic acid fragment
features an allylboration catalyzed by a chiral diol-SnCl4 complex, followed by a highly
diastereoselective directed cyclopropanation.
Available online
2014 Elsevier Ltd. All rights reserved.
Keywords:
Kinase inhibitors
Enantioselective catalysis
Directed cyclopropanation
Transfer hydrogenation
Allylboration
1. Introduction
synthesized as racemates, then resolved independently by
supercricital fluid chromatography (SFC) on a chiral stationary
Interleukin-2 inducible T-cell kinase (ITK) is a non-receptor
tyrosine kinase of the Tec family which signals downstream from
the T-cell receptor, and is implicated in T-cell development,
differentiation and effector function.1 Significant pre-clinical
data supports the role of ITK in allergic asthmatic response,
including the observation that ITK-/- mice are resistant to lung
inflammation, eosinophil infiltration and mucous production
following challenge by the antigen ovalbumin.2 This promising
pre-clinical data has prompted numerous pharmaceutical and
academic laboratories to direct research efforts toward the
development of selective inhibitors of ITK as potential treatments
for allergic asthma.3
phase prior to amide bond formation. In our second generation
approach, we were interested in exploring the possibility of
accessing 2 and 3 as single enantiomers through the use of chiral
catalysis in the stereodifferentiating transformations.
We have recently disclosed a tetrahydroindazole series of ITK
inhibitors which demonstrate excellent potency, selectivity and
ADME properties.4 Compound 1 (GNE-6688; Figure 1) is a
quintessential representative of this class that contains two
stereogenic structural features important for ITK potency and
selectivity: a benzylic pyrazole stereocenter that positions the
phenyl ring to interact in an edge-to-face -stack with Phe437
(Figure 1A), and a fused cyclopropane on the beta face of the
ligand that fits into a lipophilic pocket adjacent to Phe435 (Figure
1B).
2. Retrosynthetic Analysis
Figure 1. Structure of GNE-6688. (A) Edge-to-face -stacking
interaction with Phe437; (B) Cyclopropane occupying lipophilic
pocket adjacent to Phe435. Structures are docking models
Retrosynthetically, 1 can be disconnected via the amide bond
to form two fragments of approximately equal complexity:
aminopyrazole 2 and pyrazole carboxylic acid 3 (Scheme 1). In
our original synthesis of inhibitor 1,4b, 5 these two fragments were

2
aReagents and Conditions: (a) MeONHMe∙HCl, HATU, iPr2NEt, DMF,
87%; (b) PhMgBr, THF, 60 °C, 90%; Oxone®, MeOH, H2O, 82%.
prepared using MOE (www.chemcomp.com) and crystal
structures from related molecules. For further details see ref. 4b.
For the enantioselective reduction of ketones 5, we were
Scheme 1. Retrosynthetic analysis of GNE-6688
drawn to a report by the Wills group, where a so-called “reverse-
tethered” ruthenium complex (12) was shown to be an effective
catalyst for the highly enantioselective transfer hydrogenation of
aryl-alkyl ketones.8 Reaction conditions determined by Wills to
be optimal for the majority of substrates (cat. 12, HCO2H, Et3N,
40 °C) proved unacceptable for sulfone 5b (Table 1, entry 1).
Gratifyingly, modified conditions also reported by Wills (cat. 12,
iPrOH, KOH, 40 °C, entry 2) provided the desired benzylic
alcohol 4 in excellent yield and enantioselectivity. Sulfide 5a
also proved to be an acceptable substrate for this transformation
(entry 3), albeit with reduced yield and enantioselectivity,
presumably due to complications arising from coordination of the
sulfide to ruthenium. Completion of fragment 2 was
accomplished by a Mitsunobu reaction between alcohol 4 and 3-
nitropyazole, followed by hydrogenative reduction of the nitro
group (Scheme 3).
Table 1. Catalytic enantioselective transfer hydrogenation of
ketones 5
Our proposed synthesis of the nitropyrazole fragment 2,
mimicked the racemic synthesis disclosed previously,4b,5 which
utilized a Mitsunobu reaction6 between 3-nitropyrazole (14) and
(±)-4 as the key step. We envisioned that preparation of 4 in an
enantioselective fashion would be feasible through a transition-
metal catalyzed transfer hydrogenation of ketone 5a or 5b. We
had already shown that diethyl oxalate Claisen condensation of
(±)-6 followed by hydrazine addition is an effective method for
the regioselective synthesis of pyrazole carboxylic acid (±)-3.4b,5
Unfortunately, our previous racemic synthesis of 6 was not easily
amenable to enantioselective variation, and thus we sought a
distinct approach. Directed cyclopropanations of cyclohex-3-
enols using Simmons-Smith conditions are well precedented,7
therefore we envisioned that alcohol 7 would be a suitable
precursor for cyclopropyl ketone 6. Reterosynthetic ring-opening
of 7 provides diene 8, which contains an appropriate synthon for
an enantioselective methallyl addition onto aldehyde 9.
aReagents and Conditions: (A) 0.5 mol% 12, Et3N, HCO2H, 40 °C; (B) 0.5
mol% 12, 2.5 mol% KOH, iPrOH, 40 °C. bSee ref. 9 for details of
chromatography conditions for ee determination.
Scheme 3.a Completion of fragment 2
aReagents and Conditions: (a) 14, PPh3, DIAD, THF, rt, 75%; (b) 0.1 equiv.
Pd/C (10 wt%), H2 (1 atm), MeOH, EtOAc, rt, quant.
Our attention then turned to optimization of the
3. Results
enantioselective methallyl addition to aldehyde 9. Although
aldehyde 9 had not previously been used as a substrate in
enantioselective allyl additions, the related aldehyde
The syntheses of ketones 5a and 5b were straightforward
(Scheme 2). Weinreb amide 11 was accessible by HATU-
mediated amide bond formation from acid 10. Addition of
phenylmagnesium bromide provided ketone 5a, which could be
oxidized to the sulfone 5b with Oxone®.
dihydrocinnamaldehyde had shown to be an acceptable substrate
for the enantioselective allylborations disclosed by Hall and co-
workers.10 Through variation of ligand 16 (“vivols”), we were
able to determine that alcohol 8 could be obtained in good yields
and good to excellent levels of enantioselectivity (Table 2).11
Ligand 16b (“F-vivol-7”) proved optimal in this case, providing
alcohol 8 in 88% ee on small scale (entry 2), which improved by
a slight but reproducible margin when the scale was increased
(entry 5), presumably due to limitation of background reactivity
caused by adventitious water.
Scheme 2.a Synthesis of ketones 5a and 5b

3
With fragments 2 and 3 available in high enantiomeric
purity, all that remained to complete the stereoselective synthesis
of inhibitor 1 was to merge the fragments via amide bond
formation. Amidation using the peptide coupling reagent HATU
proved successful for fragment coupling, providing 1 in good
yield (Scheme 5). SFC on a chiral stationary phase (Whelk-1
(4.6x50 mm; 3 m ID) column with 40% MeOH/0.1%NH4OH as
eluent) was successful in resolving all four diastereoisomers of 1,
and verified that material prepared via this route was enantio- and
diastereomerically pure to the limit of detection (>20:1).
Furthermore, comparison to an authentic standard of 1 confirmed
that the material exhibited the relative and absolute
Table 2. Catalytic enantioselective methallyl addition to
aldehyde 9
stereochemistry as shown.
Scheme 5.a Completion of inhibitor 1
aReagents and Conditions: (a) 1.5 equiv. HATU, 2.5 equiv. iPr2NEt, DMF, rt,
84%.
aReagents and Conditions: (i) 4 mol% SnCl4, 5 mol% 16, toluene, rt, 15 min;
(ii) 17, -78 °C, 30 min; 1.0 mmol 9, -78 °C, 4 h; (iii) 2.0 equiv. DIBAL, -78
°C. b10.0 mmol scale.
In conclusion, we have developed a convergent,
stereoselective synthesis of ITK inhibitor GNE-6688, highlighted
by two highly enantioselective catalytic transformations. This
synthesis should find utility for the synthesis of related molecules
which contain either of these stereogenic fragments.
With an acceptable enantioselective synthesis of 8 in hand,
completion of fragment 3 proceeded as planned (Scheme 4).12
Ring-closing metathesis was accomplished in good yield using
the Grubbs Second Generation catalyst.13 Directed
Acknowledgments
cyclopropanation of alkene 7 was accomplished using modified
Simmons-Smith conditions developed by Shi,14 which provided
cyclopropane 18 as a single diastereomer as judged by 1H-NMR
spectroscopy. Following Swern oxidation to ketone 6, Claisen
condensation with diethyl oxalate provided -ketoester 19, which
was directly reacted with hydrazine to furnish pyrazole
carboxylic ester 20. Ester hydrolysis under basic conditions
completed the synthesis of fragment 3.
The authors are indebted to Prof. Dennis Hall for providing
ligands ent-16a, 16b and 16c for use in the early phase of
optimization of the allylboration reaction. Mengling Wong is
gratefully acknowledged for the SFC analyses of
enantioselectivity determination. Dr. Matthew Volgraf and
Malcolm P. Huestis are acknowledged for their careful editing of
this manuscript, and Daniel Shore is acknowledged for his
assistance in final preparation.
Scheme 4.a Completion of fragment 3
References and notes
1. (a) Berg. L. J.; Finkelstein, L. D.; Lucas, J. A.; Schwartzberg, P.
L. Annu. Rev. Immunol. 2005, 23, 549-600. (b) Felices, M.; Falk,
M.; Kosaka, Y.; Berg, L. J. Adv. Immunol. 2007, 93, 145-184.
2. Mueller, C.; August, A. J. Immunol. 2003, 170, 5056-5063.
3. Charrier, J.-D.; Knegtel, R. M. Exp. Opin. Drug Discov. 2013, 8,
369-381.
4. (a) Burch, J. D.; Lau, K.; Barker, J. J.; Brookfield, F.; Chen, Y.;
Chen, Y.; Eigenbrot, C.; Ellebrandt, C.; Ismaili, M. H. A.;
Johnson, A.; Kordt, D.; MacKinnon, C. H.; McEwan, P. A.;
Ortwine, D. F.; Stein, D. B.; Wang, X.; Winkler, D.; Yuen, P.-W.;
Zhang, Y.; Zarrin, A. A.; Pei, Z. J. Med. Chem. 2014, 57, 5714-
5727. (b) Burch, J. D.; Barrett, K.; Chen, Y.; DeVoss, J.;
Eigenbrot, C.; Goldsmith, R.; Ismaili, M. H. A.; Lau, K.; Lin, Z.;
Ortwine, D. F.; Zarrin, A.; McEwan, P. A.; Barker, J. J.;
Ellebrandt, C.; Kordt, D.; Stein, D. B.; Wang, X.; Chen, Y.; Hu.,
B.; Xu, X.; Yuen, P.-W.; Zhang, Y.; Pei, Z. J. Med. Chem. 2015,
58, 3806-3816.
aReagents and Conditions: (a) 5 mol% [1,2-Bis-(2,4,6-trimethylphenyl)-2-
imidazolidinylidene]dichloro(phenylmethylene)(tricyclohexylphosphine)
ruthenium, CH2Cl2, rt, 79%; (b) Et2Zn, CF3COOH, CH2I2, CH2Cl2, 0 °C → rt,
92%; (c) DMSO, (COCl)2, Et3N, CH2Cl2, -78 °C → rt, 94%; (d) sodium,
diethyl oxalate, EtOH, 0 °C; (e) hydrazine, AcOH, 120 °C, 34% (2 steps); (f)
LiOH, THF, MeOH, 50 °C, quant.

4
5. Brookfield, F.; Burch, J.; Goldsmith, R. A.; Hu, B.; Lau, K. H. L.;
MacKinnon, C. H.; Ortwine, D. F.; Pei, Z.; Yuen, P.-W.; Zhang,
Y. WO2014/23258 A1, 2014.
6. (a) Mitsunobu, O. Synthesis 1981, 1-28. (b) Zabierek, A. A.;
Konrad, K. M.; Haidle, A. M. Tetrahedron Lett. 2008, 49, 2996-
2998.
7. Chan, J. H.-H.; Rickborn, B. J. Am. Chem. Soc. 1968, 90, 6406-
6411.
8. Morris, D. J.; Hayes, A. M.; Wills, M. J. Org. Chem. 2006, 71,
7035-7044. For a recent review of enantioselective transfer
hydrogenation see: Wang, D.; Astruc, D. Chem. Rev. 2015, 115,
6621-6686.
9. Enantioselectivity was determined by SFC analysis on a chiral
stationary phase. For alcohol 4, a Chiralpak ID column was used
with 35% MeOH + 0.1% NH4OH as the eluent. For alcohol 13, a
Chiralpak IA column was used with 15% MeOH + 0.1% NH4OH
as the eluent. Absolute stereochemistry was assigned by analogy
(ref. 8), and verified by conversion to authentic 1.
10. (a) Rauniyar, V.; Hall, D. G. J. Org. Chem. 2009, 74, 4236-4241.
(b) Rauniyar, V.; Zhai, H.; Hall, D. G. J. Am. Chem. Soc. 2008,
130, 8481-8490. (c) Rauniyar, V.; Hall, D. G. Angew. Chem. Int.
Ed. 2006, 45, 2426-2428.
11. Enantioselectivity was determined by conversion of 9 to its 3,5-di-
nitrobenzoate (3,5-dinitrobenzoylchloride, pyridine), and SFC
analysis on a chiral stationary phase (Chiralpak AD; 5 to 50%
MeOH + 0.1% NH4OH). Absolute stereochemistry was assigned
by analogy (ref. 10) and verified by conversion to authentic 1.
12. Care must be taken when concentrating solutions of 6, 7, 8 and 18
due to the volatility of these intermediates.
13. Vougioukalakis, G. C.; Grubbs, R. H. Chem. Rev. 2010, 110,
1746-1787.
14. Yang, Z.; Lorenz, J. C.; Shi, Y. Tetrahedron Lett. 1998, 39, 8621-
8624. These conditions have previously been demonstrated to
provide excellent diastereoselectivity for directed
cyclopropanations: Evans, D. A.; Burch, J. D. Org. Lett. 2001, 3,
503-505.

5



A stereoselective synthesis of the ITK inhibitor
GNE-6688 has been accomplished.
An enantioselective transfer hydrogenation was
used to prepare the Western fragment.
An enantioselective allyl boration, and a
directed cyclopropanation were key steps for
the Eastern fragment.