1
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Nilewski C, Labadie S, Wei B, Malhotra S, Do S, Gazzard L, Liu L, Shao C, Murray J, Izrayelit Y, Gustafson A, Endres NF, Ma F, Ye X, Zou J, Evangelista M. Structure-Based Design and Evaluation of Reversible KRAS G13D Inhibitors. ACS Med Chem Lett 2024; 15:21-28. [PMID: 38229748 PMCID: PMC10788945 DOI: 10.1021/acsmedchemlett.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/18/2023] [Accepted: 11/28/2023] [Indexed: 01/18/2024] Open
Abstract
Oncogenic KRAS mutations were identified decades ago, yet the selective inhibition of specific KRAS mutant proteins represents an ongoing challenge. Recent progress has been made in targeting certain P-loop mutant proteins, in particular KRAS G12C, for which the covalent inhibition of the GDP state via the Switch II pocket is now a clinically validated strategy. Inhibition of other KRAS mutant proteins such as KRAS G13D, on the other hand, still requires clinical validation. The remoteness of the D13 residue relative to the Switch II pocket in combination with the solvent exposure and conformational flexibility of the D13 side chain, as well as the difficulties of targeting carboxylate residues covalently, renders this specific protein particularly challenging to target selectively. In this report, we describe the design and evaluation of potent and KRAS G13D-selective reversible inhibitors. Subnanomolar binding to the GDP state Switch II pocket and biochemical selectivity over WT KRAS are achieved by leveraging a salt bridge with D13.
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Affiliation(s)
- Christian Nilewski
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sharada Labadie
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Binqing Wei
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sushant Malhotra
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven Do
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lewis Gazzard
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Li Liu
- Pharmaron-Beijing
Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Cheng Shao
- Pharmaron-Beijing
Co. Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Jeremy Murray
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yevgeniy Izrayelit
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Amy Gustafson
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas F. Endres
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Fang Ma
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xin Ye
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jun Zou
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Marie Evangelista
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
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2
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Chang MT, Shanahan F, Nguyen TTT, Staben ST, Gazzard L, Yamazoe S, Wertz IE, Piskol R, Yang YA, Modrusan Z, Haley B, Evangelista M, Malek S, Foster SA, Ye X. Identifying transcriptional programs underlying cancer drug response with TraCe-seq. Nat Biotechnol 2022; 40:86-93. [PMID: 34531539 DOI: 10.1038/s41587-021-01005-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Genetic and non-genetic heterogeneity within cancer cell populations represent major challenges to anticancer therapies. We currently lack robust methods to determine how preexisting and adaptive features affect cellular responses to therapies. Here, by conducting clonal fitness mapping and transcriptional characterization using expressed barcodes and single-cell RNA sequencing (scRNA-seq), we have developed tracking differential clonal response by scRNA-seq (TraCe-seq). TraCe-seq is a method that captures at clonal resolution the origin, fate and differential early adaptive transcriptional programs of cells in a complex population in response to distinct treatments. We used TraCe-seq to benchmark how next-generation dual epidermal growth factor receptor (EGFR) inhibitor-degraders compare to standard EGFR kinase inhibitors in EGFR-mutant lung cancer cells. We identified a loss of antigrowth activity associated with targeted degradation of EGFR protein and an essential role of the endoplasmic reticulum (ER) protein processing pathway in anti-EGFR therapeutic efficacy. Our results suggest that targeted degradation is not always superior to enzymatic inhibition and establish TraCe-seq as an approach to study how preexisting transcriptional programs affect treatment responses.
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Affiliation(s)
- Matthew T Chang
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Thi Thu Thao Nguyen
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Staben
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Lewis Gazzard
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Sayumi Yamazoe
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Discovery Biotherapeutics, Bristol-Myers Squibb, Redwood City, CA, USA
| | - Ingrid E Wertz
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Robert Piskol
- Department of Computational Biology and Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Yeqing Angela Yang
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | - Marie Evangelista
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Shiva Malek
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Scott A Foster
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA.
| | - Xin Ye
- Department of Discovery Oncology, Genentech Inc., South San Francisco, CA, USA.
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3
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Chan BK, Seward E, Lainchbury M, Brewer TF, An L, Blench T, Cartwright MW, Chan GKY, Choo EF, Drummond J, Elliott RL, Gancia E, Gazzard L, Hu B, Jones GE, Luo X, Madin A, Malhotra S, Moffat JG, Pang J, Salphati L, Sneeringer CJ, Stivala CE, Wei B, Wang W, Wu P, Heffron TP. Discovery of Spiro-azaindoline Inhibitors of Hematopoietic Progenitor Kinase 1 (HPK1). ACS Med Chem Lett 2021; 13:84-91. [PMID: 35059127 PMCID: PMC8762754 DOI: 10.1021/acsmedchemlett.1c00473] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/01/2021] [Indexed: 01/16/2023] Open
Abstract
Hematopoietic progenitor kinase 1 (HPK1) is implicated as a negative regulator of T-cell receptor-induced T-cell activation. Studies using HPK1 kinase-dead knock-in animals have demonstrated the loss of HPK1 kinase activity resulted in an increase in T-cell function and tumor growth inhibition in glioma models. Herein, we describe the discovery of a series of small molecule inhibitors of HPK1. Using a structure-based drug design approach, the kinase selectivity of the molecules was significantly improved by inducing and stabilizing an unusual P-loop folded binding mode. The metabolic liabilities of the initial 7-azaindole high-throughput screening hit were mitigated by addressing a key metabolic soft spot along with physicochemical property-based optimization. The resulting spiro-azaindoline HPK1 inhibitors demonstrated improved in vitro ADME properties and the ability to induce cytokine production in primary human T-cells.
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Affiliation(s)
- Bryan K. Chan
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States,
| | - Eileen Seward
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Michael Lainchbury
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Thomas F. Brewer
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Le An
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Toby Blench
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Matthew W. Cartwright
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Grace Ka Yan Chan
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Edna F. Choo
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jason Drummond
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard L. Elliott
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Emanuela Gancia
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Lewis Gazzard
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Baihua Hu
- Pharmaron
Beijing Co, No. 6 Tai He Road, BDA, Beijing 100176, P.R. China
| | - Graham E. Jones
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Xifeng Luo
- Pharmaron
Beijing Co, No. 6 Tai He Road, BDA, Beijing 100176, P.R. China
| | - Andrew Madin
- Charles
River Laboratories, 8-9
Spire Green, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Sushant Malhotra
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - John G. Moffat
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jodie Pang
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laurent Salphati
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Craig E. Stivala
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Binqing Wei
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Weiru Wang
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ping Wu
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Timothy P. Heffron
- Genentech
Inc., 1 DNA Way, South San Francisco, California 94080, United States
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4
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Parr BT, Pastor R, Sellers BD, Pei Z, Jaipuri FA, Castanedo GM, Gazzard L, Kumar S, Li X, Liu W, Mendonca R, Pavana RK, Potturi H, Shao C, Velvadapu V, Waldo JP, Wu G, Yuen PW, Zhang Z, Zhang Y, Harris SF, Oh AJ, DiPasquale A, Dement K, La H, Goon L, Gustafson A, VanderPorten EC, Mautino MR, Liu Y. Implementation of the CYP Index for the Design of Selective Tryptophan-2,3-dioxygenase Inhibitors. ACS Med Chem Lett 2020; 11:541-549. [PMID: 32292562 DOI: 10.1021/acsmedchemlett.0c00004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/04/2020] [Indexed: 01/09/2023] Open
Abstract
A class of imidazoisoindole (III) heme-binding indoleamine-2,3-dioxygenase (IDO1) inhibitors were optimized via structure-based drug design into a series of tryptophan-2,3-dioxygenase (TDO)-selective inhibitors. Kynurenine pathway modulation was demonstrated in vivo, which enabled evaluation of TDO as a potential cancer immunotherapy target. As means of mitigating the risk of drug-drug interactions arising from cytochrome P450 inhibition, a novel property-based drug design parameter, herein referred to as the CYP Index, was implemented for the design of inhibitors with appreciable selectivity for TDO over CYP3A4. We anticipate the CYP Index will be a valuable design parameter for optimizing CYP inhibition of any small molecule inhibitor containing a Lewis basic motif capable of binding heme.
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Affiliation(s)
- Brendan T. Parr
- Genentech, South San Francisco, California 94080, United States
| | - Richard Pastor
- Genentech, South San Francisco, California 94080, United States
| | | | - Zhonghua Pei
- Genentech, South San Francisco, California 94080, United States
| | | | | | - Lewis Gazzard
- Genentech, South San Francisco, California 94080, United States
| | | | - Xiaokai Li
- NewLink Genetics, Ames, Iowa 50010, United States
| | - Wen Liu
- Genentech, South San Francisco, California 94080, United States
| | - Rohan Mendonca
- Genentech, South San Francisco, California 94080, United States
| | | | - Hima Potturi
- NewLink Genetics, Ames, Iowa 50010, United States
| | - Cheng Shao
- Pharmaron, Beijing 100176, People’s Republic of China
| | | | | | - Guosheng Wu
- Pharmaron, Beijing 100176, People’s Republic of China
| | - Po-wai Yuen
- Pharmaron, Beijing 100176, People’s Republic of China
| | - Zuhui Zhang
- NewLink Genetics, Ames, Iowa 50010, United States
| | - Yamin Zhang
- Pharmaron, Beijing 100176, People’s Republic of China
| | - Seth F. Harris
- Genentech, South San Francisco, California 94080, United States
| | - Angela J. Oh
- Genentech, South San Francisco, California 94080, United States
| | | | - Kevin Dement
- Genentech, South San Francisco, California 94080, United States
| | - Hank La
- Genentech, South San Francisco, California 94080, United States
| | - Leanne Goon
- Genentech, South San Francisco, California 94080, United States
| | - Amy Gustafson
- Genentech, South San Francisco, California 94080, United States
| | | | | | - Yichin Liu
- Genentech, South San Francisco, California 94080, United States
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5
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Pei Z, Mendonca R, Gazzard L, Pastor R, Goon L, Gustafson A, VanderPorten E, Hatzivassiliou G, Dement K, Cass R, Yuen PW, Zhang Y, Wu G, Lin X, Liu Y, Sellers BD. Aminoisoxazoles as Potent Inhibitors of Tryptophan 2,3-Dioxygenase 2 (TDO2). ACS Med Chem Lett 2018; 9:417-421. [PMID: 29795752 DOI: 10.1021/acsmedchemlett.7b00427] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 04/02/2018] [Indexed: 11/28/2022] Open
Abstract
Tryptophan 2,3-dioxygenase 2 (TDO2) catalyzes the conversion of tryptophan to the immunosuppressive metabolite kynurenine. TDO2 overexpression has been observed in a number of cancers; therefore, TDO inhibition may be a useful therapeutic intervention for cancers. We identified an aminoisoxazole series as potent TDO2 inhibitors from a high-throughput screen (HTS). An extensive medicinal chemistry effort revealed that both the amino group and the isoxazole moiety are important for TDO2 inhibitory activity. Computational modeling yielded a binding hypothesis and provided insight into the observed structure-activity relationships. The optimized compound 21 is a potent TDO2 inhibitor with modest selectivity over indolamine 2,3-dioxygenase 1 (IDO1) and with improved human whole blood stability.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Po-wai Yuen
- Pharmaron-Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Yamin Zhang
- Pharmaron-Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Guosheng Wu
- Pharmaron-Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Xingyu Lin
- Pharmaron-Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
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6
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Rudolph J, Murray LJ, Ndubaku CO, O’Brien T, Blackwood E, Wang W, Aliagas I, Gazzard L, Crawford JJ, Drobnick J, Lee W, Zhao X, Hoeflich KP, Favor DA, Dong P, Zhang H, Heise CE, Oh A, Ong CC, La H, Chakravarty P, Chan C, Jakubiak D, Epler J, Ramaswamy S, Vega R, Cain G, Diaz D, Zhong Y. Chemically Diverse Group I p21-Activated Kinase (PAK) Inhibitors Impart Acute Cardiovascular Toxicity with a Narrow Therapeutic Window. J Med Chem 2016; 59:5520-41. [DOI: 10.1021/acs.jmedchem.6b00638] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - David A. Favor
- Shanghai Chempartner Inc., 998
Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, People’s Republic of China
| | - Ping Dong
- Shanghai Chempartner Inc., 998
Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, People’s Republic of China
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7
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Ndubaku CO, Crawford JJ, Drobnick J, Aliagas I, Campbell D, Dong P, Dornan LM, Duron S, Epler J, Gazzard L, Heise CE, Hoeflich KP, Jakubiak D, La H, Lee W, Lin B, Lyssikatos JP, Maksimoska J, Marmorstein R, Murray LJ, O’Brien T, Oh A, Ramaswamy S, Wang W, Zhao X, Zhong Y, Blackwood E, Rudolph J. Design of Selective PAK1 Inhibitor G-5555: Improving Properties by Employing an Unorthodox Low-pK a Polar Moiety. ACS Med Chem Lett 2015; 6:1241-6. [PMID: 26713112 DOI: 10.1021/acsmedchemlett.5b00398] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 10/31/2015] [Indexed: 11/28/2022] Open
Abstract
Signaling pathways intersecting with the p21-activated kinases (PAKs) play important roles in tumorigenesis and cancer progression. By recognizing that the limitations of FRAX1036 (1) were chiefly associated with the highly basic amine it contained, we devised a mitigation strategy to address several issues such as hERG activity. The 5-amino-1,3-dioxanyl moiety was identified as an effective means of reducing pK a and logP simultaneously. When positioned properly within the scaffold, this group conferred several benefits including potency, pharmacokinetics, and selectivity. Mouse xenograft PK/PD studies were carried out using an advanced compound, G-5555 (12), derived from this approach. These studies concluded that dose-dependent pathway modulation was achievable and paves the way for further in vivo investigations of PAK1 function in cancer and other diseases.
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Affiliation(s)
- Chudi O. Ndubaku
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James J. Crawford
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joy Drobnick
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Ignacio Aliagas
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - David Campbell
- Afraxis, Inc., 6605 Nancy Ridge
Road, Suite 224, San Diego, California 92121, United States
| | - Ping Dong
- Shanghai ChemPartner, 576 Libing
Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, PRC
| | - Laura M. Dornan
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sergio Duron
- Afraxis, Inc., 6605 Nancy Ridge
Road, Suite 224, San Diego, California 92121, United States
| | - Jennifer Epler
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lewis Gazzard
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher E. Heise
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Klaus P. Hoeflich
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Diana Jakubiak
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hank La
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy Lee
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Baiwei Lin
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joseph P. Lyssikatos
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jasna Maksimoska
- Perelman
School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- Perelman
School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Lesley J. Murray
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Thomas O’Brien
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Angela Oh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sreemathy Ramaswamy
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Weiru Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xianrui Zhao
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yu Zhong
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Elizabeth Blackwood
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joachim Rudolph
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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8
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Gazzard L, Williams K, Chen H, Axford L, Blackwood E, Burton B, Chapman K, Crackett P, Drobnick J, Ellwood C, Epler J, Flagella M, Gancia E, Gill M, Goodacre S, Halladay J, Hewitt J, Hunt H, Kintz S, Lyssikatos J, Macleod C, Major S, Médard G, Narukulla R, Ramiscal J, Schmidt S, Seward E, Wiesmann C, Wu P, Yee S, Yen I, Malek S. Mitigation of Acetylcholine Esterase Activity in the 1,7-Diazacarbazole Series of Inhibitors of Checkpoint Kinase 1. J Med Chem 2015; 58:5053-74. [PMID: 25988399 DOI: 10.1021/acs.jmedchem.5b00464] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Checkpoint kinase 1 (ChK1) plays a key role in the DNA damage response, facilitating cell-cycle arrest to provide sufficient time for lesion repair. This leads to the hypothesis that inhibition of ChK1 might enhance the effectiveness of DNA-damaging therapies in the treatment of cancer. Lead compound 1 (GNE-783), the prototype of the 1,7-diazacarbazole class of ChK1 inhibitors, was found to be a highly potent inhibitor of acetylcholine esterase (AChE) and unsuitable for development. A campaign of analogue synthesis established SAR delineating ChK1 and AChE activities and allowing identification of new leads with improved profiles. In silico docking using a model of AChE permitted rationalization of the observed SAR. Compounds 19 (GNE-900) and 30 (GNE-145) were identified as selective, orally bioavailable ChK1 inhibitors offering excellent in vitro potency with significantly reduced AChE activity. In combination with gemcitabine, these compounds demonstrate an in vivo pharmacodynamic effect and are efficacious in a mouse p53 mutant xenograft model.
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Affiliation(s)
| | - Karen Williams
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | | | - Lorraine Axford
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | | | - Brenda Burton
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Kerry Chapman
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Peter Crackett
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | | | - Charles Ellwood
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | | | | | - Emanuela Gancia
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Matthew Gill
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Simon Goodacre
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | | | - Joanne Hewitt
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Hazel Hunt
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | | | | | - Calum Macleod
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Sarah Major
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Guillaume Médard
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | - Raman Narukulla
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
| | | | | | - Eileen Seward
- ∇Argenta, A Charles River Company, 8-9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom
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9
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Stumpf A, Cheng ZK, Wong B, Reynolds M, Angelaud R, Girotti J, Deese A, Gu C, Gazzard L. Development of an Expedient Process for the Multi-Kilogram Synthesis of Chk1 Inhibitor GDC-0425. Org Process Res Dev 2015. [DOI: 10.1021/acs.oprd.5b00105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andreas Stumpf
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Zhigang Ken Cheng
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Brian Wong
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Mark Reynolds
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Remy Angelaud
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - James Girotti
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Alan Deese
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christine Gu
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lewis Gazzard
- Small Molecule Process Chemistry, ‡Small Molecule Analytical Chemistry, §Department of Discovery
Chemistry, Genentech, A member
of the Roche Group, 1 DNA Way, South San Francisco, California 94080, United States
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10
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Blackwood E, Epler J, Yen I, Flagella M, O'Brien T, Evangelista M, Schmidt S, Xiao Y, Choi J, Kowanetz K, Ramiscal J, Wong K, Jakubiak D, Yee S, Cain G, Gazzard L, Williams K, Halladay J, Jackson PK, Malek S. Combination drug scheduling defines a "window of opportunity" for chemopotentiation of gemcitabine by an orally bioavailable, selective ChK1 inhibitor, GNE-900. Mol Cancer Ther 2013; 12:1968-80. [PMID: 23873850 DOI: 10.1158/1535-7163.mct-12-1218] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Checkpoint kinase 1 (ChK1) is a serine/threonine kinase that functions as a central mediator of the intra-S and G2-M cell-cycle checkpoints. Following DNA damage or replication stress, ChK1-mediated phosphorylation of downstream effectors delays cell-cycle progression so that the damaged genome can be repaired. As a therapeutic strategy, inhibition of ChK1 should potentiate the antitumor effect of chemotherapeutic agents by inactivating the postreplication checkpoint, causing premature entry into mitosis with damaged DNA resulting in mitotic catastrophe. Here, we describe the characterization of GNE-900, an ATP-competitive, selective, and orally bioavailable ChK1 inhibitor. In combination with chemotherapeutic agents, GNE-900 sustains ATR/ATM signaling, enhances DNA damage, and induces apoptotic cell death. The kinetics of checkpoint abrogation seems to be more rapid in p53-mutant cells, resulting in premature mitotic entry and/or accelerated cell death. Importantly, we show that GNE-900 has little single-agent activity in the absence of chemotherapy and does not grossly potentiate the cytotoxicity of gemcitabine in normal bone marrow cells. In vivo scheduling studies show that optimal administration of the ChK1 inhibitor requires a defined lag between gemcitabine and GNE-900 administration. On the refined combination treatment schedule, gemcitabine's antitumor activity against chemotolerant xenografts is significantly enhanced and dose-dependent exacerbation of DNA damage correlates with extent of tumor growth inhibition. In summary, we show that in vivo potentiation of gemcitabine activity is mechanism based, with optimal efficacy observed when S-phase arrest and release is followed by checkpoint abrogation with a ChK1 inhibitor.
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Affiliation(s)
- Elizabeth Blackwood
- Corresponding Authors: Elizabeth Blackwood and Shiva Malek, Genentech, 1 DNA Way, South San Francisco, CA 94080.
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11
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Flygare JA, Beresini M, Budha N, Chan H, Chan IT, Cheeti S, Cohen F, Deshayes K, Doerner K, Eckhardt SG, Elliott LO, Feng B, Franklin MC, Reisner SF, Gazzard L, Halladay J, Hymowitz SG, La H, LoRusso P, Maurer B, Murray L, Plise E, Quan C, Stephan JP, Young SG, Tom J, Tsui V, Um J, Varfolomeev E, Vucic D, Wagner AJ, Wallweber HJA, Wang L, Ware J, Wen Z, Wong H, Wong JM, Wong M, Wong S, Yu R, Zobel K, Fairbrother WJ. Discovery of a potent small-molecule antagonist of inhibitor of apoptosis (IAP) proteins and clinical candidate for the treatment of cancer (GDC-0152). J Med Chem 2012; 55:4101-13. [PMID: 22413863 DOI: 10.1021/jm300060k] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A series of compounds were designed and synthesized as antagonists of cIAP1/2, ML-IAP, and XIAP based on the N-terminus, AVPI, of mature Smac. Compound 1 (GDC-0152) has the best profile of these compounds; it binds to the XIAP BIR3 domain, the BIR domain of ML-IAP, and the BIR3 domains of cIAP1 and cIAP2 with K(i) values of 28, 14, 17, and 43 nM, respectively. These compounds promote degradation of cIAP1, induce activation of caspase-3/7, and lead to decreased viability of breast cancer cells without affecting normal mammary epithelial cells. Compound 1 inhibits tumor growth when dosed orally in the MDA-MB-231 breast cancer xenograft model. Compound 1 was advanced to human clinical trials, and it exhibited linear pharmacokinetics over the dose range (0.049 to 1.48 mg/kg) tested. Mean plasma clearance in humans was 9 ± 3 mL/min/kg, and the volume of distribution was 0.6 ± 0.2 L/kg.
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Affiliation(s)
- John A Flygare
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
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12
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Austin CD, Wen X, Gazzard L, Nelson C, Scheller RH, Scales SJ. Oxidizing potential of endosomes and lysosomes limits intracellular cleavage of disulfide-based antibody-drug conjugates. Proc Natl Acad Sci U S A 2005; 102:17987-92. [PMID: 16322102 PMCID: PMC1298180 DOI: 10.1073/pnas.0509035102] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibody-drug conjugate therapy entails targeted killing of cancer cells with cytotoxic compounds covalently linked to tumor-specific antibodies and shows promise in the treatment of several human cancers. Current antibody-drug conjugate designs that incorporate a disulfide linker between the antibody and cytotoxic drug are inspired by indirect evidence suggesting that the redox potential within the endosomal system is reducing. It is presumed that antigen-dependent endocytosis leads to disulfide linker reduction and intracellular release of free drug, but direct demonstration of such a mechanism is lacking. To determine whether the disulfide N-succinimidyl 4-(2-pyridyldithio)pentanoate (SPP) linker would be reduced during endocytic recycling of the anti-HER2 antibody trastuzumab (Herceptin, Genentech), we synthesized a trastuzumab-SPP-Rhodamine red conjugate and developed a linker cleavage assay by using the self-quenching property of this fluorophore. In breast carcinoma SKBr3 cells, no SPP linker cleavage was observed, as detected by fluorescence dequenching upon internalization. By contrast, the conjugate did display fluorescence dequenching when diverted to the lysosomal pathway by geldanamycin, an effect partly due to proteolytic degradation rather than disulfide reduction. To understand why linker reduction was inefficient, we measured redox potentials of endocytic compartments by expressing a redox-sensitive variant of GFP fused to various endocytic proteins. Unexpectedly, we found that recycling endosomes, late endosomes, and lysosomes are not reducing, but oxidizing and comparable with conditions in the endoplasmic reticulum. These results suggest that intracellular reduction is unlikely to account for the potency of disulfide-linked antibody-drug conjugates.
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Affiliation(s)
- Cary D Austin
- Department of Research Administration, Genentech, Inc., South San Francisco, CA 94080, USA
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13
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Magnus P, Gazzard L, Hobson L, Payne AH, Rainey TJ, Westlund N, Lynch V. Synthesis of the Kopsia alkaloids (±)-pauciflorine B, (±)-lahadinine B, (±)-kopsidasine, (±)-kopsidasine-N-oxide, (±)-kopsijasminilam and (±)-11-methoxykopsilongine. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00243-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Caddick S, Gazzard L, Motherwell W, Wilkinson J. Preparation of 1-fluoroglycosides from 1-arylthio and 1-arylselenoglycosides using 4-methyl(difluoroiodo)benzene. Tetrahedron 1996. [DOI: 10.1016/0040-4020(95)00889-g] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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