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Le K, Soth MJ, Cross JB, Liu G, Ray WJ, Ma J, Goodwani SG, Acton PJ, Buggia-Prevot V, Akkermans O, Barker J, Conner ML, Jiang Y, Liu Z, McEwan P, Warner-Schmidt J, Xu A, Zebisch M, Heijnen CJ, Abrahams B, Jones P. Discovery of IACS-52825, a Potent and Selective DLK Inhibitor for Treatment of Chemotherapy-Induced Peripheral Neuropathy. J Med Chem 2023. [PMID: 37436942 DOI: 10.1021/acs.jmedchem.3c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Chemotherapy-induced peripheral neuropathy (CIPN) is a major unmet medical need with limited treatment options. Despite different mechanisms of action, diverse chemotherapeutics can cause CIPN through a converged pathway─an active axon degeneration program that engages the dual leucine zipper kinase (DLK). DLK is a neuronally enriched kinase upstream in the MAPK-JNK cascade, and while it is dormant under physiological conditions, DLK mediates a core mechanism for neuronal injury response under stress conditions, making it an attractive target for treatment of neuronal injury and neurodegenerative diseases. We have developed potent, selective, brain penetrant DLK inhibitors with excellent PK and activity in mouse models of CIPN. Lead compound IACS-52825 (22) showed strongly effective reversal of mechanical allodynia in a mouse model of CIPN and was advanced into preclinical development.
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Affiliation(s)
- Kang Le
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Michael J Soth
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Jason B Cross
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Gang Liu
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - William J Ray
- Neurodegenerative Consortium (NDC), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Jiacheng Ma
- Neurodegenerative Consortium (NDC), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Sunil G Goodwani
- Neurodegenerative Consortium (NDC), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Paul J Acton
- Neurodegenerative Consortium (NDC), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Virginie Buggia-Prevot
- Neurodegenerative Consortium (NDC), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | | | | | - Michael L Conner
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Yongying Jiang
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Zhen Liu
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | | | - Jennifer Warner-Schmidt
- Alexandria Center for Life Science, Magnolia Neurosciences Corporation, New York, New York 10016, United States
| | - Alan Xu
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | | | - Cobi J Heijnen
- Laboratories of Neuroimmunology, Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Psychological Sciences, Rice University, Houston, Texas 77005, United States
| | - Brett Abrahams
- Alexandria Center for Life Science, Magnolia Neurosciences Corporation, New York, New York 10016, United States
| | - Philip Jones
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
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Elamin YY, Robichaux JP, Carter BW, Altan M, Tran H, Gibbons DL, Heeke S, Fossella FV, Lam VK, Le X, Negrao MV, Nilsson MB, Patel A, Vijayan RSK, Cross JB, Zhang J, Byers LA, Lu C, Cascone T, Feng L, Luthra R, San Lucas FA, Mantha G, Routbort M, Blumenschein G, Tsao AS, Heymach JV. Poziotinib for EGFR exon 20-mutant NSCLC: Clinical efficacy, resistance mechanisms, and impact of insertion location on drug sensitivity. Cancer Cell 2022; 40:754-767.e6. [PMID: 35820397 PMCID: PMC9667883 DOI: 10.1016/j.ccell.2022.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 04/14/2022] [Accepted: 06/14/2022] [Indexed: 02/06/2023]
Abstract
We report a phase II study of 50 advanced non-small cell lung cancer (NSCLC) patients with point mutations or insertions in EGFR exon 20 treated with poziotinib (NCT03066206). The study achieved its primary endpoint, with confirmed objective response rates (ORRs) of 32% and 31% by investigator and blinded independent review, respectively, with a median progression-free survival of 5.5 months. Using preclinical studies, in silico modeling, and molecular dynamics simulations, we found that poziotinib sensitivity was highly dependent on the insertion location, with near-loop insertions (amino acids A767 to P772) being more sensitive than far-loop insertions, an observation confirmed clinically with ORRs of 46% and 0% observed in near versus far-loop, respectively (p = 0.0015). Putative mechanisms of acquired resistance included EGFR T790M, MET amplifications, and epithelial-to-mesenchymal transition (EMT). Our data demonstrate that poziotinib is active in EGFR exon 20-mutant NSCLC, although this activity is influenced by insertion location.
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Affiliation(s)
- Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Jacqulyne P Robichaux
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Hai Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Frank V Fossella
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Vincent K Lam
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA; Department of Medicine, Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD 21287, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Monique B Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Anisha Patel
- Department of Dermatology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - R S K Vijayan
- Institute for Applied Cancer Science, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason B Cross
- Institute for Applied Cancer Science, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Lauren A Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Charles Lu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Lei Feng
- Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Francis A San Lucas
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Geeta Mantha
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark Routbort
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - George Blumenschein
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - Anne S Tsao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Unit 432, PO Box 301402, 1500 Holcombe Boulevard, Houston, TX 77030, USA.
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Lai Y, Tuvim MJ, Leitz J, Peters J, Pfuetzner RA, Esquivies L, Zhou Q, Czako B, Cross JB, Jones P, Dickey BF, Brunger AT. Screening of Hydrocarbon-Stapled Peptides for Inhibition of Calcium-Triggered Exocytosis. Front Pharmacol 2022; 13:891041. [PMID: 35814209 PMCID: PMC9258623 DOI: 10.3389/fphar.2022.891041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
The so-called primary interface between the SNARE complex and synaptotagmin-1 (Syt1) is essential for Ca2+-triggered neurotransmitter release in neuronal synapses. The interacting residues of the primary interface are conserved across different species for synaptotagmins (Syt1, Syt2, Syt9), SNAP-25, and syntaxin-1A homologs involved in fast synchronous release. This Ca2+-independent interface forms prior to Ca2+-triggering and plays a role in synaptic vesicle priming. This primary interface is also conserved in the fusion machinery that is responsible for mucin granule membrane fusion. Ca2+-stimulated mucin secretion is mediated by the SNAREs syntaxin-3, SNAP-23, VAMP8, Syt2, and other proteins. Here, we designed and screened a series of hydrocarbon-stapled peptides consisting of SNAP-25 fragments that included some of the key residues involved in the primary interface as observed in high-resolution crystal structures. We selected a subset of four stapled peptides that were highly α-helical as assessed by circular dichroism and that inhibited both Ca2+-independent and Ca2+-triggered ensemble lipid-mixing with neuronal SNAREs and Syt1. In a single-vesicle content-mixing assay with reconstituted neuronal SNAREs and Syt1 or with reconstituted airway SNAREs and Syt2, the selected peptides also suppressed Ca2+-triggered fusion. Taken together, hydrocarbon-stapled peptides that interfere with the primary interface consequently inhibit Ca2+-triggered exocytosis. Our inhibitor screen suggests that these compounds may be useful to combat mucus hypersecretion, which is a major cause of airway obstruction in the pathophysiology of COPD, asthma, and cystic fibrosis.
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Affiliation(s)
- Ying Lai
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,*Correspondence: Axel T. Brunger, ; Ying Lai, ; Burton F. Dickey,
| | - Michael J. Tuvim
- Department of Pulmonary Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
| | - John Peters
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
| | - Barbara Czako
- Institute for Applied Cancer Science, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Jason B. Cross
- Institute for Applied Cancer Science, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Philip Jones
- Institute for Applied Cancer Science, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Burton F. Dickey
- Department of Pulmonary Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, United States,*Correspondence: Axel T. Brunger, ; Ying Lai, ; Burton F. Dickey,
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States,*Correspondence: Axel T. Brunger, ; Ying Lai, ; Burton F. Dickey,
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4
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Vijayan RSK, Kihlberg J, Cross JB, Poongavanam V. Enhancing preclinical drug discovery with artificial intelligence. Drug Discov Today 2021; 27:967-984. [PMID: 34838731 DOI: 10.1016/j.drudis.2021.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/14/2021] [Revised: 10/15/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
Artificial intelligence (AI) is becoming an integral part of drug discovery. It has the potential to deliver across the drug discovery and development value chain, starting from target identification and reaching through clinical development. In this review, we provide an overview of current AI technologies and a glimpse of how AI is reimagining preclinical drug discovery by highlighting examples where AI has made a real impact. Considering the excitement and hyperbole surrounding AI in drug discovery, we aim to present a realistic view by discussing both opportunities and challenges in adopting AI in drug discovery.
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Affiliation(s)
- R S K Vijayan
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX, USA
| | - Jan Kihlberg
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Jason B Cross
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX, USA.
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5
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Czako B, Sun Y, McAfoos T, Cross JB, Leonard PG, Burke JP, Carroll CL, Feng N, Harris AL, Jiang Y, Kang Z, Kovacs JJ, Mandal P, Meyers BA, Mseeh F, Parker CA, Yu SS, Williams CC, Wu Q, Di Francesco ME, Draetta G, Heffernan T, Marszalek JR, Kohl NE, Jones P. Discovery of 6-[(3 S,4 S)-4-Amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-3-(2,3-dichlorophenyl)-2-methyl-3,4-dihydropyrimidin-4-one (IACS-15414), a Potent and Orally Bioavailable SHP2 Inhibitor. J Med Chem 2021; 64:15141-15169. [PMID: 34643390 DOI: 10.1021/acs.jmedchem.1c01132] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Src homology 2 (SH2) domain-containing phosphatase 2 (SHP2) plays a role in receptor tyrosine kinase (RTK), neurofibromin-1 (NF-1), and Kirsten rat sarcoma virus (KRAS) mutant-driven cancers, as well as in RTK-mediated resistance, making the identification of small-molecule therapeutics that interfere with its function of high interest. Our quest to identify potent, orally bioavailable, and safe SHP2 inhibitors led to the discovery of a promising series of pyrazolopyrimidinones that displayed excellent potency but had a suboptimal in vivo pharmacokinetic (PK) profile. Hypothesis-driven scaffold optimization led us to a series of pyrazolopyrazines with excellent PK properties across species but a narrow human Ether-à-go-go-Related Gene (hERG) window. Subsequent optimization of properties led to the discovery of the pyrimidinone series, in which multiple members possessed excellent potency, optimal in vivo PK across species, and no off-target activities including no hERG liability up to 100 μM. Importantly, compound 30 (IACS-15414) potently suppressed the mitogen-activated protein kinase (MAPK) pathway signaling and tumor growth in RTK-activated and KRASmut xenograft models in vivo.
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Affiliation(s)
- Barbara Czako
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Yuting Sun
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology) University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Timothy McAfoos
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason B Cross
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Paul G Leonard
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason P Burke
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Christopher L Carroll
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Ningping Feng
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology) University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Angela L Harris
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology) University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Yongying Jiang
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Zhijun Kang
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jeffrey J Kovacs
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology) University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Pijus Mandal
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Brooke A Meyers
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology) University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Faika Mseeh
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Connor A Parker
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Simon S Yu
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Christopher C Williams
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Qi Wu
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Maria Emilia Di Francesco
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Giulio Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Timothy Heffernan
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology) University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Joseph R Marszalek
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology) University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Nancy E Kohl
- Navire Inc., 421 Kipling Street, Palo Alto, California 94301, United States
| | - Philip Jones
- IACS (Institute for Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
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Hamilton MM, Mseeh F, McAfoos TJ, Leonard PG, Reyna NJ, Harris AL, Xu A, Han M, Soth MJ, Czako B, Theroff JP, Mandal PK, Burke JP, Virgin-Downey B, Petrocchi A, Pfaffinger D, Rogers NE, Parker CA, Yu SS, Jiang Y, Krapp S, Lammens A, Trevitt G, Tremblay MR, Mikule K, Wilcoxen K, Cross JB, Jones P, Marszalek JR, Lewis RT. Discovery of IACS-9779 and IACS-70465 as Potent Inhibitors Targeting Indoleamine 2,3-Dioxygenase 1 (IDO1) Apoenzyme. J Med Chem 2021; 64:11302-11329. [PMID: 34292726 DOI: 10.1021/acs.jmedchem.1c00679] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1), a heme-containing enzyme that mediates the rate-limiting step in the metabolism of l-tryptophan to kynurenine, has been widely explored as a potential immunotherapeutic target in oncology. We developed a class of inhibitors with a conformationally constrained bicyclo[3.1.0]hexane core. These potently inhibited IDO1 in a cellular context by binding to the apoenzyme, as elucidated by biochemical characterization and X-ray crystallography. A SKOV3 tumor model was instrumental in differentiating compounds, leading to the identification of IACS-9779 (62) and IACS-70465 (71). IACS-70465 has excellent cellular potency, a robust pharmacodynamic response, and in a human whole blood assay was more potent than linrodostat (BMS-986205). IACS-9779 with a predicted human efficacious once daily dose below 1 mg/kg to sustain >90% inhibition of IDO1 displayed an acceptable safety margin in rodent toxicology and dog cardiovascular studies to support advancement into preclinical safety evaluation for human development.
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Affiliation(s)
- Matthew M Hamilton
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Faika Mseeh
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Timothy J McAfoos
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Paul G Leonard
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Naphtali J Reyna
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Angela L Harris
- TRACTION (Translational Research to Advance Therapeutics and Innovation in Oncology), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Alan Xu
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Michelle Han
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Michael J Soth
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Barbara Czako
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jay P Theroff
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Pijus K Mandal
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason P Burke
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Brett Virgin-Downey
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Alessia Petrocchi
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Dana Pfaffinger
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Norma E Rogers
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Connor A Parker
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Simon S Yu
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Yongying Jiang
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Stephan Krapp
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Martinsried, Germany
| | - Alfred Lammens
- Proteros Biostructures GmbH, Bunsenstr. 7a, D-82152 Martinsried, Germany
| | - Graham Trevitt
- XenoGesis Ltd, BioCity Nottingham, Pennyfoot Street, Nottingham, Nottinghamshire NG1 1GF, U.K
| | - Martin R Tremblay
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451 United States
| | - Keith Mikule
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451 United States
| | - Keith Wilcoxen
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451 United States
| | - Jason B Cross
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Philip Jones
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Joseph R Marszalek
- TRACTION (Translational Research to Advance Therapeutics and Innovation in Oncology), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Richard T Lewis
- IACS (Institute for Applied Cancer Science), University of Texas, MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
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7
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Chung I, Serreli R, Cross JB, Di Francesco ME, Marszalek JR, Hirst J. Cork-in-bottle mechanism of inhibitor binding to mammalian complex I. Sci Adv 2021; 7:7/20/eabg4000. [PMID: 33990335 PMCID: PMC8121435 DOI: 10.1126/sciadv.abg4000] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/26/2021] [Indexed: 05/08/2023]
Abstract
Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a major contributor of free energy for oxidative phosphorylation, is increasingly recognized as a promising drug target for ischemia-reperfusion injury, metabolic disorders, and various cancers. Several pharmacologically relevant but structurally unrelated small molecules have been identified as specific complex I inhibitors, but their modes of action remain unclear. Here, we present a 3.0-Å resolution cryo-electron microscopy structure of mammalian complex I inhibited by a derivative of IACS-010759, which is currently in clinical development against cancers reliant on oxidative phosphorylation, revealing its unique cork-in-bottle mechanism of inhibition. We combine structural and kinetic analyses to deconvolute cross-species differences in inhibition and identify the structural motif of a "chain" of aromatic rings as a characteristic that promotes inhibition. Our findings provide insights into the importance of π-stacking residues for inhibitor binding in the long substrate-binding channel in complex I and a guide for future biorational drug design.
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Affiliation(s)
- Injae Chung
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Riccardo Serreli
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Jason B Cross
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - M Emilia Di Francesco
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Joseph R Marszalek
- TRACTION-Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Judy Hirst
- MRC Mitochondrial Biology Unit, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK.
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8
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Sun Y, Meyers BA, Czako B, Leonard P, Mseeh F, Harris AL, Wu Q, Johnson S, Parker CA, Cross JB, Di Francesco ME, Bivona BJ, Bristow CA, Burke JP, Carrillo CC, Carroll CL, Chang Q, Feng N, Gao G, Gera S, Giuliani V, Huang JK, Jiang Y, Kang Z, Kovacs JJ, Liu CY, Lopez AM, Ma X, Mandal PK, McAfoos T, Miller MA, Mullinax RA, Peoples M, Ramamoorthy V, Seth S, Spencer ND, Suzuki E, Williams CC, Yu SS, Zuniga AM, Draetta GF, Marszalek JR, Heffernan TP, Kohl NE, Jones P. Allosteric SHP2 Inhibitor, IACS-13909, Overcomes EGFR-Dependent and EGFR-Independent Resistance Mechanisms toward Osimertinib. Cancer Res 2020; 80:4840-4853. [PMID: 32928921 DOI: 10.1158/0008-5472.can-20-1634] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/04/2020] [Accepted: 09/01/2020] [Indexed: 11/16/2022]
Abstract
Src homology 2 domain-containing phosphatase (SHP2) is a phosphatase that mediates signaling downstream of multiple receptor tyrosine kinases (RTK) and is required for full activation of the MAPK pathway. SHP2 inhibition has demonstrated tumor growth inhibition in RTK-activated cancers in preclinical studies. The long-term effectiveness of tyrosine kinase inhibitors such as the EGFR inhibitor (EGFRi), osimertinib, in non-small cell lung cancer (NSCLC) is limited by acquired resistance. Multiple clinically identified mechanisms underlie resistance to osimertinib, including mutations in EGFR that preclude drug binding as well as EGFR-independent activation of the MAPK pathway through alternate RTK (RTK-bypass). It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between multiple resistance mechanisms could restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. Here, we report the discovery of IACS-13909, a specific and potent allosteric inhibitor of SHP2, that suppresses signaling through the MAPK pathway. IACS-13909 potently impeded proliferation of tumors harboring a broad spectrum of activated RTKs as the oncogenic driver. In EGFR-mutant osimertinib-resistant NSCLC models with EGFR-dependent and EGFR-independent resistance mechanisms, IACS-13909, administered as a single agent or in combination with osimertinib, potently suppressed tumor cell proliferation in vitro and caused tumor regression in vivo. Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFRi-resistant NSCLC. SIGNIFICANCE: These findings highlight the discovery of IACS-13909 as a potent, selective inhibitor of SHP2 with drug-like properties, and targeting SHP2 may serve as a therapeutic strategy to overcome tumor resistance to osimertinib.
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Affiliation(s)
- Yuting Sun
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Brooke A Meyers
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Barbara Czako
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Leonard
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Faika Mseeh
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Angela L Harris
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qi Wu
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah Johnson
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Connor A Parker
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason B Cross
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria Emilia Di Francesco
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Benjamin J Bivona
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher A Bristow
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason P Burke
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caroline C Carrillo
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher L Carroll
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qing Chang
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ningping Feng
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guang Gao
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sonal Gera
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Virginia Giuliani
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Justin K Huang
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yongying Jiang
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhijun Kang
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey J Kovacs
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chiu-Yi Liu
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anastasia M Lopez
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoyan Ma
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pijus K Mandal
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy McAfoos
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Meredith A Miller
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Mullinax
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael Peoples
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vandhana Ramamoorthy
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sahil Seth
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nakia D Spencer
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Erika Suzuki
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher C Williams
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Simon S Yu
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andy M Zuniga
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joseph R Marszalek
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- TRACTION - Translational Research to AdvanCe Therapeutics and Innovation in ONcology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Philip Jones
- Institute for Applied Cancer Science (IACS), The University of Texas MD Anderson Cancer Center, Houston, Texas
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9
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Czako B, Marszalek JR, Burke JP, Mandal P, Leonard PG, Cross JB, Mseeh F, Jiang Y, Chang EQ, Suzuki E, Kovacs JJ, Feng N, Gera S, Harris AL, Liu Z, Mullinax RA, Pang J, Parker CA, Spencer ND, Yu SS, Wu Q, Tremblay MR, Mikule K, Wilcoxen K, Heffernan TP, Draetta GF, Jones P. Discovery of IACS-9439, a Potent, Exquisitely Selective, and Orally Bioavailable Inhibitor of CSF1R. J Med Chem 2020; 63:9888-9911. [PMID: 32787110 DOI: 10.1021/acs.jmedchem.0c00936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tumor-associated macrophages (TAMs) have a significant presence in the tumor stroma across multiple human malignancies and are believed to be beneficial to tumor growth. Targeting CSF1R has been proposed as a potential therapy to reduce TAMs, especially the protumor, immune-suppressive M2 TAMs. Additionally, the high expression of CSF1R on tumor cells has been associated with poor survival in certain cancers, suggesting tumor dependency and therefore a potential therapeutic target. The CSF1-CSF1R signaling pathway modulates the production, differentiation, and function of TAMs; however, the discovery of selective CSF1R inhibitors devoid of type III kinase activity has proven to be challenging. We discovered a potent, highly selective, and orally bioavailable CSF1R inhibitor, IACS-9439 (1). Treatment with 1 led to a dose-dependent reduction in macrophages, promoted macrophage polarization toward the M1 phenotype, and led to tumor growth inhibition in MC38 and PANC02 syngeneic tumor models.
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Affiliation(s)
- Barbara Czako
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Joseph R Marszalek
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason P Burke
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Pijus Mandal
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Paul G Leonard
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jason B Cross
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Faika Mseeh
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Yongying Jiang
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Edward Q Chang
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Erika Suzuki
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jeffrey J Kovacs
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Ningping Feng
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Sonal Gera
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Angela L Harris
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Zhen Liu
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Robert A Mullinax
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Jihai Pang
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Connor A Parker
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Nakia D Spencer
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Simon S Yu
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Qi Wu
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Martin R Tremblay
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451, United States
| | - Keith Mikule
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451, United States
| | - Keith Wilcoxen
- Tesaro Inc., 1000 Winter Street, Waltham, Massachusetts 02451, United States
| | - Timothy P Heffernan
- TRACTION (Translational Research to AdvanCe Therapeutics and Innovation in Oncology), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Philip Jones
- IACS (Institute of Applied Cancer Science), University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, Texas 77054, United States
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10
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Robichaux JP, Elamin YY, Vijayan R, Nilsson MB, Hu L, He J, Zhang F, Pisegna M, Poteete A, Sun H, Li S, Chen T, Han H, Negrao MV, Ahnert JR, Diao L, Wang J, Le X, Meric-Bernstam F, Routbort M, Roeck B, Yang Z, Raymond VM, Lanman RB, Frampton GM, Miller VA, Schrock AB, Albacker LA, Wong KK, Cross JB, Heymach JV. Pan-Cancer Landscape and Analysis of ERBB2 Mutations Identifies Poziotinib as a Clinically Active Inhibitor and Enhancer of T-DM1 Activity. Cancer Cell 2020; 37:420. [PMID: 32183953 PMCID: PMC7241090 DOI: 10.1016/j.ccell.2020.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Sun Y, Meyers BA, Johnson SB, Harris AL, Czako B, Cross JB, Leonard PG, Mseeh F, Francesco MED, Parker CA, Wu Q, Bristow CA, Burke JP, Carrillo CC, Carroll CL, Chang Q, Feng N, Gera S, Guang G, Huang JKL, Jiang Y, Kang Z, Kovacs JJ, Ma X, Mandal PK, McAfoos T, Mullinax RA, Peoples MD, Ramamoorthy V, Seth S, Suzuki E, Williams CC, Yu SS, Zuniga AM, Draetta GF, Marszalek JR, Heffernan TP, Kohl NE, Jones P. Abstract C036: Discovery of IACS-13909, an allosteric SHP2 inhibitor that overcomes multiple mechanisms underlying osimertinib resistance. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-c036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Osimertinib, a third generation EGFR inhibitor, is a front-line therapy for EGFR mutated non-small lung cancer (NSCLC). The long-term effectiveness of osimertinib is limited by acquired resistance. Clinically identified resistance mechanisms include EGFR-dependent mechanisms such as mutations on EGFR that preclude drug binding, and EGFR-independent activation of the MAPK pathway, for instance via activation of alternate RTKs. It has also been noted that frequently a tumor from a single patient harbors more than one resistance mechanism, and the plasticity between the multiple resistance mechanisms will restrict the effectiveness of therapies targeting a single node of the oncogenic signaling network. SHP2 (Src homology 2 domain-containing phosphatase) is a phosphatase that mediates the signaling of multiple RTKs and is required for full activation of the MAPK pathway. Here we report IACS-13909 - a specific and potent allosteric inhibitor of SHP2 - suppresses the signaling of RTK/MAPK pathway. IACS-13909 potently impedes the proliferation of tumors with a broad spectrum of RTKs as the oncogenic driver. Importantly, in NSCLC models with acquired resistance to osimertinib, IACS-13909 administered as a single agent or in combination with osimertinib potently reduces tumor cell proliferation in vitro and in vivo. Together, our findings provide preclinical evidence for using a SHP2 inhibitor as a therapeutic strategy in acquired EGFR inhibitor-resistant NSCLC. Currently, a compound that potently inhibits SHP2 has been selected as the clinical development candidate and is undergoing IND-enabling studies with a projected first-in-human target of early 2020.
Citation Format: Yuting Sun, Brooke A Meyers, Sarah B Johnson, Angela L Harris, Barbara Czako, Jason B Cross, Paul G Leonard, Faika Mseeh, Maria E Di Francesco, Connor A Parker, Qi Wu, Christopher A Bristow, Jason P Burke, Caroline C Carrillo, Christopher L Carroll, Qing Chang, Ningping Feng, Sonal Gera, Gao Guang, Justin Kwang-Lay Huang, Yongying Jiang, Zhijun Kang, Jeffrey J Kovacs, Xiaoyan Ma, Pijus K Mandal, Timothy McAfoos, Robert A Mullinax, Michael D Peoples, Vandhana Ramamoorthy, Sahil Seth, Erika Suzuki, Christopher Conrad Williams, Simon S Yu, Andy M Zuniga, Giulio F Draetta, Joseph R Marszalek, Timothy P Heffernan, Nancy E Kohl, Philip Jones. Discovery of IACS-13909, an allosteric SHP2 inhibitor that overcomes multiple mechanisms underlying osimertinib resistance [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C036. doi:10.1158/1535-7163.TARG-19-C036
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Qi Wu
- 1MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | - Gao Guang
- 1MD Anderson Cancer Center, Houston, TX
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12
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Robichaux JP, Elamin YY, Vijayan RSK, Nilsson MB, Hu L, He J, Zhang F, Pisegna M, Poteete A, Sun H, Li S, Chen T, Han H, Negrao MV, Ahnert JR, Diao L, Wang J, Le X, Meric-Bernstam F, Routbort M, Roeck B, Yang Z, Raymond VM, Lanman RB, Frampton GM, Miller VA, Schrock AB, Albacker LA, Wong KK, Cross JB, Heymach JV. Pan-Cancer Landscape and Analysis of ERBB2 Mutations Identifies Poziotinib as a Clinically Active Inhibitor and Enhancer of T-DM1 Activity. Cancer Cell 2019; 36:444-457.e7. [PMID: 31588020 PMCID: PMC6944069 DOI: 10.1016/j.ccell.2019.09.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/29/2019] [Accepted: 09/01/2019] [Indexed: 12/16/2022]
Abstract
We characterized the landscape and drug sensitivity of ERBB2 (HER2) mutations in cancers. In 11 datasets (n = 211,726), ERBB2 mutational hotspots varied across 25 tumor types. Common HER2 mutants yielded differential sensitivities to eleven EGFR/HER2 tyrosine kinase inhibitors (TKIs) in vitro, and molecular dynamics simulations revealed that mutants with a reduced drug-binding pocket volume were associated with decreased affinity for larger TKIs. Overall, poziotinib was the most potent HER2 mutant-selective TKI tested. Phase II clinical testing in ERBB2 exon 20-mutant non-small cell lung cancer resulted in a confirmed objective response rate of 42% in the first 12 evaluable patients. In pre-clinical models, poziotinib upregulated HER2 cell-surface expression and potentiated the activity of T-DM1, resulting in complete tumor regression with combination treatment.
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Affiliation(s)
- Jacqulyne P Robichaux
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - R S K Vijayan
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Monique B Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lemei Hu
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junqin He
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fahao Zhang
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marlese Pisegna
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alissa Poteete
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huiying Sun
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shuai Li
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Ting Chen
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Han Han
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Marcelo Vailati Negrao
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jordi Rodon Ahnert
- Investigative Cancer Therapeutics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Investigative Cancer Therapeutics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark Routbort
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brent Roeck
- Spectrum Pharmaceuticals, Irvine, CA 92618, USA
| | - Zane Yang
- Spectrum Pharmaceuticals, Irvine, CA 92618, USA
| | | | | | | | | | | | | | - Kwok-Kin Wong
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jason B Cross
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA.
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13
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Mseeh F, Hamilton MM, Marszalek JR, Rogers NE, Parker CA, Yu SS, Liu Z, Reyna NJ, McAfoos T, Virgin-Downey BW, Leonard PG, Cross JB, Feng N, Harris AL, Zuniga AM, Mikule K, Tremblay M, Jiang Y, Mahendra M, Pang J, Wu Q, Xu Q, Heffernan TP, Jones P, Lewis RT. Abstract 3277: IACS-9779, a development candidate that inhibits 2,3-dioxygenase (IDO) activity by blocking heme incorporation into IDO apoenzyme. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Increased expression of IDO1 is believed to create a tumor microenvironment that is immunosuppressive. In the course of our research directed at identifying potent and selective inhibitors of IDO1, we identified a class of compounds that inhibited IDO1 activity in a cellular context, but not in isolated enzymatic assays. We have conducted detailed mechanistic studies and shown that these molecules inhibit IDO1 by binding to the apo-enzyme, thus preventing the incorporation of the heme-cofactor into the active site of the holo-enzyme.
Through an extensive medicinal chemistry campaign, we optimized a series of orally bioavailable, highly potent and selective inhibitors of IDO1 that possess excellent pharmacological properties. For several lead molecules, pharmacokinetic (PK) - pharmacodynamic (PD) relationships were established in whole blood and SKOV3 xenograft assays. The inhibition of IDO1 in a human whole-blood assay correlated well with the suppression of tumor kynurenine (KYN) that was observed in SKOV3 xenografts. At plasma concentrations of 3 µM, IACS-9779 supressed tumor KYN levels by 90%. IACS-9779 was well tolerated with excellent in vivo PK properties across multiple preclinical species, and a human PK prediction consistent with a low daily dose needed for full suppression of KYN production via IDO1.
Note: This abstract was not presented at the meeting.
Citation Format: Faika Mseeh, Matthew M. Hamilton, Joseph R. Marszalek, Norma E. Rogers, Connor A. Parker, Simon S. Yu, Zhen Liu, Naphtali J. Reyna, Timothy McAfoos, Brett W. Virgin-Downey, Paul G. Leonard, Jason B. Cross, Ningping Feng, Angela L. Harris, Andy M. Zuniga, Keith Mikule, Martin Tremblay, Yongying Jiang, Mikhila Mahendra, Jihai Pang, Qi Wu, Quanyun Xu, Timothy P. Heffernan, Philip Jones, Richard T. Lewis. IACS-9779, a development candidate that inhibits 2,3-dioxygenase (IDO) activity by blocking heme incorporation into IDO apoenzyme [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3277.
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Affiliation(s)
| | | | | | | | | | | | - Zhen Liu
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jihai Pang
- 1UT MD Anderson Cancer Center, Houston, TX
| | - Qi Wu
- 1UT MD Anderson Cancer Center, Houston, TX
| | - Quanyun Xu
- 1UT MD Anderson Cancer Center, Houston, TX
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14
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Petrocchi A, Reyna NJ, Mseeh F, Parker CA, Yu S, Xu Q, Feng N, Leonard P, Rogers N, Cross JB, Harris AL, Jiang Y, Khor TO, Mahendra MG, Pang J, Wu Q, Zuniga AM, McAfoos T, McAfoos T, Hamilton MM, Marszalek JR, Mikule K, Vancutsem P, Wilcoxen K, Tremblay M, Jones P, Lewis RT. Abstract LB-071: Discovery of an imidazopyridine series of potent human IDO1 inhibitors with robust target engagement in a preclinical tumor model. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Indoleamine 2,3-dioxygenase (IDO1 and IDO2) and tryptophan dioxygenase (TDO) are heme-containing enzymes that mediate the rate limiting step in the oxidative degradation of L-tryptophan (L-TRP) to kynurenine (KYN) metabolites. Tryptophan catabolism through the KYN metabolic pathway is now recognized as one of many mechanisms involved in tumor cell evasion of the immune surveillance system. Inhibition of the KYN pathway in the tumor microenvironment can lead to improved immune response and tumor growth suppression. Recently, clinical proof of concept of this mechanism has been demonstrated using an Indoleamine 2,3-dioxygenase (IDO1) inhibitor in combination with a PD-1 antagonist in a variety of tumor contexts. Consideration of known low molecular weight heme-co-ordinating ligands identified from the PDB, in conjunction with a virtual screen performed in-silico identified a number of potentially interesting starting points for medicinal chemistry development. Identification of an attractive indazole fragment as a starting point, and expansion into alternative bicyclic cores, resulted in the discovery of a family of imidazopyridines as potent human IDO1 inhibitors with >200 fold selectivity against TDO. Utilizing a structure-based design approach allowed rapid lead optimization that resulted in the identification of IACS-8968. Crystallography studies were conducted, and binding of IACS-8968 to the heme domain of the human IDO1 was confirmed. The homochiral imidazopyridine IACS-8968 displayed cellular IC50= 29 nM in a HeLa cell line expressing human IDO1 and IC50= 21 nM in a PANC02 mouse cell line expressing the murine IDO1 enzyme, showed satisfactory selectivity margin (> 150 fold) versus its CYP450 inhibition profile and good oral bioavailability across species. PK/PD experiments indicated that, at equivalent exposure, IACS-8968 (sodium salt) and epacadostat decreased tumor KYN at comparable levels in CT26 syngeneic mouse model.
Citation Format: Alessia Petrocchi, Naphtali J. Reyna, Faika Mseeh, Connor A. Parker, Simon Yu, Quanyun Xu, Ningping Feng, Paul Leonard, Norma Rogers, Jason B. Cross, Angela L. Harris, Yongying Jiang, Tin Oo Khor, Mikhila G. Mahendra, Jihai Pang, Qi Wu, Andy M. Zuniga, Timothy McAfoos, Timothy McAfoos, Matthew M. Hamilton, Joe R. Marszalek, Keith Mikule, Paul Vancutsem, Keith Wilcoxen, Martin Tremblay, Philip Jones, Richard T. Lewis. Discovery of an imidazopyridine series of potent human IDO1 inhibitors with robust target engagement in a preclinical tumor model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-071.
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Affiliation(s)
| | | | | | | | - Simon Yu
- 1MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | | | | | | | - Qi Wu
- 1MD Anderson Cancer Center, Houston, TX
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15
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Molina JR, Sun Y, Protopopova M, Gera S, Bandi M, Bristow C, McAfoos T, Morlacchi P, Ackroyd J, Agip ANA, Al-Atrash G, Asara J, Bardenhagen J, Carrillo CC, Carroll C, Chang E, Ciurea S, Cross JB, Czako B, Deem A, Daver N, de Groot JF, Dong JW, Feng N, Gao G, Gay J, Do MG, Greer J, Giuliani V, Han J, Han L, Henry VK, Hirst J, Huang S, Jiang Y, Kang Z, Khor T, Konoplev S, Lin YH, Liu G, Lodi A, Lofton T, Ma H, Mahendra M, Matre P, Mullinax R, Peoples M, Petrocchi A, Rodriguez-Canale J, Serreli R, Shi T, Smith M, Tabe Y, Theroff J, Tiziani S, Xu Q, Zhang Q, Muller F, DePinho RA, Toniatti C, Draetta GF, Heffernan TP, Konopleva M, Jones P, Di Francesco ME, Marszalek JR. An inhibitor of oxidative phosphorylation exploits cancer vulnerability. Nat Med 2018; 24:1036-1046. [PMID: 29892070 DOI: 10.1038/s41591-018-0052-4] [Citation(s) in RCA: 540] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/27/2018] [Indexed: 12/19/2022]
Abstract
Metabolic reprograming is an emerging hallmark of tumor biology and an actively pursued opportunity in discovery of oncology drugs. Extensive efforts have focused on therapeutic targeting of glycolysis, whereas drugging mitochondrial oxidative phosphorylation (OXPHOS) has remained largely unexplored, partly owing to an incomplete understanding of tumor contexts in which OXPHOS is essential. Here, we report the discovery of IACS-010759, a clinical-grade small-molecule inhibitor of complex I of the mitochondrial electron transport chain. Treatment with IACS-010759 robustly inhibited proliferation and induced apoptosis in models of brain cancer and acute myeloid leukemia (AML) reliant on OXPHOS, likely owing to a combination of energy depletion and reduced aspartate production that leads to impaired nucleotide biosynthesis. In models of brain cancer and AML, tumor growth was potently inhibited in vivo following IACS-010759 treatment at well-tolerated doses. IACS-010759 is currently being evaluated in phase 1 clinical trials in relapsed/refractory AML and solid tumors.
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Affiliation(s)
- Jennifer R Molina
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuting Sun
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marina Protopopova
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sonal Gera
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Madhavi Bandi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Bristow
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy McAfoos
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pietro Morlacchi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Agilent Technologies Inc., Lexington, MA, USA
| | - Jeffrey Ackroyd
- Department of Cancer Imaging Systems, University of Texas MD Cancer Center, Houston, TX, USA
| | - Ahmed-Noor A Agip
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Asara
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jennifer Bardenhagen
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline C Carrillo
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Carroll
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edward Chang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stefan Ciurea
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason B Cross
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Czako
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Angela Deem
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naval Daver
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Frederick de Groot
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian-Wen Dong
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ningping Feng
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guang Gao
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Gay
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mary Geck Do
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Greer
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Virginia Giuliani
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Han
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lina Han
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Verlene K Henry
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Sha Huang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yongying Jiang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhijun Kang
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tin Khor
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergej Konoplev
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu-Hsi Lin
- Department of Cancer Imaging Systems, University of Texas MD Cancer Center, Houston, TX, USA
| | - Gang Liu
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessia Lodi
- Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Timothy Lofton
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Helen Ma
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mikhila Mahendra
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Polina Matre
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Mullinax
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Peoples
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alessia Petrocchi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaime Rodriguez-Canale
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Riccardo Serreli
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge, UK
| | - Thomas Shi
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melinda Smith
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoko Tabe
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Next Generation Hematology Laboratory Medicine, Department of Laboratory Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Jay Theroff
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stefano Tiziani
- Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Quanyun Xu
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Zhang
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Florian Muller
- Department of Cancer Imaging Systems, University of Texas MD Cancer Center, Houston, TX, USA
| | - Ronald A DePinho
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlo Toniatti
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giulio F Draetta
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marina Konopleva
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Philip Jones
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Emilia Di Francesco
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph R Marszalek
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for Co-Clinical Trials, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Abstract
Virtual screening (VS) has become an integral part of the drug discovery process and is a valuable tool for finding novel chemical starting points for GPCR targets. Ligand-based VS makes use of biochemical data for known, active compounds and has been applied successfully to many diverse GPCRs. Recent progress in GPCR X-ray crystallography has made it possible to incorporate detailed structural information into the VS process. This chapter outlines the latest VS techniques along with examples that highlight successful applications of these methods. Best practices for increasing the likelihood of VS success, as well as ongoing challenges, are also discussed.
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Affiliation(s)
- Jason B Cross
- University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.
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17
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Zhang J, Chan A, Lippa B, Cross JB, Liu C, Yin N, Romero JAC, Lawrence J, Heney R, Herradura P, Goss J, Clark C, Abel C, Zhang Y, Poutsiaka KM, Epie F, Conrad M, Mahamoon A, Nguyen K, Chavan A, Clark E, Li TC, Cheng RK, Wood M, Andersen OA, Brooks M, Kwong J, Barker J, Parr IB, Gu Y, Ryan MD, Coleman S, Metcalf CA. Structure-based discovery of LpxC inhibitors. Bioorg Med Chem Lett 2017; 27:1670-1680. [DOI: 10.1016/j.bmcl.2017.03.006] [Citation(s) in RCA: 11] [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] [Received: 01/27/2017] [Revised: 03/01/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
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18
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Cross JB, Zhang J, Yang Q, Mesleh MF, Romero JAC, Wang B, Bevan D, Poutsiaka KM, Epie F, Moy T, Daniel A, Shotwell J, Chamberlain B, Carter N, Andersen O, Barker J, Ryan MD, Metcalf CA, Silverman J, Nguyen K, Lippa B, Dolle RE. Discovery of Pyrazolopyridones as a Novel Class of Gyrase B Inhibitors Using Structure Guided Design. ACS Med Chem Lett 2016; 7:374-8. [PMID: 27096044 DOI: 10.1021/acsmedchemlett.5b00368] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 09/20/2015] [Accepted: 02/06/2016] [Indexed: 12/20/2022] Open
Abstract
The ATPase subunit of DNA gyrase B is an attractive antibacterial target due to high conservation across bacteria and the essential role it plays in DNA replication. A novel class of pyrazolopyridone inhibitors was discovered by optimizing a fragment screening hit scaffold using structure guided design. These inhibitors show potent Gram-positive antibacterial activity and low resistance incidence against clinically important pathogens.
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Affiliation(s)
- Jason B. Cross
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Jing Zhang
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Qingyi Yang
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Michael F. Mesleh
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | | | - Bin Wang
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Doug Bevan
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Katherine M. Poutsiaka
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Felix Epie
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Terence Moy
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Anu Daniel
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Joseph Shotwell
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Brian Chamberlain
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Nicole Carter
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Ole Andersen
- Evotec U.K., Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - John Barker
- Evotec U.K., Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - M. Dominic Ryan
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Chester A. Metcalf
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Jared Silverman
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Kien Nguyen
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Blaise Lippa
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
| | - Roland E. Dolle
- Cubist Pharmaceuticals, Inc., 65 Hayden Avenue, Lexington, Massachusetts 02421, United States
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19
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Petrocchi A, Leo E, Reyna NJ, Hamilton MM, Shi X, Parker CA, Mseeh F, Bardenhagen JP, Leonard P, Cross JB, Huang S, Jiang Y, Cardozo M, Draetta G, Marszalek JR, Toniatti C, Jones P, Lewis RT. Identification of potent and selective MTH1 inhibitors. Bioorg Med Chem Lett 2016; 26:1503-1507. [PMID: 26898335 DOI: 10.1016/j.bmcl.2016.02.026] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [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: 01/15/2016] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 12/01/2022]
Abstract
Structure based design of a novel class of aminopyrimidine MTH1 (MutT homolog 1) inhibitors is described. Optimization led to identification of IACS-4759 (compound 5), a sub-nanomolar inhibitor of MTH1 with excellent cell permeability and good metabolic stability in microsomes. This compound robustly inhibited MTH1 activity in cells and proved to be an excellent tool for interrogation of the utility of MTH1 inhibition in the context of oncology.
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Affiliation(s)
- Alessia Petrocchi
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA.
| | - Elisabetta Leo
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Naphtali J Reyna
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Matthew M Hamilton
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Xi Shi
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Connor A Parker
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Faika Mseeh
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Jennifer P Bardenhagen
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Paul Leonard
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Jason B Cross
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Sha Huang
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Yongying Jiang
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Mario Cardozo
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Giulio Draetta
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Joseph R Marszalek
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Carlo Toniatti
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Philip Jones
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
| | - Richard T Lewis
- Institute for Applied Cancer Science, MD Anderson Cancer Center, 1901 East Road, Houston (TX) 77054, USA
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20
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Mesleh MF, Cross JB, Zhang J, Kahmann J, Andersen OA, Barker J, Cheng RK, Felicetti B, Wood M, Hadfield AT, Scheich C, Moy TI, Yang Q, Shotwell J, Nguyen K, Lippa B, Dolle R, Ryan MD. Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB. Bioorg Med Chem Lett 2016; 26:1314-8. [DOI: 10.1016/j.bmcl.2016.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 11/16/2022]
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21
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Zhang J, Yang Q, Cross JB, Romero JAC, Poutsiaka KM, Epie F, Bevan D, Wang B, Zhang Y, Chavan A, Zhang X, Moy T, Daniel A, Nguyen K, Chamberlain B, Carter N, Shotwell J, Silverman J, Metcalf CA, Ryan D, Lippa B, Dolle RE. Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors. J Med Chem 2015; 58:8503-12. [DOI: 10.1021/acs.jmedchem.5b00961] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jing Zhang
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Qingyi Yang
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Jason B. Cross
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | | | | | - Felix Epie
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Douglas Bevan
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Bin Wang
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Yanzhi Zhang
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Ajit Chavan
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Xin Zhang
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Terence Moy
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Anu Daniel
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Kien Nguyen
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Brian Chamberlain
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Nicole Carter
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Joseph Shotwell
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Jared Silverman
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Chester A. Metcalf
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Dominic Ryan
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Blaise Lippa
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
| | - Roland E. Dolle
- Cubist Pharmaceuticals Inc., Lexington, Massachusetts 02421, United States
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22
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Abstract
Fragment-based drug design (FBDD), which is comprised of both fragment screening and the use of fragment hits to design leads, began more than 15 years ago and has been steadily gaining in popularity and utility. Its origin lies on the fact that the coverage of chemical space and the binding efficiency of hits are directly related to the size of the compounds screened. Nevertheless, FBDD still faces challenges, among them developing fragment screening libraries that ensure optimal coverage of chemical space, physical properties and chemical tractability. Fragment screening also requires sensitive assays, often biophysical in nature, to detect weak binders. In this chapter we will introduce the technologies used to address these challenges and outline the experimental advantages that make FBDD one of the most popular new hit-to-lead process.
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Brooijmans N, Cross JB, Humblet C. Biased retrieval of chemical series in receptor-based virtual screening. J Comput Aided Mol Des 2010; 24:1053-62. [DOI: 10.1007/s10822-010-9394-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 10/19/2010] [Indexed: 11/30/2022]
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24
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Unwalla RJ, Cross JB, Salaniwal S, Shilling AD, Leung L, Kao J, Humblet C. Using a homology model of cytochrome P450 2D6 to predict substrate site of metabolism. J Comput Aided Mol Des 2010; 24:237-56. [PMID: 20361239 DOI: 10.1007/s10822-010-9336-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 03/15/2010] [Indexed: 10/19/2022]
Abstract
CYP2D6 is an important enzyme that is involved in first pass metabolism and is responsible for metabolizing ~25% of currently marketed drugs. A homology model of CYP2D6 was built using X-ray structures of ligand-bound CYP2C5 complexes as templates. This homology model was used in docking studies to rationalize and predict the site of metabolism of known CYP2D6 substrates. While the homology model was generally found to be in good agreement with the recently solved apo (ligand-free) X-ray structure of CYP2D6, significant differences between the structures were observed in the B' and F-G helical region. These structural differences are similar to those observed between ligand-free and ligand-bound structures of other CYPs and suggest that these conformational changes result from induced-fit adaptations upon ligand binding. By docking to the homology model using Glide, it was possible to identify the correct site of metabolism for a set of 16 CYP2D6 substrates 85% of the time when the 5 top scoring poses were examined. On the other hand, docking to the apo CYP2D6 X-ray structure led to a loss in accuracy in predicting the sites of metabolism for many of the CYP2D6 substrates considered in this study. These results demonstrate the importance of describing substrate-induced conformational changes that occur upon binding. The best results were obtained using Glide SP with van der Waals scaling set to 0.8 for both the receptor and ligand atoms. A discussion of putative binding modes that explain the distribution of metabolic sites for substrates, as well as a relationship between the number of metabolic sites and substrate size, are also presented. In addition, analysis of these binding modes enabled us to rationalize the typical hydroxylation and O-demethylation reactions catalyzed by CYP2D6 as well as the less common N-dealkylation.
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Affiliation(s)
- Rayomand J Unwalla
- Chemical Sciences, Wyeth Research, S-2421, 500 Arcola Road, Collegeville, PA 19426, USA.
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25
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Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 2009; 49:1455-74. [PMID: 19476350 DOI: 10.1021/ci900056c] [Citation(s) in RCA: 329] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular docking programs are widely used modeling tools for predicting ligand binding modes and structure based virtual screening. In this study, six molecular docking programs (DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex) were evaluated using metrics intended to assess docking pose and virtual screening accuracy. Cognate ligand docking to 68 diverse, high-resolution X-ray complexes revealed that ICM, GLIDE, and Surflex generated ligand poses close to the X-ray conformation more often than the other docking programs. GLIDE and Surflex also outperformed the other docking programs when used for virtual screening, based on mean ROC AUC and ROC enrichment values obtained for the 40 protein targets in the Directory of Useful Decoys (DUD). Further analysis uncovered general trends in accuracy that are specific for particular protein families. Modifying basic parameters in the software was shown to have a significant effect on docking and virtual screening results, suggesting that expert knowledge is critical for optimizing the accuracy of these methods.
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Affiliation(s)
- Jason B Cross
- Wyeth Research, Chemical Sciences, Collegeville, Pennsylvania 19426, USA.
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26
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Affiliation(s)
- J. Christian Baber
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - David C. Thompson
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - Jason B. Cross
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
| | - Christine Humblet
- Chemical Sciences, Wyeth Research, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140 and 865 Ridge Road, Princeton, New Jersey 08543, and Chemical Sciences, Wyeth Pharmaceuticals and Research Headquarters, 500 Arcola Road, Collegeville, Pennsylvania 19426
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27
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Cross JB, Vreven T, Meroueh SO, Mobashery S, Schlegel HB. Computational investigation of irreversible inactivation of the zinc-dependent protease carboxypeptidase A. J Phys Chem B 2007; 109:4761-9. [PMID: 16851559 DOI: 10.1021/jp0455172] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 11/30/2022]
Abstract
Zinc proteases are ubiquitous and the zinc ion plays a central function in the catalytic mechanism of these enzymes. A novel class of mechanism-based inhibitors takes advantage of the zinc ion chemistry in carboxypeptidase A (CPA) to promote covalent attachment of an inhibitor to the carboxylate of Glu-270, resulting in irreversible inhibition of the enzyme. The effect of the active site zinc ion on irreversible inactivation of CPA was probed by molecular orbital (MO) calculations on a series of active site models and the Cl(-) + CH(3)Cl S(N)2 reaction fragment. Point charge models representing the active site reproduced energetics from full MO calculations at 12.0 A separation between the zinc and the central carbon of the S(N)2 reaction, but at 5.0 A polarization played an important role in moderating barrier suppression. ONIOM MO/MO calculations that included the residues within 10 A of the active site zinc suggest that about 75% of the barrier suppression arises from the zinc ion and its ligands. A model of the pre-reactive complex of the 2-benzyl-3-iodopropanoate inactivator with CPA was constructed from the X-ray structure of l-phenyl lactate bound in the active site of the enzyme. The model was fully solvated and minimized by using the AMBER force field to generate the starting structure for the ONIOM QM/MM calculations. Optimization of this structure led to the barrierless S(N)2 displacement of the iodide of the inhibitor by Glu-270, assisted by interaction of the zinc ion with the leaving group. The resulting product is in good agreement with the X-ray structure of the covalently modified enzyme obtained by irreversible inhibition of CPA by 2-benzyl-3-iodopropanoate.
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Affiliation(s)
- Jason B Cross
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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28
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Abstract
An increasing number of proteins are being shown to have an N(zeta)-carboxylated lysine in their structures, a posttranslational modification of proteins that proceeds without the intervention of a specific enzyme. The role of the carboxylated lysine in these proteins is typically structural (hydrogen bonding or metal coordination). However, carboxylated lysines in the active sites of OXA-10 and OXA-1 beta-lactamases and the sensor domain of BlaR signal-transducer protein serve in proton transfer events required for the functions of these proteins. These examples demonstrate the utility of this unusual amino acid in acid-base chemistry, in expansion of function beyond those of the 20 standard amino acids. In this study, the ONIOM quantum-mechanical/molecular-mechanical (QM/MM) method is used to study the carboxylation of lysine in the OXA-10 beta-lactamase. Lys-70 and the active site of the OXA-10 beta-lactamase were treated with B3LYP/6-31G(d,p) density functional calculations and the remainder of the enzyme with the AMBER molecular mechanics force field. The barriers for unassisted carboxylation of neutral lysine by carbon dioxide or bicarbonate are high. However, when the reaction with CO2 is catalyzed by a molecule of water in the active site, it is exothermic by about 13 kcal/mol, with a barrier of approximately 14 kcal/mol. The calculations show that the carboxylation and decarboxylation of Lys-70 are likely to be accompanied by deprotonation and protonation of the carbamate, respectively. The analysis may also be relevant for other proteins with carboxylated lysines, a feature that may be more common in nature than previously appreciated.
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Affiliation(s)
- Jie Li
- Department of Chemistry and Institute for Scientific Computing, Wayne State University, Detroit, Michigan 48202, USA
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29
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Cross JB, Currier RP, Torraco DJ, Vanderberg LA, Wagner GL, Gladen PD. Killing of bacillus spores by aqueous dissolved oxygen, ascorbic acid, and copper ions. Appl Environ Microbiol 2003; 69:2245-52. [PMID: 12676707 PMCID: PMC154791 DOI: 10.1128/aem.69.4.2245-2252.2003] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [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: 01/02/2023] Open
Abstract
An approach to decontamination of biological endospores is discussed. Specifically, the performance of an aqueous modified Fenton reagent is examined. A modified Fenton reagent formulation of cupric chloride, ascorbic acid, and sodium chloride is shown to be an effective sporicide under aerobic conditions. The traditional Fenton reaction involves the conversion of hydrogen peroxide to hydroxyl radical by aqueous ionic catalysts such as the transition metal ions. Our modified Fenton reaction involves the conversion of aqueous dissolved oxygen to hydrogen peroxide by an ionic catalyst (Cu(2+)) and then subsequent conversion to hydroxyl radicals. Results are given for the modified Fenton reagent deactivating spores of Bacillus globigii. A biocidal mechanism is proposed that is consistent with our experimental results and independently derived information found in the literature. This mechanism requires diffusion of relatively benign species into the interior of the spore, where dissolved O(2) is then converted through a series of reactions which ultimately produce hydroxyl radicals that perform the killing action.
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Affiliation(s)
- J B Cross
- Chemistry Division, Los Alamos National Laboratory, New Mexico 87545, USA
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30
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Cross JB, Duca JS, Kaminski JJ, Madison VS. The active site of a zinc-dependent metalloproteinase influences the computed pK(a) of ligands coordinated to the catalytic zinc ion. J Am Chem Soc 2002; 124:11004-7. [PMID: 12224947 DOI: 10.1021/ja0201810] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [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: 11/30/2022]
Abstract
TNF-alpha converting enzyme (TACE) is a multidomain, membrane-anchored protein that includes a Zn-dependent protease domain. It releases the soluble form of cytokine tumor necrosis factor-alpha (TNF-alpha) from its membrane-bound precursor. TACE is a metalloprotease containing a catalytic glutamic acid, Glu-406, and a Zn(2+) ion ligated to three imidazoles. The protonation states of the active site glutamic acid and inhibitors are important factors in understanding the potency of inhibitors with acidic zinc-ligating groups such as hydroxamic and carboxylic acids. Density functional methods were utilized to compute pK(a) values using a model of the catalytic site of TACE and to predict a concomitant mechanism of binding, consistent with lowering the pK(a) of the bound ligand and raising the pK(a) of the active site Glu-406. Weak acids, such as hydroxamic acids, bind in their neutral form and then transfer an acidic proton to Glu-406. Stronger acids, such as carboxylic acids, bind in their anionic form and require preprotonation of Glu-406. Similar binding events would be expected for other zinc-dependent proteases.
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Affiliation(s)
- Jason B Cross
- Contribution from the Department of Structural Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA
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31
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Kotra LP, Cross JB, Shimura Y, Fridman R, Schlegel HB, Mobashery S. Insight into the complex and dynamic process of activation of matrix metalloproteinases. J Am Chem Soc 2001; 123:3108-13. [PMID: 11457021 DOI: 10.1021/ja001896a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Matrix metalloproteinases (MMPs) are important hydrolytic enzymes with profound physiological and pathological functions in living organisms. MMPs are produced in their inactive zymogenic forms, which are subsequently proteolytically activated in an elaborate set of events. The propeptide in the zymogen blocks the active site, with a cysteine side-chain thiolate from this propeptide achieving coordination with the catalytically important zinc ion in the active site. Molecular dynamics simulations, ab initio calculations, and wet chemistry experiments presented herein argue for the critical importance of a protonation event at the coordinated thiolate as a prerequisite for the departure of the propeptide from the active site. Furthermore, a catalytically important glutamate is shown to coordinate transiently to the active-site zinc ion to "mask" the positive potential of the zinc ion and lower the energy barrier for dissociation of the protonated cysteine side chain from the zinc ion. In addition, a subtle conformational change by the propeptide is needed in the course of zymogen activation. These elaborate processes take place in concert in the activation process of MMPs, and the insight into these processes presented herein sheds light on a highly regulated physiological process with profound consequences for eukaryotic organisms.
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Affiliation(s)
- L P Kotra
- Department of Pathology, Institute for Drug Design, Wayne State University, Detroit, Michigan 48202-3489, USA
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32
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Cross JB. Technique for Making Spreads of Omentum from Small Animals. Science 1949; 109:314. [PMID: 17782723 DOI: 10.1126/science.109.2830.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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