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Welsch ME, Kaplan A, Chambers JM, Stokes ME, Bos PH, Zask A, Zhang Y, Sanchez-Martin M, Badgley MA, Huang CS, Tran TH, Akkiraju H, Brown LM, Nandakumar R, Cremers S, Yang WS, Tong L, Olive KP, Ferrando A, Stockwell BR. Multivalent Small-Molecule Pan-RAS Inhibitors. Cell 2017; 168:878-889.e29. [PMID: 28235199 DOI: 10.1016/j.cell.2017.02.006] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 10/23/2016] [Accepted: 02/01/2017] [Indexed: 12/30/2022]
Abstract
Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, may provide chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small-molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy, and isothermal titration calorimetry and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins.
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Affiliation(s)
- Matthew E Welsch
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Anna Kaplan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jennifer M Chambers
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Michael E Stokes
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Pieter H Bos
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Arie Zask
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yan Zhang
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Marta Sanchez-Martin
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael A Badgley
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Diseases in the Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Christine S Huang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Hemanth Akkiraju
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Lewis M Brown
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA
| | - Renu Nandakumar
- Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Serge Cremers
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Wan Seok Yang
- Department of Biological Sciences, St. John's University, Queens, NY 11439, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Kenneth P Olive
- Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Diseases in the Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Brent R Stockwell
- Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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Welsch ME, Zhou J, Gao Y, Yan Y, Porter G, Agnihotri G, Li Y, Lu H, Chen Z, Thomas SB. Discovery of Potent and Selective Leads against Toxoplasma gondii Dihydrofolate Reductase via Structure-Based Design. ACS Med Chem Lett 2016; 7:1124-1129. [PMID: 27994750 DOI: 10.1021/acsmedchemlett.6b00328] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/16/2016] [Indexed: 11/28/2022] Open
Abstract
Current treatment of toxoplasmosis targets the parasite's folate metabolism through inhibition of dihydrofolate reductase (DHFR). The most widely used DHFR antagonist, pyrimethamine, was introduced over 60 years ago and is associated with toxicity that can be largely attributed to a similar affinity for parasite and human DHFR. Computational analysis of biochemical differences between Toxoplasma gondii and human DHFR enabled the design of inhibitors with both improved potency and selectivity. The approach described herein yielded TRC-19, a promising lead with an IC50 of 9 nM and 89-fold selectivity in favor of Toxoplasma gondii DHFR, as well as crystallographic data to substantiate in silico methodology. Overall, 50% of synthesized in silico designs met hit threshold criteria of IC50 < 10 μM and >2-fold selectivity favoring Toxoplasma gondii, further demonstrating the efficiency of our structure-based drug design approach.
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Affiliation(s)
- Matthew E. Welsch
- Turing Pharmaceuticals AG, Research & Development, 1177 Avenue of the Americas, 39th Floor, New York, New York 10036, United States
| | - Jian Zhou
- WuXi AppTec, International Discovery Service Unit & Research Service Division, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yueqiang Gao
- WuXi AppTec, International Discovery Service Unit & Research Service Division, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yunqing Yan
- WuXi AppTec, International Discovery Service Unit & Research Service Division, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Gene Porter
- WuXi AppTec, In Vitro Biology US, 107 Morgan Lane, Plainsborough, New Jersey 08536, United States
| | - Gautam Agnihotri
- WuXi AppTec, In Vitro Biology US, 107 Morgan Lane, Plainsborough, New Jersey 08536, United States
| | - Yingjie Li
- WuXi AppTec, International Discovery Service Unit & Research Service Division, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Henry Lu
- WuXi AppTec, International Discovery Service Unit & Research Service Division, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zhongguo Chen
- WuXi AppTec, International Discovery Service Unit & Research Service Division, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Stephen B. Thomas
- Turing Pharmaceuticals AG, Research & Development, 1177 Avenue of the Americas, 39th Floor, New York, New York 10036, United States
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Yang WS, SriRamaratnam R, Welsch ME, Shimada K, Skouta R, Viswanathan VS, Cheah JH, Clemons PA, Shamji AF, Clish CB, Brown LM, Girotti AW, Cornish VW, Schreiber SL, Stockwell BR. Regulation of ferroptotic cancer cell death by GPX4. Cell 2014; 156:317-331. [PMID: 24439385 DOI: 10.1016/j.cell.2013.12.010] [Citation(s) in RCA: 3823] [Impact Index Per Article: 382.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/30/2013] [Accepted: 12/04/2013] [Indexed: 02/06/2023]
Abstract
Ferroptosis is a form of nonapoptotic cell death for which key regulators remain unknown. We sought a common mediator for the lethality of 12 ferroptosis-inducing small molecules. We used targeted metabolomic profiling to discover that depletion of glutathione causes inactivation of glutathione peroxidases (GPXs) in response to one class of compounds and a chemoproteomics strategy to discover that GPX4 is directly inhibited by a second class of compounds. GPX4 overexpression and knockdown modulated the lethality of 12 ferroptosis inducers, but not of 11 compounds with other lethal mechanisms. In addition, two representative ferroptosis inducers prevented tumor growth in xenograft mouse tumor models. Sensitivity profiling in 177 cancer cell lines revealed that diffuse large B cell lymphomas and renal cell carcinomas are particularly susceptible to GPX4-regulated ferroptosis. Thus, GPX4 is an essential regulator of ferroptotic cancer cell death.
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Affiliation(s)
- Wan Seok Yang
- Department of Biological Sciences, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA
| | - Rohitha SriRamaratnam
- Department of Chemistry, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA
| | - Matthew E Welsch
- Department of Chemistry, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA
| | - Kenichi Shimada
- Department of Biological Sciences, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA
| | - Rachid Skouta
- Department of Biological Sciences, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA
| | - Vasanthi S Viswanathan
- Department of Biological Sciences, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jaime H Cheah
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Paul A Clemons
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Lewis M Brown
- Department of Biological Sciences, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA.,Quantitative Proteomics Center, Columbia University, New York, NY 10027, USA
| | - Albert W Girotti
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Virginia W Cornish
- Department of Chemistry, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA
| | | | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA.,Department of Chemistry, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA.,Howard Hughes Medical Institute, Columbia University, 1208 Northwest Corner Building, 12 Floor, 550 West 120 Street, MC 4846, New York, NY 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
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Welsch ME, Snyder SA, Stockwell BR. Privileged scaffolds for library design and drug discovery. Curr Opin Chem Biol 2010; 14:347-61. [PMID: 20303320 DOI: 10.1016/j.cbpa.2010.02.018] [Citation(s) in RCA: 1056] [Impact Index Per Article: 75.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 02/09/2010] [Accepted: 02/18/2010] [Indexed: 02/07/2023]
Abstract
This review explores the concept of using privileged scaffolds to identify biologically active compounds through building chemical libraries. We hope to accomplish three main objectives: to provide one of the most comprehensive listings of privileged scaffolds; to reveal through four selected examples the present state of the art in privileged scaffold library synthesis (in hopes of inspiring new and even more creative approaches); and also to offer some thoughts on how new privileged scaffolds might be identified and exploited.
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Affiliation(s)
- Matthew E Welsch
- Columbia University, Department of Chemistry, Havemeyer Hall, MC 3129, 3000 Broadway, New York, NY 10027, USA
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