1
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Moison C, Gracias D, Schmitt J, Girard S, Spinella JF, Fortier S, Boivin I, Mendoza-Sanchez R, Thavonekham B, MacRae T, Mayotte N, Bonneil E, Wittman M, Carmichael J, Ruel R, Thibault P, Hébert J, Marinier A, Sauvageau G. SF3B1 mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia. Sci Adv 2024; 10:eadl4018. [PMID: 38517966 PMCID: PMC10959413 DOI: 10.1126/sciadv.adl4018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/20/2024] [Indexed: 03/24/2024]
Abstract
In a phenotypical screen of 56 acute myeloid leukemia (AML) patient samples and using a library of 10,000 compounds, we identified a hit with increased sensitivity toward SF3B1-mutated and adverse risk AMLs. Through structure-activity relationship studies, this hit was optimized into a potent, specific, and nongenotoxic molecule called UM4118. We demonstrated that UM4118 acts as a copper ionophore that initiates a mitochondrial-based noncanonical form of cell death known as cuproptosis. CRISPR-Cas9 loss-of-function screen further revealed that iron-sulfur cluster (ISC) deficiency enhances copper-mediated cell death. Specifically, we found that loss of the mitochondrial ISC transporter ABCB7 is synthetic lethal to UM4118. ABCB7 is misspliced and down-regulated in SF3B1-mutated leukemia, creating a vulnerability to copper ionophores. Accordingly, ABCB7 overexpression partially rescued SF3B1-mutated cells to copper overload. Together, our work provides mechanistic insights that link ISC deficiency to cuproptosis, as exemplified by the high sensitivity of SF3B1-mutated AMLs. We thus propose SF3B1 mutations as a biomarker for future copper ionophore-based therapies.
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Affiliation(s)
- Céline Moison
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Deanne Gracias
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Julie Schmitt
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Simon Girard
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Jean-François Spinella
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Simon Fortier
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Isabel Boivin
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | | | - Bounkham Thavonekham
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Tara MacRae
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Nadine Mayotte
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Mark Wittman
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA, USA
| | - James Carmichael
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA, USA
| | - Réjean Ruel
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Chemistry, Université de Montréal, Montréal, Canada
| | - Josée Hébert
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Division of Hematology-Oncology and Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Chemistry, Université de Montréal, Montréal, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Division of Hematology-Oncology and Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
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2
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Mader P, Mendoza-Sanchez R, Iqbal A, Dong A, Dobrovetsky E, Corless VB, Liew SK, Houliston SR, De Freitas RF, Smil D, Sena CCD, Kennedy S, Diaz DB, Wu H, Dombrovski L, Allali-Hassani A, Min J, Schapira M, Vedadi M, Brown PJ, Santhakumar V, Yudin AK, Arrowsmith CH. Identification and characterization of the first fragment hits for SETDB1 Tudor domain. Bioorg Med Chem 2019; 27:3866-3878. [PMID: 31327677 DOI: 10.1016/j.bmc.2019.07.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 11/26/2022]
Abstract
SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the Tandem Tudor Domain (TTD) of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.
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Affiliation(s)
- Pavel Mader
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | | | - Aman Iqbal
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Elena Dobrovetsky
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | | | - Sean K Liew
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Scott R Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | | | - David Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Carlo C Dela Sena
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Steven Kennedy
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Diego B Diaz
- Department of Chemistry, University of Toronto, Toronto, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | | | | | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | | | - Andrei K Yudin
- Department of Chemistry, University of Toronto, Toronto, Canada.
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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3
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Corless VB, Holownia A, Foy H, Mendoza-Sanchez R, Adachi S, Dudding T, Yudin AK. Synthesis of α-Borylated Ketones by Regioselective Wacker Oxidation of Alkenylboronates. Org Lett 2018; 20:5300-5303. [DOI: 10.1021/acs.orglett.8b02234] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victoria B. Corless
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Aleksandra Holownia
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Hayden Foy
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catherines, ON L2S 3A1, Canada
| | - Rodrigo Mendoza-Sanchez
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Shinya Adachi
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Travis Dudding
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catherines, ON L2S 3A1, Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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4
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Mendoza-Sanchez R, Corless VB, Nguyen QNN, Bergeron-Brlek M, Frost J, Adachi S, Tantillo DJ, Yudin AK. Cyclols Revisited: Facile Synthesis of Medium-Sized Cyclic Peptides. Chemistry 2017; 23:13319-13322. [PMID: 28771904 DOI: 10.1002/chem.201703616] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Indexed: 12/21/2022]
Abstract
Medium-sized rings, particularly the corresponding cyclic peptides, are challenging synthetic targets. In the present study, we report an approach to medium-sized cyclic peptides through targeted formation and collapse of cyclol intermediates. This methodology operates on β-amino imides derived from 2,5-diketopiperazines and offers a straightforward transition from frequently examined scaffolds in drug discovery to a rarely visited class of medium-sized rings.
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Affiliation(s)
- Rodrigo Mendoza-Sanchez
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Victoria B Corless
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Q Nhu N Nguyen
- Department of Chemistry, University of California Davis, 1 Shields Avenue, Davis, CA, USA
| | - Milan Bergeron-Brlek
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - John Frost
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Shinya Adachi
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Dean J Tantillo
- Department of Chemistry, University of California Davis, 1 Shields Avenue, Davis, CA, USA
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
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5
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Kaldas SJ, O'Keefe KTV, Mendoza-Sanchez R, Yudin AK. Frontispiece: Amphoteric Borylketenimines: Versatile Intermediates in the Synthesis of Borylated Heterocycles. Chemistry 2017. [DOI: 10.1002/chem.201784162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sherif J. Kaldas
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Kowan T. V. O'Keefe
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Rodrigo Mendoza-Sanchez
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
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Kaldas SJ, O'Keefe KTV, Mendoza-Sanchez R, Yudin AK. Amphoteric Borylketenimines: Versatile Intermediates in the Synthesis of Borylated Heterocycles. Chemistry 2017; 23:9711-9715. [DOI: 10.1002/chem.201702008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Sherif J. Kaldas
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Kowan T. V. O'Keefe
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Rodrigo Mendoza-Sanchez
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
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Mendoza-Sanchez R, Cotnoir-White D, Kulpa J, Jutras I, Pottel J, Moitessier N, Mader S, Gleason JL. Design, synthesis and evaluation of antiestrogen and histone deacetylase inhibitor molecular hybrids. Bioorg Med Chem 2015; 23:7597-606. [DOI: 10.1016/j.bmc.2015.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/28/2015] [Accepted: 11/05/2015] [Indexed: 01/28/2023]
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Therrien E, Englebienne P, Arrowsmith AG, Mendoza-Sanchez R, Corbeil CR, Weill N, Campagna-Slater V, Moitessier N. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery. J Chem Inf Model 2011; 52:210-24. [PMID: 22133077 DOI: 10.1021/ci2004779] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.
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Affiliation(s)
- Eric Therrien
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, QC, Canada H3A 2K6
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