1
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Ding M, Bell C, Willis MC. The Modular Synthesis of Sulfondiimidoyl Fluorides and their Application to Sulfondiimidamide and Sulfondiimine Synthesis. Angew Chem Int Ed Engl 2024; 63:e202409240. [PMID: 38923337 DOI: 10.1002/anie.202409240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 06/28/2024]
Abstract
A modular synthesis of sulfondiimidoyl fluorides-the double aza-analogues of sulfonyl fluorides-allowing variation of the carbon and both nitrogen-substituents is reported. The chemistry uses readily available organometallic reagents, commercial sulfinylamines, simple electrophiles, and N-fluorobenzenesulfonimide (NFSI), as the starting materials. The reactions are broad in scope, efficient, and scalable. We show that the sulfondiimidoyl fluoride products can be combined with amines to provide sulfondiimidamides, and with organolithium reagents to provide sulfondiimines, and that reactivity in these transformations can be modulated by variation of the N-substituents.
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Affiliation(s)
- Mingyan Ding
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Charles Bell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Michael C Willis
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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2
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Schnaider L, Tan S, Singh PR, Capuano F, Scott AJ, Hambley R, Lu L, Yang H, Wallace EJ, Jo H, DeGrado WF. SuFEx Chemistry Enables Covalent Assembly of a 280-kDa 18-Subunit Pore-Forming Complex. J Am Chem Soc 2024; 146:25047-25057. [PMID: 39190920 DOI: 10.1021/jacs.4c07920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Proximity-enhanced chemical cross-linking is an invaluable tool for probing protein-protein interactions and enhancing the potency of potential peptide and protein drugs. Here, we extend this approach to covalently stabilize large macromolecular assemblies. We used SuFEx chemistry to covalently stabilize an 18-subunit pore-forming complex, CsgG:CsgF, consisting of nine CsgG membrane protein subunits that noncovalently associate with nine CsgF peptides. Derivatives of the CsgG:CsgF pore have been used for DNA sequencing, which places high demands on the structural stability and homogeneity of the complex. To increase the robustness of the pore, we designed and synthesized derivatives of CsgF-bearing sulfonyl fluorides, which react with CsgG in very high yield to form a covalently stabilized CsgG:CsgF complex. The resulting pores formed highly homogeneous channels when added to artificial membranes. The high yield and rapid reaction rate of the SuFEx reaction prompted molecular dynamics simulations, which revealed that the SO2F groups in the initially formed complex are poised for nucleophilic reaction with a targeted Tyr. These results demonstrate the utility of SuFEx chemistry to structurally stabilize very large (here, 280 kDa) assemblies.
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Affiliation(s)
- Lee Schnaider
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Sophia Tan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | | | | | | | | | - Lei Lu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - Hyunjun Yang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | | | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94143, United States
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94143, United States
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3
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Ábrányi-Balogh P, Bajusz D, Orgován Z, Keeley AB, Petri L, Péczka N, Szalai TV, Pálfy G, Gadanecz M, Grant EK, Imre T, Takács T, Ranđelović I, Baranyi M, Marton A, Schlosser G, Ashraf QF, de Araujo ED, Karancsi T, Buday L, Tóvári J, Perczel A, Bush JT, Keserű GM. Mapping protein binding sites by photoreactive fragment pharmacophores. Commun Chem 2024; 7:168. [PMID: 39085342 PMCID: PMC11292009 DOI: 10.1038/s42004-024-01252-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024] Open
Abstract
Fragment screening is a popular strategy of generating viable chemical starting points especially for challenging targets. Although fragments provide a better coverage of chemical space and they have typically higher chance of binding, their weak affinity necessitates highly sensitive biophysical assays. Here, we introduce a screening concept that combines evolutionary optimized fragment pharmacophores with the use of a photoaffinity handle that enables high hit rates by LC-MS-based detection. The sensitivity of our screening protocol was further improved by a target-conjugated photocatalyst. We have designed, synthesized, and screened 100 diazirine-tagged fragments against three benchmark and three therapeutically relevant protein targets of different tractability. Our therapeutic targets included a conventional enzyme, the first bromodomain of BRD4, a protein-protein interaction represented by the oncogenic KRasG12D protein, and the yet unliganded N-terminal domain of the STAT5B transcription factor. We have discovered several fragment hits against all three targets and identified their binding sites via enzymatic digestion, structural studies and modeling. Our results revealed that this protocol outperforms screening traditional fully functionalized and photoaffinity fragments in better exploration of the available binding sites and higher hit rates observed for even difficult targets.
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Affiliation(s)
- Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Orgován
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Aaron B Keeley
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Nikolett Péczka
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Tibor Viktor Szalai
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology & HUN-REN-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - Márton Gadanecz
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Laboratory of Structural Chemistry and Biology & HUN-REN-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | | | - Tímea Imre
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- MS Metabolomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Takács
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Signal Transduction and Functional Genomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ivan Ranđelović
- National Tumor Biology Laboratory and Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
- KINETO Lab Ltd, Budapest, Hungary
| | - Marcell Baranyi
- KINETO Lab Ltd, Budapest, Hungary
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - András Marton
- Department of Chemical and Environmental Process Engineering, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Waters Research Center, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Eötvös Loránd University, Budapest, Hungary
| | - Qirat F Ashraf
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Elvin D de Araujo
- Centre for Medicinal Chemistry, University of Toronto at Mississauga, Mississauga, ON, Canada
| | - Tamás Karancsi
- Department of Chemical and Environmental Process Engineering, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
- Waters Research Center, Budapest, Hungary
| | - László Buday
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Signal Transduction and Functional Genomics Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - József Tóvári
- National Tumor Biology Laboratory and Department of Experimental Pharmacology, National Institute of Oncology, Budapest, Hungary
| | - András Perczel
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Laboratory of Structural Chemistry and Biology & HUN-REN-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | | | - György M Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
- National Drug Research and Development Laboratory, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
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4
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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5
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Hong J, Li C, Zhao K, Wang X, Feng R, Chen X, Wei C, Gong X, Zheng F, Zheng C. Stereoselective Fluorosulfonylation of Vinylboronic Acids for ( E)-Vinyl Sulfonyl Fluorides with Copper Participation. Org Lett 2024; 26:2332-2337. [PMID: 38478713 DOI: 10.1021/acs.orglett.4c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
A practical synthetic method for the synthesis of vinyl sulfonyl fluorides through copper-promoted direct fluorosulfonylation has been developed. The reaction of the vinylboronic acids with DABSO and then NFSI is performed under mild reaction conditions. This transformation efficiently affords aryl or alkyl vinyl sulfonyl fluorides with good reaction yields, exclusive E-configuration, broad substrate scope, excellent compatibility, and operational simplicity.
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Affiliation(s)
- Jianquan Hong
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Chunxiang Li
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Kui Zhao
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Xiaoyu Wang
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Ruilong Feng
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Xifei Chen
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Chongbin Wei
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Xinxin Gong
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Feng Zheng
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Changge Zheng
- Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
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6
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Tang G, Wang W, Zhu C, Huang H, Chen P, Wang X, Xu M, Sun J, Zhang CJ, Xiao Q, Gao L, Zhang ZM, Yao SQ. Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development. Angew Chem Int Ed Engl 2024; 63:e202316394. [PMID: 38248139 DOI: 10.1002/anie.202316394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/23/2024]
Abstract
Advances in targeted covalent inhibitors (TCIs) have been made by using lysine-reactive chemistries. Few aminophiles possessing balanced reactivity/stability for the development of cell-active TCIs are however available. We report herein lysine-reactive activity-based probes (ABPs; 2-14) based on the chemistry of aryl fluorosulfates (ArOSO2 F) capable of global reactivity profiling of the catalytic lysine in human kinome from mammalian cells. We concurrently developed reversible covalent ABPs (15/16) by installing salicylaldehydes (SA) onto a promiscuous kinase-binding scaffold. The stability and amine reactivity of these probes exhibited a broad range of tunability. X-ray crystallography and mass spectrometry (MS) confirmed the successful covalent engagement between ArOSO2 F on 9 and the catalytic lysine of SRC kinase. Chemoproteomic studies enabled the profiling of >300 endogenous kinases, thus providing a global landscape of ligandable catalytic lysines of the kinome. By further introducing these aminophiles into VX-680 (a noncovalent inhibitor of AURKA kinase), we generated novel lysine-reactive TCIs that exhibited excellent in vitro potency and reasonable cellular activities with prolonged residence time. Our work serves as a general guide for the development of lysine-reactive ArOSO2 F-based TCIs.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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7
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Anderson JM, Poole DL, Cook GC, Murphy JA, Measom ND. Organometallic Bridge Diversification of Bicyclo[1.1.1]pentanes. Chemistry 2024; 30:e202304070. [PMID: 38117748 DOI: 10.1002/chem.202304070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/22/2023]
Abstract
Bicyclo[1.1.1]pentane (BCP) derivatives have attracted significant recent interest in drug discovery as alkyne, tert-butyl and arene bioisosteres, where their incorporation is frequently associated with increased compound solubility and metabolic stability. While strategies for functionalisation of the bridgehead (1,3) positions are extensively developed, platforms allowing divergent substitution at the bridge (2,4,5) positions remain limited. Recent reports have introduced 1-electron strategies for arylation and incorporation of a small range of other substituents, but are limited in terms of scope, yields or practical complexity. Herein, we show the synthesis of diverse 1,2,3-trifunctionalised BCPs through lithium-halogen exchange of a readily accessible BCP bromide. When coupled with medicinally relevant product derivatisations, our developed 2-electron "late stage" approach provides rapid and straightforward access to unprecedented BCP structural diversity (>20 hitherto-unknown motifs reported). Additionally, we describe a method for the synthesis of enantioenriched "chiral-at-BCP" bicyclo[1.1.1]pentanes through a novel stereoselective bridgehead desymmetrisation.
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Affiliation(s)
- Joseph M Anderson
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, UK, G1 1XL
| | - Darren L Poole
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
| | - Gemma C Cook
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
| | - John A Murphy
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, UK, G1 1XL
| | - Nicholas D Measom
- Medicinal Chemistry, GSK, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, UK, SG1 2NY
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8
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Fleetwood TD, Kerr WJ, Mason J. Copper-Mediated N-Trifluoromethylation of O-Benzoylhydroxylamines. Chemistry 2024; 30:e202303314. [PMID: 38018464 PMCID: PMC10952365 DOI: 10.1002/chem.202303314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
The use of trifluoromethyl containing compounds is well established within medicinal chemistry, with a range of approved drugs containing C-CF3 and O-CF3 moieties. However, the utilisation of the N-CF3 functional group remains relatively unexplored. This may be attributed to the challenging synthesis of this unit, with many current methods employing harsh conditions or less accessible reagents. A robust methodology for the N-trifluoromethylation of secondary amines has been developed, which employs an umpolung strategy in the form of a copper-catalysed electrophilic amination. The method is operationally simple, uses mild, inexpensive reagents, and has been used to synthesise a range of novel, structurally complex N-CF3 containing compounds.
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Affiliation(s)
- Thomas D. Fleetwood
- Medicinal ChemistryGSK Medicines Research CentreGunnels Wood RoadSG1 2NYStevenageEnglandU.K.
- Department of Pure and Applied ChemistryUniversity of StrathclydeG1 1XLGlasgowScotlandU.K.
| | - William J. Kerr
- Department of Pure and Applied ChemistryUniversity of StrathclydeG1 1XLGlasgowScotlandU.K.
| | - Joseph Mason
- Medicinal ChemistryGSK Medicines Research CentreGunnels Wood RoadSG1 2NYStevenageEnglandU.K.
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9
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Grob NM, Remarcik C, Rössler SL, Wong JYK, Wang JCK, Tao J, Smith CL, Loas A, Buchwald SL, Eaton DL, López MP, Pentelute BL. Electrophile Scanning Reveals Reactivity Hotspots for the Design of Covalent Peptide Binders. ACS Chem Biol 2024; 19:101-109. [PMID: 38069818 DOI: 10.1021/acschembio.3c00538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Protein-protein interactions (PPIs) are intriguing targets in drug discovery and development. Peptides are well suited to target PPIs, which typically present with large surface areas lacking distinct features and deep binding pockets. To improve binding interactions with these topologies and advance the development of PPI-focused therapeutics, potential ligands can be equipped with electrophilic groups to enable binding through covalent mechanisms of action. We report a strategy termed electrophile scanning to identify reactivity hotspots in a known peptide ligand and demonstrate its application in a model PPI. Cysteine mutants of a known ligand are used to install protein-reactive modifiers via a palladium oxidative addition complex (Pd-OAC). Reactivity hotspots are revealed by cross-linking reactions with the target protein under physiological conditions. In a model PPI with the 9-mer peptide antigen VL9 and major histocompatibility complex (MHC) class I protein HLA-E, we identify two reactivity hotspots that afford up to 87% conversion to the protein-peptide conjugate within 4 h. The reactions are specific to the target protein in vitro and dependent on the peptide sequence. Moreover, the cross-linked peptide successfully inhibits molecular recognition of HLA-E by CD94-NKG2A possibly due to structural changes enacted at the PPI interface. The results illustrate the potential application of electrophile scanning as a tool for rapid discovery and development of covalent peptide binders.
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Affiliation(s)
- Nathalie M Grob
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Clint Remarcik
- Calico Life Sciences LLC, San Francisco, California 94080, United States of America
| | - Simon L Rössler
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Jeffrey Y K Wong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - John C K Wang
- Calico Life Sciences LLC, San Francisco, California 94080, United States of America
| | - Jason Tao
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Corey L Smith
- AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States of America
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
| | - Dan L Eaton
- Calico Life Sciences LLC, San Francisco, California 94080, United States of America
| | | | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States of America
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10
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Zhang Y, Zhang J, Li M, Qiao Y, Wang W, Ma L, Liu K. Target discovery of bioactive natural products with native-compound-coupled CNBr-activated Sepharose 4B beads (NCCB): Applications, mechanisms and outlooks. Bioorg Med Chem 2023; 96:117483. [PMID: 37951136 DOI: 10.1016/j.bmc.2023.117483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 11/13/2023]
Abstract
Natural products (NPs) represent a treasure trove for drug discovery and development due to their chemical structural diversity and a broad spectrum of biological activities. Uncovering the biological targets and understanding their molecular mechanism of actions are crucial steps in the development of clinical therapeutics. However, the structural complexity of NPs and intricate nature of biological system present formidable challenges in target identification of NPs. Although significant advances have been made in the development of new chemical tools, these methods often require high levels of synthetic skills for preparing chemical probes. This can be costly and time-consuming relaying on operationally complicated procedures and instruments. In recent efforts, we and others have successfully developed an operationally simple and practical chemical tool known as native-compound-coupled CNBr-activated Sepharose 4B beads (NCCB) for NP target identification. In this approach, a native compound readily reacts with commercial CNBr-activated Sepharose 4B beads with a process that is easily performed in any biology laboratory. Based on NCCB, our group has identified the direct targets of more than 60 NPs. In this review, we will elucidate the application scopes, including flavonoids, quinones, terpenoids and others, characteristics, chemical mechanisms, procedures, advantages, disadvantages, and future directions of NCCB in specific target discovery.
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Affiliation(s)
- Yueteng Zhang
- Basic Medical Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Junjie Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Menglong Li
- Basic Medical Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yan Qiao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wei Wang
- Departments of Pharmacology & Toxicology and Chemistry & Biochemistry, and BIO5 Institute, University of Arizona, Tucson, AZ 85721, United States
| | - Lu Ma
- Basic Medical Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Kangdong Liu
- Basic Medical Research Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China; Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
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11
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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12
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Cosgrove B, Grant EK, Bertrand S, Down KD, Somers DO, P Evans J, Tomkinson NCO, Barker MD. Covalent targeting of non-cysteine residues in PI4KIIIβ. RSC Chem Biol 2023; 4:1111-1122. [PMID: 38033723 PMCID: PMC10685791 DOI: 10.1039/d3cb00142c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 12/02/2023] Open
Abstract
The synthesis and characterisation of fluorosulfate covalent inhibitors of the lipid kinase PI4KIIIβ is described. The conserved lysine residue located within the ATP binding site was targeted, and optimised compounds based upon reversible inhibitors with good activity and physicochemical profile showed strong reversible interactions and slow onset times for the covalent inhibition, resulting in an excellent selectivity profile for the lipid kinase target. X-Ray crystallography demonstrated a distal tyrosine residue could also be targeted using a fluorosulfate strategy. Combination of this knowledge showed that a dual covalent inhibitor could be developed which reveals potential in addressing the challenges associated with drug resistant mutations.
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Affiliation(s)
- Brett Cosgrove
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
- Department of Pure and Applied Chemistry, University of Strathclyde Glasgow G1 1XL UK
| | - Emma K Grant
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Sophie Bertrand
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Kenneth D Down
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Don O Somers
- Structural and Biophysical Science, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - John P Evans
- Screening, Profiling and Mechanistic Biology, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | | | - Michael D Barker
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
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13
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Lake BM, Rullo AF. Offsetting Low-Affinity Carbohydrate Binding with Covalency to Engage Sugar-Specific Proteins for Tumor-Immune Proximity Induction. ACS CENTRAL SCIENCE 2023; 9:2064-2075. [PMID: 38033792 PMCID: PMC10683482 DOI: 10.1021/acscentsci.3c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Indexed: 12/02/2023]
Abstract
Carbohydrate-binding receptors are often used by the innate immune system to potentiate inflammation, target endocytosis/destruction, and adaptive immunity (e.g., CD206, DC-SIGN, MBL, and anticarbohydrate antibodies). To access this class of receptors for cancer immunotherapy, a growing repertoire of bifunctional proximity-inducing therapeutics use high-avidity multivalent carbohydrate binding domains to offset the intrinsically low affinity associated with monomeric carbohydrate-protein binding interactions (Kd ≈ 10-3-10-6 M). For applications aimed at recruiting anticarbohydrate antibodies to tumor cells, large synthetic scaffolds are used that contain both a tumor-binding domain (TBD) and a multivalent antibody-binding domain (ABD) comprising multiple l-rhamnose monosaccharides. This allows for stable bridging between tumor cells and antibodies, which activates tumoricidal immune function. Problematically, such multivalent macromolecules can face limitations including synthetic and/or structural complexity and the potential for off-target immune engagement. We envisioned that small bifunctional "proximity-inducing" molecules containing a low-affinity monovalent ABD could efficiently engage carbohydrate-binding receptors for tumor-immune proximity by coupling weak binding with covalent engagement. Typical covalent drugs and electrophilic chimeras use high-affinity ligands to promote the fast covalent engagement of target proteins (i.e., large kinact/KI), driven by a favorably small KI for binding. We hypothesized the much less favorable KI associated with carbohydrate-protein binding interactions can be offset by a favorably large kinact for the covalent labeling step. In the current study, we test this hypothesis in the context of a model system that uses rhamnose-specific antibodies to induce tumor-immune proximity and tumoricidal function. We discovered that synthetic chimeric molecules capable of preorganizing an optimal electrophile (i.e., SuFEx vs activated ester) for protein engagement can rapidly covalently engage natural sources of antirhamnose antibody using only a single low-affinity rhamnose monosaccharide ABD. Strikingly, we observe chimeric molecules lacking an electrophile, which can only noncovalently bind the antibody, completely lack tumoricidal function. This is in stark contrast to previous work targeting small molecule hapten and peptide-specific antibodies. Our findings underscore the utility of covalency as a strategy to engage low-affinity carbohydrate-specific proteins for tumor-immune proximity induction.
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Affiliation(s)
- Benjamin
P. M. Lake
- Department
of Medicine, McMaster Immunology Research Center, Center
for Discovery in Cancer Research, Department of Biochemistry and Biomedical
Sciences, and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton Ontario, Canada
| | - Anthony F. Rullo
- Department
of Medicine, McMaster Immunology Research Center, Center
for Discovery in Cancer Research, Department of Biochemistry and Biomedical
Sciences, and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton Ontario, Canada
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14
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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15
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Tang G, Wang W, Wang X, Ding K, Ngan SC, Chen JY, Sze SK, Gao L, Yuan P, Lu X, Yao SQ. Cell-active, irreversible covalent inhibitors that selectively target the catalytic lysine of EGFR by using fluorosulfate-based SuFEx chemistry. Eur J Med Chem 2023; 259:115671. [PMID: 37499291 DOI: 10.1016/j.ejmech.2023.115671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
EGFR signaling is involved in multiple cellular processes including cell proliferation, differentiation and development, making this protein kinase one of the most valuable drug targets for the treatment of non-small cell lung carcinomas (NSCLC). Herein, we describe the design and synthesis of a series of potential covalent inhibitors targeting the catalytically conserved lysine (K745) of EGFR on the basis of Erlotinib, an FDA-approved first-generation EGFR drug. Different amine-reactive electrophiles were introduced at positions on the Erlotinib scaffold proximal to K745 in EGFR. The optimized compound 26 (as well as its close analog 30), possessing a novel arylfluorosulfate group (ArOSO2F), showed excellent in vitro potency (as low as 0.19 nM in independent IC50 determination) and selectivity against EGFR and many of its drug-resistant mutants. Both intact protein mass spectrometry (MS) and site-mapping analysis revealed that compound 26 covalently bound to EGFR at K745 through the formation of a sulfamate. In addition, compound 26 displayed good anti-proliferative potency against EGFR-overexpressing HCC827 cells by inhibiting endogenous EGFR autophosphorylation. The pharmacokinetic studies of compound 26 demonstrated the druggable potential of other ArOSO2F-containing compounds. Finally, competitive activity-based protein profiling (ABPP), cellular thermal shift assay (CETSA), as well as cellular wash-out experiments, all showed compound 26 to be the first cell-active, fluorosulfate-based targeted covalent inhibitor (TCI) of protein kinases capable of covalently engaging the catalytically conserved lysine of its target in live mammalian cells.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China; State Key Laboratory of Bioorganic & Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Jiao-Yu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Siu Kwan Sze
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China.
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore.
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16
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Aatkar A, Vuorinen A, Longfield OE, Gilbert K, Peltier-Heap R, Wagner CD, Zappacosta F, Rittinger K, Chung CW, House D, Tomkinson NCO, Bush JT. Efficient Ligand Discovery Using Sulfur(VI) Fluoride Reactive Fragments. ACS Chem Biol 2023; 18:1926-1937. [PMID: 37084287 PMCID: PMC10510102 DOI: 10.1021/acschembio.3c00034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Sulfur(VI) fluorides (SFs) have emerged as valuable electrophiles for the design of "beyond-cysteine" covalent inhibitors and offer potential for expansion of the liganded proteome. Since SFs target a broad range of nucleophilic amino acids, they deliver an approach for the covalent modification of proteins without requirement for a proximal cysteine residue. Further to this, libraries of reactive fragments present an innovative approach for the discovery of ligands and tools for proteins of interest by leveraging a breadth of mass spectrometry analytical approaches. Herein, we report a screening approach that exploits the unique properties of SFs for this purpose. Libraries of SF-containing reactive fragments were synthesized, and a direct-to-biology workflow was taken to efficiently identify hit compounds for CAII and BCL6. The most promising hits were further characterized to establish the site(s) of covalent modification, modification kinetics, and target engagement in cells. Crystallography was used to gain a detailed molecular understanding of how these reactive fragments bind to their target. It is anticipated that this screening protocol can be used for the accelerated discovery of "beyond-cysteine" covalent inhibitors.
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Affiliation(s)
- Arron Aatkar
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Aini Vuorinen
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
| | - Oliver E. Longfield
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Katharine Gilbert
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Rachel Peltier-Heap
- GSK, South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Craig D. Wagner
- GSK, South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | | | | | - Chun-wa Chung
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | - David House
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
| | - Nicholas C. O. Tomkinson
- Department
of Pure and Applied Chemistry, University
of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Jacob T. Bush
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
- The
Francis Crick Institute, London NW1 1AT, U.K.
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17
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White MEH, Gil J, Tate EW. Proteome-wide structural analysis identifies warhead- and coverage-specific biases in cysteine-focused chemoproteomics. Cell Chem Biol 2023; 30:828-838.e4. [PMID: 37451266 DOI: 10.1016/j.chembiol.2023.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/20/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Covalent drug discovery has undergone a resurgence over the past two decades and reactive cysteine profiling has emerged in parallel as a platform for ligand discovery through on- and off-target profiling; however, the scope of this approach has not been fully explored at the whole-proteome level. We combined AlphaFold2-predicted side-chain accessibilities for >95% of the human proteome with a meta-analysis of eighteen public cysteine profiling datasets, totaling 44,187 unique cysteine residues, revealing accessibility biases in sampled cysteines primarily dictated by warhead chemistry. Analysis of >3.5 million cysteine-fragment interactions further showed that hit elaboration and optimization drives increased bias against buried cysteine residues. Based on these data, we suggest that current profiling approaches cover a small proportion of potential ligandable cysteine residues and propose future directions for increasing coverage, focusing on high-priority residues and depth. All analysis and produced resources are freely available and extendable to other reactive amino acids.
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Affiliation(s)
- Matthew E H White
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; The Francis Crick Institute, London NW1 1AT, UK.
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18
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Petri L, Ábrányi-Balogh P, Csorba N, Keeley A, Simon J, Ranđelović I, Tóvári J, Schlosser G, Szabó D, Drahos L, Keserű GM. Activation-Free Sulfonyl Fluoride Probes for Fragment Screening. Molecules 2023; 28:molecules28073042. [PMID: 37049805 PMCID: PMC10096327 DOI: 10.3390/molecules28073042] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
SuFEx chemistry is based on the unique reactivity of the sulfonyl fluoride group with a range of nucleophiles. Accordingly, sulfonyl fluorides label multiple nucleophilic amino acid residues, making these reagents popular in both chemical biology and medicinal chemistry applications. The reactivity of sulfonyl fluorides nominates this warhead chemotype as a candidate for an external, activation-free general labelling tag. Here, we report the synthesis and characterization of a small sulfonyl fluoride library that yielded the 3-carboxybenzenesulfonyl fluoride warhead for tagging tractable targets at nucleophilic residues. Based on these results, we propose that coupling diverse fragments to this warhead would result in a library of sulfonyl fluoride bits (SuFBits), available for screening against protein targets. SuFBits will label the target if it binds to the core fragment, which facilitates the identification of weak fragments by mass spectrometry.
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Affiliation(s)
- László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Noémi Csorba
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - József Simon
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Research Centre for Natural Sciences, MS Metabolomics Research Group, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | | | - József Tóvári
- Department of Experimental Pharmacology and National Tumor Biology Laboratory POB 21, National Institute of Oncology, 1525 Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, 1117 Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, 1117 Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
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19
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Faucher FF, Abegg D, Ipock P, Adibekian A, Lovell S, Bogyo M. Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.529022. [PMID: 36824748 PMCID: PMC9949109 DOI: 10.1101/2023.02.17.529022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Macrocyclic peptides are attractive for chemoproteomic applications due to their modular synthesis and potential for high target selectivity. We describe a solid phase synthesis method for the efficient generation of libraries of small macrocycles that contain an electrophile and alkyne handle. The modular synthesis produces libraries that can be directly screened using simple SDS-PAGE readouts and then optimal lead molecules applied to proteomic analysis. We generated a library of 480 macrocyclic peptides containing the weakly reactive fluorosulfate (OSF) electrophile. Initial screening of a subset of the library containing each of the various diversity elements identified initial molecules of interest. The corresponding positional and confirmational isomers were then screened to select molecules that showed specific protein labeling patterns that were dependent on the probe structure. The most promising hits were applied to standard chemoproteomic workflows to identify protein targets. Our results demonstrate the feasibility of rapid, on-resin synthesis of diverse macrocyclic electrophiles to generate new classes of covalent ligands.
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Affiliation(s)
| | - Daniel Abegg
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | | | - Alexander Adibekian
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Scott Lovell
- Current Address: Department of Life Sciences, University of Bath, Bath BA2 7AX, U.K
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
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20
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Arafet K, Scalvini L, Galvani F, Martí S, Moliner V, Mor M, Lodola A. Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents. J Chem Inf Model 2023; 63:1301-1312. [PMID: 36762429 PMCID: PMC9976278 DOI: 10.1021/acs.jcim.2c01586] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Targeted covalent inhibitors hold promise for drug discovery, particularly for kinases. Targeting the catalytic lysine of epidermal growth factor receptor (EGFR) has attracted attention as a new strategy to overcome resistance due to the emergence of C797S mutation. Sulfonyl fluoride derivatives able to inhibit EGFRL858R/T790M/C797S by sulfonylation of Lys745 have been reported. However, atomistic details of this process are still poorly understood. Here, we describe the mechanism of inhibition of an innovative class of compounds that covalently engage the catalytic lysine of EGFR, through a sulfur(VI) fluoride exchange (SuFEx) process, with the help of hybrid quantum mechanics/molecular mechanics (QM/MM) and path collective variables (PCVs) approaches. Our simulations identify the chemical determinants accounting for the irreversible activity of agents targeting Lys745 and provide hints for the further optimization of sulfonyl fluoride agents.
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Affiliation(s)
- Kemel Arafet
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy,BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Laura Scalvini
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Francesca Galvani
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy
| | - Sergio Martí
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Vicent Moliner
- BioComp
Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castelló, Spain
| | - Marco Mor
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy,Microbiome
Research Hub, University of Parma, Parco Area delle Scienze 11/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I- 43124 Parma, Italy,. Phone: +39 0521 905062. Fax: +39 0521 905006
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Thomas RP, Grant EK, Dickinson ER, Zappacosta F, Edwards LJ, Hann MM, House D, Tomkinson NCO, Bush JT. Reactive fragments targeting carboxylate residues employing direct to biology, high-throughput chemistry. RSC Med Chem 2023; 14:671-679. [PMID: 37122547 PMCID: PMC10131605 DOI: 10.1039/d2md00453d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
We present a carboxylate-targeting reactive fragment screening platform using 2-aryl-5-carboxytetrazole (ACT) as the photoreactive functionality. This work will provide a simple accessible method to rapidly discover tool molecules to interrogate important biological targets.
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Affiliation(s)
- Ross P. Thomas
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Emma K. Grant
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | | | | | - Lee J. Edwards
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Michael M. Hann
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - David House
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Nicholas C. O. Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Jacob T. Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
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