1
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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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2
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Jiang Z, Tang Y, Lu J, Xu C, Niu Y, Zhang G, Yang Y, Cheng X, Tong L, Chen Z, Tang B. Identification of sulfhydryl-containing proteins and further evaluation of the selenium-tagged redox homeostasis-regulating proteins. Redox Biol 2024; 69:102969. [PMID: 38064764 PMCID: PMC10755098 DOI: 10.1016/j.redox.2023.102969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 01/01/2024] Open
Abstract
Chemoproteomic profiling of sulfhydryl-containing proteins has consistently been an attractive research hotspot. However, there remains a dearth of probes that are specifically designed for sulfhydryl-containing proteins, possessing sufficient reactivity, specificity, distinctive isotopic signature, as well as efficient labeling and evaluation capabilities for proteins implicated in the regulation of redox homeostasis. Here, the specific selenium-containing probes (Se-probes) in this work displayed high specificity and reactivity toward cysteine thiols on small molecules, peptides and purified proteins and showed very good competitive effect of proteins labeling in gel-ABPP. We identified more than 6000 candidate proteins. In TOP-ABPP, we investigated the peptide labeled by Se-probes, which revealed a distinct isotopic envelope pattern of selenium in both the primary and secondary mass spectra. This unique pattern can provide compelling evidence for identifying redox regulatory proteins and other target peptides. Furthermore, our examiation of post-translational modification (PTMs) of the cysteine site residues showed that oxidation PTMs was predominantly observed. We anticipate that Se-probes will enable broader and deeper proteome-wide profiling of sulfhydryl-containing proteins, provide an ideal tool for focusing on proteins that regulate redox homeostasis and advance the development of innovative selenium-based pharmaceuticals.
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Affiliation(s)
- Zhongyao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yue Tang
- Department of Emergency Medicine, Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, PR China.
| | - Jun Lu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Chang Xu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yaxin Niu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Guanglu Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Xiufen Cheng
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China.
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Minis-try of Education, Institute of Molecular and Nano Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan, 250014, PR China; Laoshan Laboratory, Qingdao, 266200, PR China.
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3
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Nao SC, Kong L, Chan DSH, Liu J, Huang LS, Wu L, Wu J, Wong CY, Wang W, Leung CH. Covalent inhibition of epidermal growth factor receptor using a long-lived iridium(III)-afatinib probe. Int J Biol Macromol 2024; 259:129211. [PMID: 38184034 DOI: 10.1016/j.ijbiomac.2024.129211] [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: 11/16/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
The overexpression and overactivation of epidermal growth factor receptor (EGFR) are frequently observed in human cancers, including squamous cell carcinoma and adenocarcinoma. In this study, a covalent EGFR probe was developed by conjugating afatinib to an iridium(III) scaffold. Complex 1 showed enhanced luminescence in living epidermoid squamous carcinoma A431 cells compared to other cell lines, via engaging EGFR as confirmed via CETSA and knockdown experiments. Moreover, complex 1 inhibited downstream targets of EGFR in cellulo with repression persisting after removal of the complex, indicating an irreversible mode of inhibition. Finally, complex 1 showed potent antiproliferative activity against A431 cells with comparable potency to afatinib alone. To our knowledge, complex 1 is the first EGFR covalent inhibitor based on an iridium scaffold reported in the literature, with the potential to be further explored as a theranostic agent in the future.
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Affiliation(s)
- Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Lingtan Kong
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China
| | - Daniel Shiu-Hin Chan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR
| | - Jianhua Liu
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China
| | - Le-Sheng Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Lei Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau
| | - Chun-Yuen Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR.
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau; Macao Centre for Research and Development in Chinese Medicine, University of Macau, Taipa, Macau; MoE Frontiers Science Centre for Precision Oncology, University of Macau, Taipa, Macau.
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4
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Goullieux M, Zoete V, Röhrig UF. Two-Step Covalent Docking with Attracting Cavities. J Chem Inf Model 2023; 63:7847-7859. [PMID: 38049143 PMCID: PMC10751798 DOI: 10.1021/acs.jcim.3c01055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 12/06/2023]
Abstract
Due to their various advantages, interest in the development of covalent drugs has been renewed in the past few years. It is therefore important to accurately describe and predict their interactions with biological targets by computer-aided drug design tools such as docking algorithms. Here, we report a covalent docking procedure for our in-house docking code Attracting Cavities (AC), which mimics the two-step mechanism of covalent ligand binding. Ligand binding to the protein cavity is driven by nonbonded interactions, followed by the formation of a covalent bond between the ligand and the protein through a chemical reaction. To test the performance of this method, we developed a diverse, high-quality, openly accessible re-docking benchmark set of 95 covalent complexes bound by 8 chemical reactions to 5 different reactive amino acids. Combination with structures from previous studies resulted in a set of 304 complexes, on which AC obtained a success rate (rmsd ≤ 2 Å) of 78%, outperforming two state-of-the-art covalent docking codes, genetic optimization for ligand docking (GOLD (66%)) and AutoDock (AD (35%)). Using a more stringent success criterion (rmsd ≤ 1.5 Å), AC reached a success rate of 71 vs 55% for GOLD and 26% for AD. We additionally assessed the cross-docking performance of AC on a set of 76 covalent complexes of the SARS-CoV-2 main protease. On this challenging test set of mainly small and highly solvent-exposed ligands, AC yielded success rates of 58 and 28% for re-docking and cross-docking, respectively, compared to 45 and 17% for GOLD.
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Affiliation(s)
- Mathilde Goullieux
- SIB
Swiss Institute of Bioinformatics, Molecular Modeling Group, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- SIB
Swiss Institute of Bioinformatics, Molecular Modeling Group, CH-1015 Lausanne, Switzerland
- Department
of Oncology UNIL-CHUV, Lausanne University, Ludwig Institute for Cancer Research
Lausanne Branch, CH-1066 Epalinges, Switzerland
| | - Ute F. Röhrig
- SIB
Swiss Institute of Bioinformatics, Molecular Modeling Group, CH-1015 Lausanne, Switzerland
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5
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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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6
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Spitzbarth B, Eelkema R. Chemical reaction networks based on conjugate additions on β'-substituted Michael acceptors. Chem Commun (Camb) 2023; 59:11174-11187. [PMID: 37529876 PMCID: PMC10508045 DOI: 10.1039/d3cc02126b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Over the last few decades, the study of more complex, chemical systems closer to those found in nature, and the interactions within those systems, has grown immensely. Despite great efforts, the need for new, versatile, and robust chemistry to apply in CRNs remains. In this Feature Article, we give a brief overview over previous developments in the field of systems chemistry and how β'-substituted Michael acceptors (MAs) can be a great addition to the systems chemist's toolbox. We illustrate their versatility by showcasing a range of examples of applying β'-substituted MAs in CRNs, both as chemical signals and as substrates, to open up the path to many applications ranging from responsive materials, to pathway control in CRNs, drug delivery, analyte detection, and beyond.
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Affiliation(s)
- Benjamin Spitzbarth
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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7
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Morese PA, Anthony N, Bodnarchuk M, Jennings C, Martin MP, Noble RA, Phillips N, Thomas HD, Wang LZ, Lister A, Noble MEM, Ward RA, Wedge SR, Stewart HL, Waring MJ. Targeting Cytotoxic Agents through EGFR-Mediated Covalent Binding and Release. J Med Chem 2023; 66:12324-12341. [PMID: 37647129 PMCID: PMC10510387 DOI: 10.1021/acs.jmedchem.3c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Indexed: 09/01/2023]
Abstract
A major drawback of cytotoxic chemotherapy is the lack of selectivity toward noncancerous cells. The targeted delivery of cytotoxic drugs to tumor cells is a longstanding goal in cancer research. We proposed that covalent inhibitors could be adapted to deliver cytotoxic agents, conjugated to the β-position of the Michael acceptor, via an addition-elimination mechanism promoted by covalent binding. Studies on model systems showed that conjugated 5-fluorouracil (5FU) could be released upon thiol addition in relevant time scales. A series of covalent epidermal growth factor receptor (EGFR) inhibitors were synthesized as their 5FU derivatives. Achieving the desired release of 5FU was demonstrated to depend on the electronics and geometry of the compounds. Mass spectrometry and NMR studies demonstrated an anilinoquinazoline acrylate ester conjugate bound to EGFR with the release of 5FU. This work establishes that acrylates can be used to release conjugated molecules upon covalent binding to proteins and could be used to develop targeted therapeutics.
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Affiliation(s)
- Pasquale A Morese
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Nahoum Anthony
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | | | - Claire Jennings
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Richard A Noble
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Nicole Phillips
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Huw D Thomas
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | | | - Andrew Lister
- Oncology iMed, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | | | - Stephen R Wedge
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Hannah L Stewart
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Michael J Waring
- Cancer Research Horizons Therapeutic Innovation, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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8
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Gayatri SK, Chhabra V, Kumar H, Sobhia ME. Identification of prospective covalent inhibitors for SARS-CoV-2 main protease using structure-based approach. J Biomol Struct Dyn 2023; 41:7913-7930. [PMID: 36200615 DOI: 10.1080/07391102.2022.2129453] [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: 03/08/2022] [Accepted: 09/16/2022] [Indexed: 10/10/2022]
Abstract
The rapid global spread of SARS-CoV-2 has recently caused havoc and forced the world into a state of the pandemic causing respiratory, gastrointestinal, hepatic, and neurologic diseases. It persistently, through mutation, develops into new variants of the virus that have appeared over time. As main protease (Mpro) is involved in proteolysis of two overlapping polyproteins pp1a and pp1ab to produce 16 non-structural proteins having a paramount factor in the virus replication that have a cysteine-histidine catalytic dyad. A computational approach, guiding a covalent docking as it offers higher potency, long duration of action and decreased drug resistance advantages over the conventional docking of the ligands on a catalytic dyad, is applied for SARS-CoV-2 main protease (Mpro) in this manuscript to divulge better molecules. Mpro active site contains Cys145 residue which act as a nucleophile and can donate its electron to an electrophilic molecule by interacting covalently. Furthermore, the ligand-protein complexes are allowed to simulate their dynamic studies to look into their time-based interaction stability and also, a parallel study of ADME properties for the hit molecules is also performed. Important insights from the studies revealed that the interactions are persistent and molecules may be considered for further optimization in clinical investigation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shenvi Kudchadker Gayatri
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - Vaishnavi Chhabra
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Mohali, Punjab, India
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9
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Pergu R, Shoba VM, Chaudhary SK, Munkanatta Godage DNP, Deb A, Singha S, Dhawa U, Singh P, Anokhina V, Singh S, Siriwardena SU, Choudhary A. Development and Applications of Chimera Platforms for Tyrosine Phosphorylation. ACS CENTRAL SCIENCE 2023; 9:1558-1566. [PMID: 37637727 PMCID: PMC10450875 DOI: 10.1021/acscentsci.3c00200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Indexed: 08/29/2023]
Abstract
Chimeric small molecules that induce post-translational modification (PTM) on a target protein by bringing it into proximity to a PTM-inducing enzyme are furnishing novel modalities to perturb protein function. Despite recent advances, such molecules are unavailable for a critical PTM, tyrosine phosphorylation. Furthermore, the contemporary design paradigm of chimeric molecules, formed by joining a noninhibitory binder of the PTM-inducing enzyme with the binder of the target protein, prohibits the recruitment of most PTM-inducing enzymes as their noninhibitory binders are unavailable. Here, we report two platforms to generate phosphorylation-inducing chimeric small molecules (PHICS) for tyrosine phosphorylation. We generate PHICS from both noninhibitory binders (scantily available, platform 1) and kinase inhibitors (abundantly available, platform 2) using cysteine-based group transfer chemistry. PHICS triggered phosphorylation on tyrosine residues in diverse sequence contexts and target proteins (e.g., membrane-associated, cytosolic) and displayed multiple bioactivities, including the initiation of a growth receptor signaling cascade and the death of drug-resistant cancer cells. These studies provide an approach to induce biologically relevant PTM and lay the foundation for pharmacologic PTM editing (i.e., induction or removal) of target proteins using abundantly available inhibitors of PTM-inducing or -erasing enzymes.
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Affiliation(s)
- Rajaiah Pergu
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Veronika M. Shoba
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Santosh K. Chaudhary
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | | | - Arghya Deb
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Santanu Singha
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Uttam Dhawa
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Prashant Singh
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Viktoriya Anokhina
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Sameek Singh
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Sachini U. Siriwardena
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Amit Choudhary
- Chemical
Biology and Therapeutics Science, Broad
Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
- Divisions
of Renal Medicine and Engineering, Brigham
and Women’s Hospital, Boston, Massachusetts 02115, United States
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10
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Lu H, Ye H, Zhang M, Liu Z, Zou H, You L. Photoswitchable dynamic conjugate addition-elimination reactions as a tool for light-mediated click and clip chemistry. Nat Commun 2023; 14:4015. [PMID: 37419874 DOI: 10.1038/s41467-023-39669-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 06/22/2023] [Indexed: 07/09/2023] Open
Abstract
Phototriggered click and clip reactions can endow chemical processes with high spatiotemporal resolution and sustainability, but are challenging with a limited scope. Herein we report photoswitchable reversible covalent conjugate addition-elimination reactions toward light-addressed modular covalent connection and disconnection. By coupling between photochromic dithienylethene switch and Michael acceptors, the reactivity of Michael reactions was tuned through closed-ring and open-ring forms of dithienylethene, allowing switching on and off dynamic exchange of a wide scope of thiol and amine nucleophiles. The breaking of antiaromaticity in transition states and enol intermediates of addition-elimination reactions provides the driving force for photoinduced change in kinetic barriers. To showcase the versatile application, light-mediated modification of solid surfaces, regulation of amphiphilic assemblies, and creation/degradation of covalent polymers on demand were achieved. The manipulation of dynamic click/clip reactions with light should set the stage for future endeavors, including responsive assemblies, biological delivery, and intelligent materials.
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Affiliation(s)
- Hanwei Lu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fuzhou, Fujian, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fuzhou, Fujian, China
| | - Meilan Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fuzhou, Fujian, China
| | - Zimu Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fuzhou, Fujian, China
| | - Hanxun Zou
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fuzhou, Fujian, China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 350002, Fuzhou, Fujian, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, 350002, Fuzhou, Fujian, China.
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11
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Yamane D, Tetsukawa R, Zenmyo N, Tabata K, Yoshida Y, Matsunaga N, Shindo N, Ojida A. Expanding the Chemistry of Dihaloacetamides as Tunable Electrophiles for Reversible Covalent Targeting of Cysteines. J Med Chem 2023. [PMID: 37393576 DOI: 10.1021/acs.jmedchem.3c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The choice of an appropriate electrophile is crucial in the design of targeted covalent inhibitors (TCIs). In this report, we systematically investigated the glutathione (GSH) reactivity of various haloacetamides and the aqueous stability of their thiol adducts. Our findings revealed that dihaloacetamides cover a broad range of GSH reactivity depending on the combination of the halogen atoms and the structure of the amine scaffold. Among the dihaloacetamides, dichloroacetamide (DCA) exhibited slightly lower GSH reactivity than chlorofluoroacetamide (CFA). The DCA-thiol adduct is readily hydrolyzed under aqueous conditions, but it can stably exist in the solvent-sequestered binding pocket of the protein. These reactivity profiles of DCA were successfully exploited in the design of TCIs targeting noncatalytic cysteines of KRASG12C and EGFRL858R/T790M. These inhibitors exhibited strong antiproliferative activities against cancer cells. Our findings provide valuable insights for designing dihaloacetamide-based reversible covalent inhibitors.
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Affiliation(s)
- Daiki Yamane
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ryo Tetsukawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoki Zenmyo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kaori Tabata
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuya Yoshida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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12
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Mahía A, Kiib AE, Nisavic M, Svenningsen EB, Palmfeldt J, Poulsen TB. α-Lactam Electrophiles for Covalent Chemical Biology. Angew Chem Int Ed Engl 2023; 62:e202304142. [PMID: 37114559 DOI: 10.1002/anie.202304142] [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: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 04/29/2023]
Abstract
Electrophilic groups are one of the key pillars of contemporary chemical biology and medicinal chemistry. For instance, 3-membered N-heterocyclic compounds-such as aziridines, azirines, and oxaziridines-possess unique electronic and structural properties which underlie their potential and applicability as covalent tools. The α-lactams are also members of this group of compounds, however, their utility within the field remains unexplored. Here, we demonstrate an α-lactam reagent (AM2) that is tolerant to aqueous buffers while being reactive towards biologically relevant nucleophiles. Interestingly, carboxylesterases 1 and 2 (CES1/2), both serine hydrolases with key roles in endo- and xenobiotic metabolism, were found as primary covalent targets for AM2 in HepG2 liver cancer cells. All in all, this study constitutes the starting point for the further development and exploration of α-lactam-based electrophilic probes in covalent chemical biology.
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Affiliation(s)
- Alejandro Mahía
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Anders E Kiib
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Marija Nisavic
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Department of Clinical Medicine-Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Esben B Svenningsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine-Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
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13
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Kurbanov M, Kirsch ZJ, Krishna J, Dutta R, Vachet RW, Thayumanavan S. Multisite Labeling of Proteins Using the Ligand-Directed Reactivity of Triggerable Michael Acceptors. Bioconjug Chem 2023; 34:1130-1138. [PMID: 37220065 PMCID: PMC10363337 DOI: 10.1021/acs.bioconjchem.3c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Targeted modification of endogenous proteins without genetic manipulation of protein expression machinery has a range of applications from chemical biology to drug discovery. Despite being demonstrated to be effective in various applications, target-specific protein labeling using ligand-directed strategies is limited by stringent amino acid selectivity. Here, we present highly reactive ligand-directed triggerable Michael acceptors (LD-TMAcs) that feature rapid protein labeling. Unlike previous approaches, the unique reactivity of LD-TMAcs enables multiple modifications on a single target protein, effectively mapping the ligand binding site. This capability is attributed to the tunable reactivity of TMAcs that enable the labeling of several amino acid functionalities via a binding-induced increase in local concentration while remaining fully dormant in the absence of protein binding. We demonstrate the target selectivity of these molecules in cell lysates using carbonic anhydrase as the model protein. Furthermore, we demonstrate the utility of this method by selectively labeling membrane-bound carbonic anhydrase XII in live cells. We envision that the unique features of LD-TMAcs will find use in target identification, investigation of binding/allosteric sites, and studying membrane proteins.
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Affiliation(s)
- Myrat Kurbanov
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Zachary J Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Jithu Krishna
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Ranit Dutta
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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14
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Sharko A, Spitzbarth B, Hermans TM, Eelkema R. Redox-Controlled Shunts in a Synthetic Chemical Reaction Cycle. J Am Chem Soc 2023; 145:9672-9678. [PMID: 37092741 PMCID: PMC10161229 DOI: 10.1021/jacs.3c00985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Shunts, alternative pathways in chemical reaction networks (CRNs), are ubiquitous in nature, enabling adaptability to external and internal stimuli. We introduce a CRN in which the recovery of Michael-accepting species is driven by oxidation chemistry. Using weak oxidants can enable access to two shunts within this CRN with different kinetics and a reduced number of side reactions compared to the main cycle that is driven by strong oxidants. Furthermore, we introduce a strategy to recycle one of the main products under flow conditions to partially reverse the CRN and control product speciation throughout time. These findings introduce new levels of control over artificial CRNs, driven by redox chemistry, narrowing the gap between synthetic and natural systems.
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Affiliation(s)
| | - Benjamin Spitzbarth
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Thomas M Hermans
- University of Strasbourg & CNRS, UMR7140, 67083 Strasbourg, France
| | - Rienk Eelkema
- Department of Chemical Engineering, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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15
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein–drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein–drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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16
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Jiang S, Huang H. Mechanism-Guided Design of Chain-Growth Click Polymerization Based on a Thiol-Michael Reaction. Angew Chem Int Ed Engl 2023; 62:e202217895. [PMID: 36734515 DOI: 10.1002/anie.202217895] [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: 12/05/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/04/2023]
Abstract
The development of chain-growth click polymerization is challenging yet desirable in modern polymer chemistry. In this work, we reported a novel chain-growth click polymerization based on the thiol-Michael reaction. This polymerization could be performed efficiently under ambient conditions and spatiotemporally regulated by ultraviolet light, allowing the synthesis of sulfur-containing polymers in excellent yields and high molecular weights. Density functional theory calculations indicated that the thiolate addition to the Michael acceptor is the rate-determining step, and introducing the phenyl group could facilitate the chain-growth process. This polymerization is a new type of chain-growth click polymerization, which will provide a unique approach to creating functional polymers.
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Affiliation(s)
- Suqiu Jiang
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Hanchu Huang
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
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17
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Wang Y, Li Z, Mo F, Chen-Mayfield TJ, Saini A, LaMere AM, Hu Q. Chemically engineering cells for precision medicine. Chem Soc Rev 2023; 52:1068-1102. [PMID: 36633324 DOI: 10.1039/d2cs00142j] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Cell-based therapy holds great potential to address unmet medical needs and revolutionize the healthcare industry, as demonstrated by several therapeutics such as CAR-T cell therapy and stem cell transplantation that have achieved great success clinically. Nevertheless, natural cells are often restricted by their unsatisfactory in vivo trafficking and lack of therapeutic payloads. Chemical engineering offers a cost-effective, easy-to-implement engineering tool that allows for strengthening the inherent favorable features of cells and confers them new functionalities. Moreover, in accordance with the trend of precision medicine, leveraging chemical engineering tools to tailor cells to accommodate patients individual needs has become important for the development of cell-based treatment modalities. This review presents a comprehensive summary of the currently available chemically engineered tools, introduces their application in advanced diagnosis and precision therapy, and discusses the current challenges and future opportunities.
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Affiliation(s)
- Yixin Wang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA. .,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zhaoting Li
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA. .,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Fanyi Mo
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Ting-Jing Chen-Mayfield
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Aryan Saini
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Afton Martin LaMere
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA. .,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.,Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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18
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Reddi RN, Rogel A, Gabizon R, Rawale DG, Harish B, Marom S, Tivon B, Arbel YS, Gurwicz N, Oren R, David K, Liu J, Duberstein S, Itkin M, Malitsky S, Barr H, Katz BZ, Herishanu Y, Shachar I, Shulman Z, London N. Sulfamate Acetamides as Self-Immolative Electrophiles for Covalent Ligand-Directed Release Chemistry. J Am Chem Soc 2023; 145:3346-3360. [PMID: 36738297 PMCID: PMC9936582 DOI: 10.1021/jacs.2c08853] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Electrophiles for covalent inhibitors that are suitable for in vivo administration are rare. While acrylamides are prevalent in FDA-approved covalent drugs, chloroacetamides are considered too reactive for such purposes. We report sulfamate-based electrophiles that maintain chloroacetamide-like geometry with tunable reactivity. In the context of the BTK inhibitor ibrutinib, sulfamate analogues showed low reactivity with comparable potency in protein labeling, in vitro, and cellular kinase activity assays and were effective in a mouse model of CLL. In a second example, we converted a chloroacetamide Pin1 inhibitor to a potent and selective sulfamate acetamide with improved buffer stability. Finally, we show that sulfamate acetamides can be used for covalent ligand-directed release (CoLDR) chemistry, both for the generation of "turn-on" probes as well as for traceless ligand-directed site-specific labeling of proteins. Taken together, this chemistry represents a promising addition to the list of electrophiles suitable for in vivo covalent targeting.
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Affiliation(s)
- Rambabu N. Reddi
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel,
| | - Adi Rogel
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ronen Gabizon
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dattatraya Gautam Rawale
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Battu Harish
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shir Marom
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Barr Tivon
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yamit Shorer Arbel
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Neta Gurwicz
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Roni Oren
- Department
of Veterinary Resources, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Keren David
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Jingjing Liu
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Shirly Duberstein
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Life Sciences
Core Facilities, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Life Sciences
Core Facilities, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Haim Barr
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ben-Zion Katz
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel,Department
of Hematology, Tel Aviv Sourasky Medical
Center, Tel Aviv 6423906, Israel
| | - Yair Herishanu
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel,Department
of Hematology, Tel Aviv Sourasky Medical
Center, Tel Aviv 6423906, Israel
| | - Idit Shachar
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Ziv Shulman
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Nir London
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel,
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19
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He YL, Zhong M, Song ZL, Shen YK, Zhao L, Fang J. Synthesis and discovery of Baylis-Hillman adducts as potent and selective thioredoxin reductase inhibitors for cancer treatment. Bioorg Med Chem 2023; 79:117169. [PMID: 36657375 DOI: 10.1016/j.bmc.2023.117169] [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: 05/24/2022] [Revised: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
The selenoprotein thioredoxin reductase (TrxR) is of paramount importance in maintaining cellular redox homeostasis, and aberrant upregulation of TrxR is frequently observed in various cancers due to their elevated oxidative stress in cells. Thus, it seems promising and feasible to target the ablation of intracellular TrxR for the treatment of cancers. We report herein the design and synthesis of a series of Baylis-Hillman adducts, and identified a typical adduct that possesses the superior cytotoxicity against HepG2 cells over other types of cancer cells. The biological investigation shows the selected typical adduct selectively targets TrxR in HepG2 cells, which thereafter results in the collapse of intracellular redox homeostasis. Further mechanistic studies reveal that the selected typical adduct arrests the cell cycle in G1/G0 phase. Importantly, the malignant metastasis of HepG2 cells is significantly restrained by the selected typical adduct. With well-defined molecular target and mechanism of action, the selected typical adduct, even other Baylis-Hillman skeleton-bearing compounds, merits further development as candidate or ancillary agent for the treatment of various cancers.
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Affiliation(s)
- Yi-Lin He
- Natural Medicine Research & Development Center, Lanzhou Jiaotong University, Lanzhou, Gansu 730070, China; State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Miao Zhong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Zi-Long Song
- Natural Medicine Research & Development Center, Lanzhou Jiaotong University, Lanzhou, Gansu 730070, China; State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yu-Kai Shen
- Lizhi College, Xi'an Jiaotong University, No. 28, Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Lanning Zhao
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, Gansu 730000, China
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20
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Wang D, Zhang J, huang Z, Yang Y, Fu T, Yang Y, Lyu Y, Jiang J, Qiu L, Cao Z, Zhang X, You Q, Lin Y, Zhao Z, Tan W. Robust Covalent Aptamer Strategy Enables Sensitive Detection and Enhanced Inhibition of SARS-CoV-2 Proteins. ACS CENTRAL SCIENCE 2023; 9:72-83. [PMID: 36712483 PMCID: PMC9881204 DOI: 10.1021/acscentsci.2c01263] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Indexed: 06/18/2023]
Abstract
Aptamer-based detection and therapy have made substantial progress with cost control and easy modification. However, the conformation lability of an aptamer typically causes the dissociation of aptamer-target complexes during harsh washes and other environmental stresses, resulting in only moderate detection sensitivity and a decreasing therapeutic effect. Herein, we report a robust covalent aptamer strategy to sensitively detect nucleocapsid protein and potently neutralize spike protein receptor binding domain (RBD), two of the most important proteins of SARS-CoV-2, after testing different cross-link electrophilic groups via integrating the specificity and efficiency. Covalent aptamers can specifically convert aptamer-protein complexes from the dynamic equilibrium state to stable and irreversible covalent complexes even in harsh environments. Covalent aptamer-based ELISA detection of nucleocapsid protein can surpass the gold standard, antibody-based sandwich ELISA. Further, covalent aptamer performs enhanced functional inhibition to RBD protein even in a blood vessel-mimicking flowing circulation system. The robust covalent aptamer-based strategy is expected to inspire more applications in accurate molecular modification, disease biomarker discovery, and other theranostic fields.
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Affiliation(s)
- Dan Wang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- LIMES
Chemical Biology Unit, Universität
Bonn, 53121 Bonn, Germany
| | - Jing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zhiyong huang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yuhang Yang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ting Fu
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yu Yang
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yifan Lyu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Jianhui Jiang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Liping Qiu
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Zehui Cao
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaobing Zhang
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qimin You
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Ustar
Biotechnologies (Hangzhou) Ltd., Hangzhou, Zhejiang 310053, China
| | - Yuankui Lin
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Ustar
Biotechnologies (Hangzhou) Ltd., Hangzhou, Zhejiang 310053, China
| | - Zilong Zhao
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular
Science and Biomedicine Laboratory (MBL), State Key Laboratory of
Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical
Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Zhejiang
Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute
of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University
School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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21
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McAulay K, Bilsland A, Bon M. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery. Pharmaceuticals (Basel) 2022; 15:1366. [PMID: 36355538 PMCID: PMC9694498 DOI: 10.3390/ph15111366] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 09/27/2023] Open
Abstract
Fragment based drug discovery has long been used for the identification of new ligands and interest in targeted covalent inhibitors has continued to grow in recent years, with high profile drugs such as osimertinib and sotorasib gaining FDA approval. It is therefore unsurprising that covalent fragment-based approaches have become popular and have recently led to the identification of novel targets and binding sites, as well as ligands for targets previously thought to be 'undruggable'. Understanding the properties of such covalent fragments is important, and characterizing and/or predicting reactivity can be highly useful. This review aims to discuss the requirements for an electrophilic fragment library and the importance of differing warhead reactivity. Successful case studies from the world of drug discovery are then be examined.
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Affiliation(s)
- Kirsten McAulay
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Centre for Targeted Protein Degradation, University of Dundee, Nethergate, Dundee DD1 4HN, UK
| | - Alan Bilsland
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marta Bon
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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22
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Temporally programmed polymer - solvent interactions using a chemical reaction network. Nat Commun 2022; 13:6242. [PMID: 36271045 PMCID: PMC9587023 DOI: 10.1038/s41467-022-33810-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 10/04/2022] [Indexed: 12/25/2022] Open
Abstract
Out of equilibrium operation of chemical reaction networks (CRNs) enables artificial materials to autonomously respond to their environment by activation and deactivation of intermolecular interactions. Generally, their activation can be driven by various chemical conversions, yet their deactivation to non-interacting building blocks remains largely limited to hydrolysis and internal pH change. To achieve control over deactivation, we present a new, modular CRN that enables reversible formation of positive charges on a tertiary amine substrate, which are removed using nucleophilic signals that control the deactivation kinetics. The modular nature of the CRN enables incorporation in diverse polymer materials, leading to a temporally programmed transition from collapsed and hydrophobic to solvated, hydrophilic polymer chains by controlling polymer-solvent interactions. Depending on the layout of the CRN, we can create stimuli-responsive or autonomously responding materials. This concept will not only offer new opportunities in molecular cargo delivery but also pave the way for next-generation interactive materials.
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23
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Reddy NC, Molla R, Joshi PN, T. K. S, Basu I, Kawadkar J, Kalra N, Mishra RK, Chakrabarty S, Shukla S, Rai V. Traceless cysteine-linchpin enables precision engineering of lysine in native proteins. Nat Commun 2022; 13:6038. [PMID: 36229616 PMCID: PMC9561114 DOI: 10.1038/s41467-022-33772-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
The maintenance of machinery requires its operational understanding and a toolbox for repair. The methods for the precision engineering of native proteins meet a similar requirement in biosystems. Its success hinges on the principles regulating chemical reactions with a protein. Here, we report a technology that delivers high-level control over reactivity, chemoselectivity, site-selectivity, modularity, dual-probe installation, and protein-selectivity. It utilizes cysteine-based chemoselective Linchpin-Directed site-selective Modification of lysine residue in a protein (LDMC-K). The efficiency of the end-user-friendly protocol is evident in quantitative conversions within an hour. A chemically orthogonal C-S bond-formation and bond-dissociation are essential among multiple regulatory attributes. The method offers protein selectivity by targeting a single lysine residue of a single protein in a complex biomolecular mixture. The protocol renders analytically pure single-site probe-engineered protein bioconjugate. Also, it provides access to homogeneous antibody conjugates (AFC and ADC). The LDMC-K-ADC exhibits highly selective anti-proliferative activity towards breast cancer cells.
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Affiliation(s)
- Neelesh C. Reddy
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Rajib Molla
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Pralhad Namdev Joshi
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Sajeev T. K.
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Ipsita Basu
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Jyotsna Kawadkar
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | | | - Ram Kumar Mishra
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Suman Chakrabarty
- grid.452759.80000 0001 2188 427XDepartment of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, 700 106 W.B. India
| | - Sanjeev Shukla
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
| | - Vishal Rai
- grid.462376.20000 0004 1763 8131Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462 066 M.P. India
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24
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Wang Y, Zhao R, Wan C, Guo X, Yang F, Hou Z, Wang R, Li S, Feng T, Yin F, Li Z. A Peptide-Based Ligand-Directed Chemistry Enables Protein Functionalization. Org Lett 2022; 24:7205-7209. [PMID: 36169233 DOI: 10.1021/acs.orglett.2c02974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ligand-directed (LD) chemistry provides powerful tools for site-specific modification of proteins. We utilized a peptide with an appended methionine (Met) as a ligand; then, the Met thioether was modified into sulfonium which enabled a proximity induced group transfer onto protein cysteine in the vicinity upon peptide-target binding. The sulfonium warhead could be easily constructed with unprotected peptides, and the transferable group scope was conducted on model protein PDZ and its ligand peptides. In addition, a living cell labeling was successfully achieved.
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Affiliation(s)
- Yuena Wang
- Center for Disease Control and Prevention, Shenzhen, 518055, China.,State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Rongtong Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fenfang Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
| | - Shuiming Li
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, Shenzhen University, Shenzhen, 518055, China
| | - Tiejian Feng
- Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
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25
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Fenbendazole and its synthetic analog interfere with HeLa cells’ proliferation and energy metabolism via inducing oxidative stress and modulating MEK3/6-p38-MAPK pathway. Chem Biol Interact 2022; 361:109983. [DOI: 10.1016/j.cbi.2022.109983] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 02/03/2023]
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26
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Montaño JL, Wang BJ, Volk RF, Warrington SE, Garda VG, Hofmann KL, Chen LC, Zaro BW. Improved Electrophile Design for Exquisite Covalent Molecule Selectivity. ACS Chem Biol 2022; 17:1440-1449. [PMID: 35587148 DOI: 10.1021/acschembio.1c00980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Covalent inhibitors are viable therapeutics. However, off-target reactivity challenges the field. Chemists have attempted to solve this issue by varying the reactivity attributes of electrophilic warheads. Here, we report the development of an approach to increase the selectivity of covalent molecules that is independent of warhead reactivity features and can be used in concert with existing methods. Using the scaffold of the Bruton's tyrosine kinase (BTK) inhibitor Ibrutinib for our proof-of-concept, we reasoned that increasing the steric bulk of fumarate-based electrophiles on Ibrutinib should improve selectivity via the steric exclusion of off-targets but retain rates of cysteine reactivity comparable to that of an acrylamide. Using chemical proteomic techniques, we demonstrate that elaboration of the electrophile to a tert-butyl (t-Bu) fumarate ester decreases time-dependent off-target reactivity and abolishes time-independent off-target reactivity. While an alkyne-bearing probe analogue of Ibrutinib has 247 protein targets, our t-Bu fumarate probe analogue has only 7. Of these 7 targets, BTK is the only time-independent target. The t-Bu inhibitor itself is also more selective for BTK, reducing off-targets by 70%. We investigated the consequences of treatment with Ibrutinib and our t-Bu analogue and discovered that only 8 proteins are downregulated in response to treatment with the t-Bu analogue compared to 107 with Ibrutinib. Of these 8 proteins, 7 are also downregulated by Ibrutinib and a majority of these targets are associated with BTK biology. Taken together, these findings reveal an opportunity to increase cysteine-reactive covalent inhibitor selectivity through electrophilic structure optimization.
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Affiliation(s)
- José L. Montaño
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Brian J. Wang
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Sara E. Warrington
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Virginia G. Garda
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Katherine L. Hofmann
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Leo C. Chen
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, California 94158, United States
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27
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Veale CGL, Talukdar A, Vauzeilles B. ICBS 2021: Looking Toward the Next Decade of Chemical Biology. ACS Chem Biol 2022; 17:728-743. [PMID: 35293726 DOI: 10.1021/acschembio.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton G. L. Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
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28
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Zhao L, Qu Y, Zhang F, Ma D, Gao H, Gan L, Zhang H, Zhang S, Fang J. Baylis–Hillman Adducts as a Versatile Module for Constructing Fluorogenic Release System. J Med Chem 2022; 65:6056-6069. [DOI: 10.1021/acs.jmedchem.1c01940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lanning Zhao
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yuan Qu
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fang Zhang
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Di Ma
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Hao Gao
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Lu Gan
- Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Hong Zhang
- Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Shengxiang Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry and College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
- School of Chemistry and Chemical Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
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29
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Kline GM, Nugroho K, Kelly JW. Inverse Drug Discovery identifies weak electrophiles affording protein conjugates. Curr Opin Chem Biol 2022; 67:102113. [PMID: 35065430 PMCID: PMC8940698 DOI: 10.1016/j.cbpa.2021.102113] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 01/01/2023]
Abstract
Traditional biochemical target-based and phenotypic cell-based screening approaches to drug discovery have produced the current covalent and non-covalent pharmacopoeia. Strategies to expand the druggable proteome include Inverse Drug Discovery, which involves incubating one weak organic electrophile at a time with the proteins of a living cell to identify the conjugates formed. An alkyne substructure in each organic electrophile enables affinity chromatography-mass spectrometry, which produces a list of proteins that each distinct compound reacts with. Herein, we review Inverse Drug Discovery in the context of organic compounds of intermediate complexity harboring Sulfur(VI)-fluoride exchange (SuFEx) electrophiles used to expand the cellular proteins that can be targeted covalently.
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Affiliation(s)
- Gabriel M Kline
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Karina Nugroho
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
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30
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Grams RJ, Hsu KL. Reactive chemistry for covalent probe and therapeutic development. Trends Pharmacol Sci 2022; 43:249-262. [PMID: 34998611 PMCID: PMC8840975 DOI: 10.1016/j.tips.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 02/06/2023]
Abstract
Bioactive small molecules that form covalent bonds with a target protein are important tools for basic research and can be highly effective drugs. This review highlights reactive groups found in a collection of thiophilic and oxophilic drugs that mediate pharmacological activity through a covalent mechanism of action (MOA). We describe the application of advanced proteomic and bioanalytical methodologies for assessing selectivity of these covalent agents to guide and inspire the search for additional electrophiles suitable for covalent probe and therapeutic development. While the emphasis is on chemistry for modifying catalytic serine, threonine or cysteine residues, we devote a substantial fraction of the review to a collection of exploratory reactive groups of understudied residues on proteins.
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Affiliation(s)
- R. Justin Grams
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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31
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M Serafim RA, da Silva Santiago A, Schwalm MP, Hu Z, Dos Reis CV, Takarada JE, Mezzomo P, Massirer KB, Kudolo M, Gerstenecker S, Chaikuad A, Zender L, Knapp S, Laufer S, Couñago RM, Gehringer M. Development of the First Covalent Monopolar Spindle Kinase 1 (MPS1/TTK) Inhibitor. J Med Chem 2022; 65:3173-3192. [PMID: 35167750 DOI: 10.1021/acs.jmedchem.1c01165] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Monopolar spindle kinase 1 (MPS1/TTK) is a key element of the mitotic checkpoint and clinically evaluated as a target in the treatment of aggressive tumors such as triple-negative breast cancer. While long drug-target residence times have been suggested to be beneficial in the context of therapeutic MPS1 inhibition, no irreversible inhibitors have been reported. Here we present the design and characterization of the first irreversible covalent MPS1 inhibitor, RMS-07, targeting a poorly conserved cysteine in the kinase's hinge region. RMS-07 shows potent MPS1 inhibitory activity and selectivity against all protein kinases with an equivalent cysteine but also in a broader kinase panel. We demonstrate potent cellular target engagement and pronounced activity against various cancer cell lines. The covalent binding mode was validated by mass spectrometry and an X-ray crystal structure. This proof of MPS1 covalent ligandability may open new avenues for the design of MPS1-specific chemical probes or drugs.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.,Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
| | - André da Silva Santiago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.,Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
| | - Martin P Schwalm
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Zexi Hu
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, 72076 Tübingen, Germany
| | - Caio V Dos Reis
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.,Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
| | - Jessica E Takarada
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.,Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
| | - Priscila Mezzomo
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.,Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
| | - Katlin B Massirer
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.,Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
| | - Mark Kudolo
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan Gerstenecker
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Apirat Chaikuad
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, 72076 Tübingen, Germany.,German Consortium for Translational Cancer Research (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), 72076 Tübingen, Germany
| | - Stefan Knapp
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany.,Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,Frankfurt Cancer Institute (FCI) and German Translational Cancer Network (DKTK) Site Frankfurt/Mainz, 60596 Frankfurt am Main, Germany
| | - Stefan Laufer
- 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.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.,Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP, Campinas, SP 13083-886, Brazil
| | - 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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32
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Reddi RN, Rogel A, Resnick E, Gabizon R, Prasad PK, Gurwicz N, Barr H, Shulman Z, London N. Site-Specific Labeling of Endogenous Proteins Using CoLDR Chemistry. J Am Chem Soc 2021; 143:20095-20108. [PMID: 34817989 PMCID: PMC8662641 DOI: 10.1021/jacs.1c06167] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Chemical modifications
of native proteins can affect their stability,
activity, interactions, localization, and more. However, there are
few nongenetic methods for the installation of chemical modifications
at a specific protein site in cells. Here we report a covalent ligand
directed release (CoLDR) site-specific labeling strategy, which enables
the installation of a variety of functional tags on a target protein
while releasing the directing ligand. Using this approach, we were
able to label various proteins such as BTK, K-RasG12C,
and SARS-CoV-2 PLpro with different tags. For BTK we have
shown selective labeling in cells of both alkyne and fluorophores
tags. Protein labeling by traditional affinity methods often inhibits
protein activity since the directing ligand permanently occupies the
target binding pocket. We have shown that using CoLDR chemistry, modification
of BTK by these probes in cells preserves its activity. We demonstrated
several applications for this approach including determining the half-life
of BTK in its native environment with minimal perturbation, as well
as quantification of BTK degradation by a noncovalent proteolysis
targeting chimera (PROTAC) by in-gel fluorescence. Using an environment-sensitive
“turn-on” fluorescent probe, we were able to monitor
ligand binding to the active site of BTK. Finally, we have demonstrated
efficient CoLDR-based BTK PROTACs (DC50 < 100 nM), which
installed a CRBN binder onto BTK. This approach joins very few available
labeling strategies that maintain the target protein activity and
thus makes an important addition to the toolbox of chemical biology.
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Affiliation(s)
- Rambabu N Reddi
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Efrat Resnick
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ronen Gabizon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Pragati Kishore Prasad
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Neta Gurwicz
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ziv Shulman
- Department of Immunology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, 7610001, Israel
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33
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Shindo N, Ojida A. Recent progress in covalent warheads for in vivo targeting of endogenous proteins. Bioorg Med Chem 2021; 47:116386. [PMID: 34509863 DOI: 10.1016/j.bmc.2021.116386] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/21/2023]
Abstract
Covalent drugs exert potent and durable activity by chemical modification of the endogenous target protein in vivo. To maximize the pharmacological efficacy while alleviating the risk of toxicity due to nonspecific off-target reactions, current covalent drug discovery focuses on the development of targeted covalent inhibitors (TCIs), wherein a reactive group (warhead) is strategically incorporated onto a reversible ligand of the target protein to facilitate specific covalent engagement. Various aspects of warheads, such as intrinsic reactivity, chemoselectivity, mode of reaction, and reversibility of the covalent engagement, would affect the target selectivity of TCIs. Although TCIs clinically approved to date largely rely on Michael acceptor-type electrophiles for cysteine targeting, a wide array of novel warheads have been devised and tested in TCI development in recent years. In this short review, we provide an overview of recent progress in chemistry for selective covalent targeting of proteins and their applications in TCI designs.
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Affiliation(s)
- Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan.
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34
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- 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.,Tübingen Center for Academic Drug Discovery, 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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35
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein–Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Itai Bloch
- Biotechnology Department MIGAL-Galilee Research Institute Kiryat-Shmona 11016 Israel
| | - Maayan Gal
- Department of Oral Biology The Goldschleger School of Dental Medicine Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Nir London
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michal Sharon
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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36
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein-Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021; 60:19637-19642. [PMID: 34101963 PMCID: PMC8457057 DOI: 10.1002/anie.202104947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/23/2021] [Indexed: 12/22/2022]
Abstract
Understanding protein–ligand interactions in a cellular context is an important goal in molecular biology and biochemistry, and particularly for drug development. Investigators must demonstrate that drugs penetrate cells and specifically bind their targets. Towards that end, we present a native mass spectrometry (MS)‐based method for analyzing drug uptake and target engagement in eukaryotic cells. This method is based on our previously introduced direct‐MS method for rapid analysis of proteins directly from crude samples. Here, direct‐MS enables label‐free studies of protein–drug binding in human cells and is used to determine binding affinities of lead compounds in crude samples. We anticipate that this method will enable the application of native MS to a range of problems where cellular context is important, including protein–protein interactions, drug uptake and binding, and characterization of therapeutic proteins.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Itai Bloch
- Biotechnology Department, MIGAL-Galilee Research Institute, Kiryat-Shmona, 11016, Israel
| | - Maayan Gal
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
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