1
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Sun J, Lou L, Zhu C, Chen P, Tang G, Gu M, Xia S, Dong X, Zhang ZM, Gao L, Yao SQ, Xiao Q. Rationally designed BCR-ABL kinase inhibitors for improved leukemia treatment via covalent and pro-/dual-drug targeting strategies. J Adv Res 2024:S2090-1232(24)00392-8. [PMID: 39255927 DOI: 10.1016/j.jare.2024.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/08/2024] [Accepted: 09/04/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND Chronic Myeloid Leukemia (CML) is a blood cancer that remains challenging to cure due to drug resistance and side effects from current BCR-ABL inhibitors. There is an urgent need for novel and more effective BCR-ABL targeting inhibitors and therapeutic strategies to combat this deadly disease. METHOD We disclose an "OH-implant" strategy to improve a noncovalent BCR-ABL inhibitor, PPY-A, by adding a hydroxyl group to its scaffold. By taking advantage of this OH "hot spot", we designed a panel of irreversible covalent kinase inhibitors and hypoxia-responsive pro-/dual-drugs, and their biological activities were studied in vitro, in cellulo and in vivo. RESULT The resulting compound B1 showed enhanced solubility and biological activity. B4 achieved sustained BCR-ABL inhibition by forming a stable covalent bond with ABL kinase. Hypoxia-responsive prodrug P1 and dual-drugs D1/D2/D3 demonstrated significant anti-tumor effects under hypoxic conditions. The in vivo studies using K562-xenografted mice showed that B1 displayed superior antitumor activity than PPY-A, while P1 and D3 offered better safety profiles alongside significant tumor control. CONCLUSION We have successfully developed a chemical biology approach to convert a known noncovalent BCR-ABL inhibitor into more potent and safer inhibitors through covalent and pro-/dual-drug targeting strategies. Our "OH-implant" approach and the resulting drug design strategies have general applicability and hold promise for improvement the performance of various other reported drugs/drug candidates, thereby providing advanced medicines for disease treatment.
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Affiliation(s)
- Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Liang Lou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Mingxi Gu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Shu Xia
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai 200444, China.
| | - Xiao Dong
- Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Shanghai 200444, China.
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, and Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; State Key Laboratory of Targeting Oncology, National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
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2
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Dey G, Sinai-Turyansky R, Yakobovich E, Merquiol E, Loboda J, Sridharan N, Houri-Haddad Y, Polak D, Yona S, Turk D, Wald O, Blum G. Development and Application of Reversible and Irreversible Covalent Probes for Human and Mouse Cathepsin-K Activity Detection, Revealing Nuclear Activity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401518. [PMID: 38970171 DOI: 10.1002/advs.202401518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 05/30/2024] [Indexed: 07/08/2024]
Abstract
Cathepsin-K (CTSK) is an osteoclast-secreted cysteine protease that efficiently cleaves extracellular matrices and promotes bone homeostasis and remodeling, making it an excellent therapeutic target. Detection of CTSK activity in complex biological samples using tailored tools such as activity-based probes (ABPs) will aid tremendously in drug development. Here, potent and selective CTSK probes are designed and created, comparing irreversible and reversible covalent ABPs with improved recognition components and electrophiles. The newly developed CTSK ABPs precisely detect active CTSK in mouse and human cells and tissues, from diseased and healthy states such as inflamed tooth implants, osteoclasts, and lung samples, indicating changes in CTSK's activity in the pathological samples. These probes are used to study how acidic pH stimulates mature CTSK activation, specifically, its transition from pro-form to mature form. Furthermore, this study reveals for the first time, why intact cells and cell lysate exhibit diverse CTSK activity while having equal levels of mature CTSK enzyme. Interestingly, these tools enabled the discovery of active CTSK in human osteoclast nuclei and in the nucleoli. Altogether, these novel probes are excellent research tools and can be applied in vivo to examine CTSK activity and inhibition in diverse diseases without immunogenicity hazards.
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Affiliation(s)
- Gourab Dey
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Reut Sinai-Turyansky
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Evalyn Yakobovich
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Emmanuelle Merquiol
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Jure Loboda
- Department of Biochemistry, Molecular and Structural Biology, J. Stefan Institute, Ljubljana, SI-1000, Slovenia
| | - Nikhila Sridharan
- The Institute of Biomedical and Oral Research, The Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Yael Houri-Haddad
- Department of Prosthodontics, The Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - David Polak
- Department of Prosthodontics, The Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Simon Yona
- The Institute of Biomedical and Oral Research, The Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Dusan Turk
- Department of Biochemistry, Molecular and Structural Biology, J. Stefan Institute, Ljubljana, SI-1000, Slovenia
| | - Ori Wald
- Department of Cardiothoracic Surgery, Hadassah Hebrew University Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Galia Blum
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
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3
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Li Z, Jiang J, Ficarro SB, Beyett TS, To C, Tavares I, Zhu Y, Li J, Eck MJ, Jänne PA, Marto JA, Zhang T, Che J, Gray NS. Molecular Bidents with Two Electrophilic Warheads as a New Pharmacological Modality. ACS CENTRAL SCIENCE 2024; 10:1156-1166. [PMID: 38947214 PMCID: PMC11212140 DOI: 10.1021/acscentsci.3c01245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 07/02/2024]
Abstract
A systematic strategy to develop dual-warhead inhibitors is introduced to circumvent the limitations of conventional covalent inhibitors such as vulnerability to mutations of the corresponding nucleophilic residue. Currently, all FDA-approved covalent small molecules feature one electrophile, leaving open a facile route to acquired resistance. We conducted a systematic analysis of human proteins in the protein data bank to reveal ∼400 unique targets amendable to dual covalent inhibitors, which we term "molecular bidents". We demonstrated this strategy by targeting two kinases: MKK7 and EGFR. The designed compounds, ZNL-8162 and ZNL-0056, are ATP-competitive inhibitors that form two covalent bonds with cysteines and retain potency against single cysteine mutants. Therefore, molecular bidents represent a new pharmacological modality with the potential for improved selectivity, potency, and drug resistance profile.
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Affiliation(s)
- Zhengnian Li
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jie Jiang
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Scott B. Ficarro
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tyler S. Beyett
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Ciric To
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Isidoro Tavares
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Yingde Zhu
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jiaqi Li
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Michael J. Eck
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Pasi A. Jänne
- Lowe
Center for Thoracic Oncology, Dana-Farber
Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Medical Oncology, Dana-Farber Cancer
Institute, Boston, Massachusetts 02215, United States
- Department
of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jarrod A. Marto
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Blais
Proteomics Center, Center for Emergent Drug
Targets, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Pathology, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Tinghu Zhang
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Jianwei Che
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Nathanael S. Gray
- Department
of Chemical and Systems Biology, Stanford Cancer Institute, ChEM-H, Stanford University, Stanford, California 94305, United States
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4
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Alboreggia G, Udompholkul P, Baggio C, Muzzarelli K, Assar Z, Pellecchia M. Histidine-Covalent Stapled Alpha-Helical Peptides Targeting hMcl-1. J Med Chem 2024; 67:8172-8185. [PMID: 38695666 PMCID: PMC11129181 DOI: 10.1021/acs.jmedchem.4c00277] [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: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/24/2024] [Indexed: 05/24/2024]
Abstract
Several novel and effective cysteine targeting (Cys) covalent drugs are in clinical use. However, the target area containing a druggable Cys residue is limited. Therefore, methods for creating covalent drugs that target different residues are being looked for; examples of such ligands include those that target the residues lysine (Lys) and tyrosine (Tyr). Though the histidine (His) side chain is more frequently found in protein binding locations and has higher desirable nucleophilicity, surprisingly limited research has been done to specifically target this residue, and there are not many examples of His-targeting ligands that have been rationally designed. In the current work, we created novel stapled peptides that are intended to target hMcl-1 His 252 covalently. We describe the in vitro (biochemical, NMR, and X-ray) and cellular design and characterization of such agents. Our findings further suggest that the use of electrophiles to specifically target His residues is warranted.
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Affiliation(s)
- Giulia Alboreggia
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Parima Udompholkul
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Carlo Baggio
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Kendall Muzzarelli
- Cayman
Chemical Co., 1180 E. Ellsworth road, Ann Arbor, Michigan 48108, United States
| | - Zahra Assar
- Cayman
Chemical Co., 1180 E. Ellsworth road, Ann Arbor, Michigan 48108, United States
| | - Maurizio Pellecchia
- Division
of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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5
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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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6
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Li L, Liu S, Luo Y. Application of covalent modality in proximity-induced drug pharmacology: Early development, current strategy, and feature directions. Eur J Med Chem 2024; 271:116394. [PMID: 38643668 DOI: 10.1016/j.ejmech.2024.116394] [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: 02/07/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/23/2024]
Abstract
With a growing number of covalent drugs securing FDA approval as successful therapies across various indications, particularly in the realm of cancer treatment, the covalent modulating strategy is undergoing a resurgence. The renewed interest in covalent bioactive compounds has captured significant attention from both the academic and biopharmaceutical industry sectors. Covalent chemistry presents several advantages over traditional noncovalent proximity-induced drugs, including heightened potency, reduced molecular size, and the ability to target "undruggable" entities. Within this perspective, we have compiled a comprehensive overview of current covalent modalities applied to proximity-induced molecules, delving into their advantages and drawbacks. Our aim is to stimulate more profound insights and ideas within the scientific community, guiding future research endeavors in this dynamic field.
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Affiliation(s)
- Linjie Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China
| | - Song Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, 610041, China.
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7
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Lucas SCC, Blackwell JH, Hewitt SH, Semple H, Whitehurst BC, Xu H. Covalent hits and where to find them. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100142. [PMID: 38278484 DOI: 10.1016/j.slasd.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK.
| | | | - Sarah H Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | | | - Hua Xu
- Mechanistic and structural Biology, Discovery Sciences, AstraZeneca R&D, Waltham, USA
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8
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Tang G, Wang W, Zhu C, Huang H, Chen P, Wang X, Xu M, Sun J, Zhang CJ, Xiao Q, Gao L, Zhang ZM, Yao SQ. Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development. Angew Chem Int Ed Engl 2024; 63:e202316394. [PMID: 38248139 DOI: 10.1002/anie.202316394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/23/2024]
Abstract
Advances in targeted covalent inhibitors (TCIs) have been made by using lysine-reactive chemistries. Few aminophiles possessing balanced reactivity/stability for the development of cell-active TCIs are however available. We report herein lysine-reactive activity-based probes (ABPs; 2-14) based on the chemistry of aryl fluorosulfates (ArOSO2 F) capable of global reactivity profiling of the catalytic lysine in human kinome from mammalian cells. We concurrently developed reversible covalent ABPs (15/16) by installing salicylaldehydes (SA) onto a promiscuous kinase-binding scaffold. The stability and amine reactivity of these probes exhibited a broad range of tunability. X-ray crystallography and mass spectrometry (MS) confirmed the successful covalent engagement between ArOSO2 F on 9 and the catalytic lysine of SRC kinase. Chemoproteomic studies enabled the profiling of >300 endogenous kinases, thus providing a global landscape of ligandable catalytic lysines of the kinome. By further introducing these aminophiles into VX-680 (a noncovalent inhibitor of AURKA kinase), we generated novel lysine-reactive TCIs that exhibited excellent in vitro potency and reasonable cellular activities with prolonged residence time. Our work serves as a general guide for the development of lysine-reactive ArOSO2 F-based TCIs.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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9
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Tillmanns J, Kicuntod J, Lösing J, Marschall M. 'Getting Better'-Is It a Feasible Strategy of Broad Pan-Antiherpesviral Drug Targeting by Using the Nuclear Egress-Directed Mechanism? Int J Mol Sci 2024; 25:2823. [PMID: 38474070 DOI: 10.3390/ijms25052823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The herpesviral nuclear egress represents an essential step of viral replication efficiency in host cells, as it defines the nucleocytoplasmic release of viral capsids. Due to the size limitation of the nuclear pores, viral nuclear capsids are unable to traverse the nuclear envelope without a destabilization of this natural host-specific barrier. To this end, herpesviruses evolved the regulatory nuclear egress complex (NEC), composed of a heterodimer unit of two conserved viral NEC proteins (core NEC) and a large-size extension of this complex including various viral and cellular NEC-associated proteins (multicomponent NEC). Notably, the NEC harbors the pronounced ability to oligomerize (core NEC hexamers and lattices), to multimerize into higher-order complexes, and, ultimately, to closely interact with the migrating nuclear capsids. Moreover, most, if not all, of these NEC proteins comprise regulatory modifications by phosphorylation, so that the responsible kinases, and additional enzymatic activities, are part of the multicomponent NEC. This sophisticated basis of NEC-specific structural and functional interactions offers a variety of different modes of antiviral interference by pharmacological or nonconventional inhibitors. Since the multifaceted combination of NEC activities represents a highly conserved key regulatory stage of herpesviral replication, it may provide a unique opportunity towards a broad, pan-antiherpesviral mechanism of drug targeting. This review presents an update on chances, challenges, and current achievements in the development of NEC-directed antiherpesviral strategies.
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Affiliation(s)
- Julia Tillmanns
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Josephine Lösing
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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10
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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11
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Keeley A, Kopranovic A, Di Lorenzo V, Ábrányi-Balogh P, Jänsch N, Lai LN, Petri L, Orgován Z, Pölöske D, Orlova A, Németh A, Desczyk C, Imre T, Bajusz D, Moriggl R, Meyer-Almes FJ, Keserü GM. Electrophilic MiniFrags Revealed Unprecedented Binding Sites for Covalent HDAC8 Inhibitors. J Med Chem 2024; 67:572-585. [PMID: 38113354 PMCID: PMC10788917 DOI: 10.1021/acs.jmedchem.3c01779] [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: 09/25/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
Screening of ultra-low-molecular weight ligands (MiniFrags) successfully identified viable chemical starting points for a variety of drug targets. Here we report the electrophilic analogues of MiniFrags that allow the mapping of potential binding sites for covalent inhibitors by biochemical screening and mass spectrometry. Small electrophilic heterocycles and their N-quaternized analogues were first characterized in the glutathione assay to analyze their electrophilic reactivity. Next, the library was used for systematic mapping of potential covalent binding sites available in human histone deacetylase 8 (HDAC8). The covalent labeling of HDAC8 cysteines has been proven by tandem mass spectrometry measurements, and the observations were explained by mutating HDAC8 cysteines. As a result, screening of electrophilic MiniFrags identified three potential binding sites suitable for the development of allosteric covalent HDAC8 inhibitors. One of the hit fragments was merged with a known HDAC8 inhibitor fragment using different linkers, and the linker length was optimized to result in a lead-like covalent inhibitor.
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Affiliation(s)
- Aaron
B. Keeley
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Aleksandra Kopranovic
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Vincenzo Di Lorenzo
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Niklas Jänsch
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Linh N. Lai
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - László Petri
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Orgován
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Daniel Pölöske
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Anna Orlova
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - András
György Németh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Charlotte Desczyk
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Tímea Imre
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- MS
Metabolomics
Research Group, Research Centre for Natural
Sciences, Magyar tudósok
krt 2, H-1117 Budapest, Hungary
| | - Dávid Bajusz
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Richard Moriggl
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Franz-Josef Meyer-Almes
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - György M. Keserü
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
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12
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Mihalovits LM, Kollár L, Bajusz D, Knez D, Bozovičar K, Imre T, Ferenczy GG, Gobec S, Keserű GM. Molecular Mechanism of Labelling Functional Cysteines by Heterocyclic Thiones. Chemphyschem 2024; 25:e202300596. [PMID: 37888491 DOI: 10.1002/cphc.202300596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023]
Abstract
Heterocyclic thiones have recently been identified as reversible covalent warheads, consistent with their mild electrophilic nature. Little is known so far about their mechanism of action in labelling nucleophilic sidechains, especially cysteines. The vast number of tractable cysteines promotes a wide range of target proteins to examine; however, our focus was put on functional cysteines. We chose the main protease of SARS-CoV-2 harboring Cys145 at the active site that is a structurally characterized and clinically validated target of covalent inhibitors. We screened an in-house, cysteine-targeting covalent inhibitor library which resulted in several covalent fragment hits with benzoxazole, benzothiazole and benzimidazole cores. Thione derivatives and Michael acceptors were selected for further investigations with the objective of exploring the mechanism of inhibition of the thiones and using the thoroughly characterized Michael acceptors for benchmarking our studies. Classical and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were carried out that revealed a new mechanism of covalent cysteine labelling by thione derivatives, which was supported by QM and free energy calculations and by a wide range of experimental results. Our study shows that the molecular recognition step plays a crucial role in the overall binding of both sets of molecules.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Levente Kollár
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Damijan Knez
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Krištof Bozovičar
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tímea Imre
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- MS Metabolomics Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Stanislav Gobec
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
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13
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Dyba M, Denson JP, Maciag AE. MALDI-TOF Mass Spectrometry-Based Assay for Measuring Covalent Target Engagement of KRAS G12C Inhibitors. Methods Mol Biol 2024; 2797:145-157. [PMID: 38570458 DOI: 10.1007/978-1-0716-3822-4_11] [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] [Indexed: 04/05/2024]
Abstract
MALDI-TOF mass spectrometry enables high-throughput screening of covalent fragment libraries and SAR compound progressions of selective KRAS G12C inhibitors. Using the MALDI-TOF platform instead of the more traditional ESI-MS TOF/orbitrap instrumentation can radically shorten sample acquisition time, allowing up to 384 samples to be screened in 30 min. The typical throughput for a covalent library screen is 1152 samples per 8 h, including processing, calculation, and reporting steps. The throughput can be doubled without any significant assay modification.
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Affiliation(s)
- Marcin Dyba
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - John-Paul Denson
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anna E Maciag
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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14
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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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15
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Jiang L, Liu S, Jia X, Gong Q, Wen X, Lu W, Yang J, Wu X, Wang X, Suo Y, Li Y, Uesugi M, Qu ZB, Tan M, Lu X, Zhou L. ABPP-CoDEL: Activity-Based Proteome Profiling-Guided Discovery of Tyrosine-Targeting Covalent Inhibitors from DNA-Encoded Libraries. J Am Chem Soc 2023; 145:25283-25292. [PMID: 37857329 DOI: 10.1021/jacs.3c08852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
DNA-encoded chemical library (DEL) has been extensively used for lead compound discovery for decades in academia and industry. Incorporating an electrophile warhead into DNA-encoded compounds recently permitted the discovery of covalent ligands that selectively react with a particular cysteine residue. However, noncysteine residues remain underexplored as modification sites of covalent DELs. Herein, we report the design and utility of tyrosine-targeting DELs of 67 million compounds. Proteome-wide reactivity analysis of tyrosine-reactive sulfonyl fluoride (SF) covalent probes suggested three enzymes (phosphoglycerate mutase 1, glutathione s-transferase 1, and dipeptidyl peptidase 3) as models of tyrosine-targetable proteins. Enrichment with SF-functionalized DELs led to the identification of a series of tyrosine-targeting covalent inhibitors of the model enzymes. In-depth mechanistic investigation revealed their novel modes of action and reactive ligand-accessible hotspots of the enzymes. Our strategy of combining activity-based proteome profiling and covalent DEL enrichment (ABPP-CoDEL), which generated selective covalent binders against a variety of target proteins, illustrates the potential use of this methodology in further covalent drug discovery.
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Affiliation(s)
- Lulu Jiang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xinglong Jia
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Qinting Gong
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jintong Yang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanrui Suo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yilin Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Motonari Uesugi
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Zhi-Bei Qu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong 528400, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai 201203, China
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16
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Thomas AM, Serafini M, Grant EK, Coombs EAJ, Bluck JP, Schiedel M, McDonough MA, Reynolds JK, Lee B, Platt M, Sharlandjieva V, Biggin PC, Duarte F, Milne TA, Bush JT, Conway SJ. Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation. ACS Chem Biol 2023; 18:2405-2417. [PMID: 37874862 PMCID: PMC10660337 DOI: 10.1021/acschembio.3c00437] [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: 07/26/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023]
Abstract
Target validation remains a challenge in drug discovery, which leads to a high attrition rate in the drug discovery process, particularly in Phase II clinical trials. Consequently, new approaches to enhance target validation are valuable tools to improve the drug discovery process. Here, we report the combination of site-directed mutagenesis and electrophilic fragments to enable the rapid identification of small molecules that selectively inhibit the mutant protein. Using the bromodomain-containing protein BRD4 as an example, we employed a structure-based approach to identify the L94C mutation in the first bromodomain of BRD4 [BRD4(1)] as having a minimal effect on BRD4(1) function. We then screened a focused, KAc mimic-containing fragment set and a diverse fragment library against the mutant and wild-type proteins and identified a series of fragments that showed high selectivity for the mutant protein. These compounds were elaborated to include an alkyne click tag to enable the attachment of a fluorescent dye. These clickable compounds were then assessed in HEK293T cells, transiently expressing BRD4(1)WT or BRD4(1)L94C, to determine their selectivity for BRD4(1)L94C over other possible cellular targets. One compound was identified that shows very high selectivity for BRD4(1)L94C over all other proteins. This work provides a proof-of-concept that the combination of site-directed mutagenesis and electrophilic fragments, in a mutate and conjugate approach, can enable rapid identification of small molecule inhibitors for an appropriately mutated protein of interest. This technology can be used to assess the cellular phenotype of inhibiting the protein of interest, and the electrophilic ligand provides a starting point for noncovalent ligand development.
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Affiliation(s)
- Adam M. Thomas
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Marta Serafini
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emma K. Grant
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Edward A. J. Coombs
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Joseph P. Bluck
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Matthias Schiedel
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A. McDonough
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jessica K. Reynolds
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bernadette Lee
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael Platt
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Vassilena Sharlandjieva
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Philip C. Biggin
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Fernanda Duarte
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Thomas A. Milne
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Jacob T. Bush
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Chemistry & Biochemistry, University
of California Los Angeles, 607 Charles E. Young Drive East, P.O. Box 951569, Los Angeles, California 90095-1569, United States
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17
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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18
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Tang G, Wang W, Wang X, Ding K, Ngan SC, Chen JY, Sze SK, Gao L, Yuan P, Lu X, Yao SQ. Cell-active, irreversible covalent inhibitors that selectively target the catalytic lysine of EGFR by using fluorosulfate-based SuFEx chemistry. Eur J Med Chem 2023; 259:115671. [PMID: 37499291 DOI: 10.1016/j.ejmech.2023.115671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
EGFR signaling is involved in multiple cellular processes including cell proliferation, differentiation and development, making this protein kinase one of the most valuable drug targets for the treatment of non-small cell lung carcinomas (NSCLC). Herein, we describe the design and synthesis of a series of potential covalent inhibitors targeting the catalytically conserved lysine (K745) of EGFR on the basis of Erlotinib, an FDA-approved first-generation EGFR drug. Different amine-reactive electrophiles were introduced at positions on the Erlotinib scaffold proximal to K745 in EGFR. The optimized compound 26 (as well as its close analog 30), possessing a novel arylfluorosulfate group (ArOSO2F), showed excellent in vitro potency (as low as 0.19 nM in independent IC50 determination) and selectivity against EGFR and many of its drug-resistant mutants. Both intact protein mass spectrometry (MS) and site-mapping analysis revealed that compound 26 covalently bound to EGFR at K745 through the formation of a sulfamate. In addition, compound 26 displayed good anti-proliferative potency against EGFR-overexpressing HCC827 cells by inhibiting endogenous EGFR autophosphorylation. The pharmacokinetic studies of compound 26 demonstrated the druggable potential of other ArOSO2F-containing compounds. Finally, competitive activity-based protein profiling (ABPP), cellular thermal shift assay (CETSA), as well as cellular wash-out experiments, all showed compound 26 to be the first cell-active, fluorosulfate-based targeted covalent inhibitor (TCI) of protein kinases capable of covalently engaging the catalytically conserved lysine of its target in live mammalian cells.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China; State Key Laboratory of Bioorganic & Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Jiao-Yu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Siu Kwan Sze
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China.
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore.
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19
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Fu L, Jung Y, Tian C, Ferreira RB, Cheng R, He F, Yang J, Carroll KS. Nucleophilic covalent ligand discovery for the cysteine redoxome. Nat Chem Biol 2023; 19:1309-1319. [PMID: 37248412 DOI: 10.1038/s41589-023-01330-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 04/07/2023] [Indexed: 05/31/2023]
Abstract
With an eye toward expanding chemistries used for covalent ligand discovery, we elaborated an umpolung strategy that exploits the 'polarity reversal' of sulfur when cysteine is oxidized to sulfenic acid, a widespread post-translational modification, for selective bioconjugation with C-nucleophiles. Here we present a global map of a human sulfenome that is susceptible to covalent modification by members of a nucleophilic fragment library. More than 500 liganded sulfenic acids were identified on proteins across diverse functional classes, and, of these, more than 80% were not targeted by electrophilic fragment analogs. We further show that members of our nucleophilic fragment library can impair functional protein-protein interactions involved in nuclear oncoprotein transport and DNA damage repair. Our findings reveal a vast expanse of ligandable sulfenic acids in the human proteome and highlight the utility of nucleophilic small molecules in the fragment-based covalent ligand discovery pipeline, presaging further opportunities using non-traditional chemistries for targeting proteins.
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Affiliation(s)
- Ling Fu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing, Beijing Institute of Lifeomics, Beijing, China
| | - Youngeun Jung
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Caiping Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing, Beijing Institute of Lifeomics, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Renan B Ferreira
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL, USA
| | - Ruifeng Cheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing, Beijing Institute of Lifeomics, Beijing, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing, Beijing Institute of Lifeomics, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Jing Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing, Beijing Institute of Lifeomics, Beijing, China.
| | - Kate S Carroll
- Department of Chemistry, UF Scripps Biomedical Research, Jupiter, FL, USA.
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20
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Hassan MM, Li YD, Ma MW, Teng M, Byun WS, Puvar K, Lumpkin R, Sandoval B, Rutter JC, Jin CY, Wang MY, Xu S, Schmoker AM, Cheong H, Groendyke BJ, Qi J, Fischer ES, Ebert BL, Gray NS. Exploration of the Tunability of BRD4 Degradation by DCAF16 Trans-labelling Covalent Glues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.07.561308. [PMID: 37873358 PMCID: PMC10592706 DOI: 10.1101/2023.10.07.561308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Small molecules that can induce protein degradation by inducing proximity between a desired target and an E3 ligase have the potential to greatly expand the number of proteins that can be manipulated pharmacologically. Current strategies for targeted protein degradation are mostly limited in their target scope to proteins with preexisting ligands. Alternate modalities such as molecular glues, as exemplified by the glutarimide class of ligands for the CUL4CRBN ligase, have been mostly discovered serendipitously. We recently reported a trans-labelling covalent glue mechanism which we named 'Template-assisted covalent modification', where an electrophile decorated small molecule binder of BRD4 was effectively delivered to a cysteine residue on an E3 ligase DCAF16 as a consequence of a BRD4-DCAF16 protein-protein interaction. Herein, we report our medicinal chemistry efforts to evaluate how various electrophilic modifications to the BRD4 binder, JQ1, affect DCAF16 trans-labeling and subsequent BRD4 degradation efficiency. We discovered a decent correlation between the ability of the electrophilic small molecule to induce ternary complex formation between BRD4 and DCAF16 with its ability to induce BRD4 degradation. Moreover, we show that a more solvent-exposed warhead presentation is optimal for DCAF16 recruitment and subsequent BRD4 degradation. Unlike the sensitivity of CUL4CRBN glue degraders to chemical modifications, the diversity of covalent attachments in this class of BRD4 glue degraders suggests a high tolerance and tunability for the BRD4-DCAF16 interaction. This offers a potential new avenue for a rational design of covalent glue degraders by introducing covalent warheads to known binders.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michelle W. Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Ryan Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cyrus Y. Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Michelle Y. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna M. Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Hakyung Cheong
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | | | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
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21
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Xie X, Yu T, Li X, Zhang N, Foster LJ, Peng C, Huang W, He G. Recent advances in targeting the "undruggable" proteins: from drug discovery to clinical trials. Signal Transduct Target Ther 2023; 8:335. [PMID: 37669923 PMCID: PMC10480221 DOI: 10.1038/s41392-023-01589-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/22/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Undruggable proteins are a class of proteins that are often characterized by large, complex structures or functions that are difficult to interfere with using conventional drug design strategies. Targeting such undruggable targets has been considered also a great opportunity for treatment of human diseases and has attracted substantial efforts in the field of medicine. Therefore, in this review, we focus on the recent development of drug discovery targeting "undruggable" proteins and their application in clinic. To make this review well organized, we discuss the design strategies targeting the undruggable proteins, including covalent regulation, allosteric inhibition, protein-protein/DNA interaction inhibition, targeted proteins regulation, nucleic acid-based approach, immunotherapy and others.
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Affiliation(s)
- Xin Xie
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Tingting Yu
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Xiang Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Nan Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Wei Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
| | - Gu He
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, Chengdu, China.
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22
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Srinivasan B. Non-equilibrium modalities of inhibition: Characterizing irreversible inhibition for the ErbB receptor family members. Methods Enzymol 2023; 690:85-108. [PMID: 37858541 DOI: 10.1016/bs.mie.2023.08.004] [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] [Indexed: 10/21/2023]
Abstract
Most drug target interactions for clinically approved small-molecules are non-equilibrium slow-onset, tight-binding or irreversible in nature, with pronounced element of time-dependence of inhibition. Analysis of such modality of inhibition requires a continuous enzyme kinetic measurement that can yield complete progress curves and an automated high-throughput analysis pipeline. Given the increasing emphasis on designing non-equilibrium modes of inhibiting an enzyme target (especially irreversible), the above specified pipeline for data generation and analysis is essential for extracting parameters to guide decisions in early drug discovery. In this manuscript, the methodology and data analysis protocol from our irreversible inhibitor characterization campaigns for the ErbB receptor family members is presented. Guidance is provided on the appropriate design of assay to generate quality data, setting up the analysis and estimation of inactivation rate (kinact) and the pseudo-equilibrium binding affinity (KI) constant (or their ratio kinact/KI) in a high-throughput manner for the inhibitor interacting with the protein target of interest.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom.
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23
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Zhao WS, Chen KF, Liu M, Jia XL, Huang YQ, Hao BB, Hu H, Shen XY, Yu Q, Tan MJ. Investigation of targets and anticancer mechanisms of covalently acting natural products by functional proteomics. Acta Pharmacol Sin 2023; 44:1701-1711. [PMID: 36932232 PMCID: PMC10374574 DOI: 10.1038/s41401-023-01072-z] [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: 10/31/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Eriocalyxin B (EB), 17-hydroxy-jolkinolide B (HJB), parthenolide (PN), xanthatin (XT) and andrographolide (AG) are terpenoid natural products with a variety of promising antitumor activities, which commonly bear electrophilic groups (α,β-unsaturated carbonyl groups and/or epoxides) capable of covalently modifying protein cysteine residues. However, their direct targets and underlying molecular mechanisms are still largely unclear, which limits the development of these compounds. In this study, we integrated activity-based protein profiling (ABPP) and quantitative proteomics approach to systematically characterize the covalent targets of these natural products and their involved cellular pathways. We first demonstrated the anti-proliferation activities of these five compounds in triple-negative breast cancer cell MDA-MB-231. Tandem mass tag (TMT)-based quantitative proteomics showed all five compounds commonly affected the ubiquitin mediated proteolysis pathways. ABPP platform identified the preferentially modified targets of EB and PN, two natural products with high anti-proliferation activity. Biochemical experiments showed that PN inhibited the cell proliferation through targeting ubiquitin carboxyl-terminal hydrolase 10 (USP10). Together, this study uncovered the covalently modified targets of these natural products and potential molecular mechanisms of their antitumor activities.
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Affiliation(s)
- Wen-Si Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
| | - Man Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xing-Long Jia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yu-Qi Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Yan Shen
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qiang Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
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24
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Hartung IV, Rudolph J, Mader MM, Mulder MPC, Workman P. Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes. J Med Chem 2023; 66:9297-9312. [PMID: 37403870 PMCID: PMC10388296 DOI: 10.1021/acs.jmedchem.3c00550] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Indexed: 07/06/2023]
Abstract
Within druggable target space, new small-molecule modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal chemists. Molecules with such modes of action have a large potential not only as drugs but also as chemical probes. Criteria have previously been established to describe the potency, selectivity, and properties of small-molecule probes that are qualified to enable the interrogation and validation of drug targets. These definitions have been tailored to reversibly acting modulators but fall short in their applicability to other modalities. While initial guidelines have been proposed, we delineate here a full set of criteria for the characterization of covalent, irreversible inhibitors as well as heterobifunctional degraders ("proteolysis-targeting chimeras", or PROTACs) and molecular glue degraders. We propose modified potency and selectivity criteria compared to those for reversible inhibitors. We discuss their relevance and highlight examples of suitable probe and pathfinder compounds.
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Affiliation(s)
- Ingo V. Hartung
- Medicinal
Chemistry, Global Research & Development, Merck Healthcare KGaA, 64293 Darmstadt, Germany
| | - Joachim Rudolph
- Discovery
Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Mary M. Mader
- Molecular
Innovation, Indiana Biosciences Research
Institute, Indianapolis, Indiana 64202, United States
| | - Monique P. C. Mulder
- Department
of Cell and Chemical Biology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul Workman
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London, Sutton SM2 5NG, United Kingdom
- Chemical
Probes Portal, https://www.chemicalprobes.org/
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25
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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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26
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Kim D, Orr MJ, Kwong AJ, Deibler KK, Munshi HH, Bridges CS, Chen TJ, Zhang X, Lacorazza HD, Scheidt KA. Rational Design of Highly Potent and Selective Covalent MAP2K7 Inhibitors. ACS Med Chem Lett 2023; 14:606-613. [PMID: 37197477 PMCID: PMC10184151 DOI: 10.1021/acsmedchemlett.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
The mitogen-activated protein kinase signaling cascade is conserved across eukaryotes, where it plays a critical role in the regulation of activities including proliferation, differentiation, and stress responses. This pathway propagates external stimuli through a series of phosphorylation events, which allows external signals to influence metabolic and transcriptional activities. Within the cascade, MEK, or MAP2K, enzymes occupy a molecular crossroads immediately upstream to significant signal divergence and cross-talk. One such kinase, MAP2K7, also known as MEK7 and MKK7, is a protein of great interest in the molecular pathophysiology underlying pediatric T cell acute lymphoblastic leukemia (T-ALL). Herein, we describe the rational design, synthesis, evaluation, and optimization of a novel class of irreversible MAP2K7 inhibitors. With a streamlined one-pot synthesis, favorable in vitro potency and selectivity, and promising cellular activity, this novel class of compounds wields promise as a powerful tool in the study of pediatric T-ALL.
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Affiliation(s)
- Dalton
R. Kim
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Meghan J. Orr
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Ada J. Kwong
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kristine K. Deibler
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hasan H. Munshi
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Cory Seth Bridges
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Taylor Jie Chen
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Xiaoyu Zhang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
| | - H. Daniel Lacorazza
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Karl A. Scheidt
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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27
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Tillmanns J, Häge S, Borst EM, Wardin J, Eickhoff J, Klebl B, Wagner S, Wangen C, Hahn F, Socher E, Marschall M. Assessment of Covalently Binding Warhead Compounds in the Validation of the Cytomegalovirus Nuclear Egress Complex as an Antiviral Target. Cells 2023; 12:cells12081162. [PMID: 37190072 DOI: 10.3390/cells12081162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Herpesviral nuclear egress is a regulated process of viral capsid nucleocytoplasmic release. Due to the large capsid size, a regular transport via the nuclear pores is unfeasible, so that a multistage-regulated export pathway through the nuclear lamina and both leaflets of the nuclear membrane has evolved. This process involves regulatory proteins, which support the local distortion of the nuclear envelope. For human cytomegalovirus (HCMV), the nuclear egress complex (NEC) is determined by the pUL50-pUL53 core that initiates multicomponent assembly with NEC-associated proteins and capsids. The transmembrane NEC protein pUL50 serves as a multi-interacting determinant that recruits regulatory proteins by direct and indirect contacts. The nucleoplasmic core NEC component pUL53 is strictly associated with pUL50 in a structurally defined hook-into-groove complex and is considered as the potential capsid-binding factor. Recently, we validated the concept of blocking the pUL50-pUL53 interaction by small molecules as well as cell-penetrating peptides or an overexpression of hook-like constructs, which can lead to a pronounced degree of antiviral activity. In this study, we extended this strategy by utilizing covalently binding warhead compounds, originally designed as binders of distinct cysteine residues in target proteins, such as regulatory kinases. Here, we addressed the possibility that warheads may likewise target viral NEC proteins, building on our previous crystallization-based structural analyses that revealed distinct cysteine residues in positions exposed from the hook-into-groove binding surface. To this end, the antiviral and NEC-binding properties of a selection of 21 warhead compounds were investigated. The combined findings are as follows: (i) warhead compounds exhibited a pronounced anti-HCMV potential in cell-culture-based infection models; (ii) computational analysis of NEC primary sequences and 3D structures revealed cysteine residues exposed to the hook-into-groove interaction surface; (iii) several of the active hit compounds exhibited NEC-blocking activity, as shown at the single-cell level by confocal imaging; (iv) the clinically approved warhead drug ibrutinib exerted a strong inhibitory impact on the pUL50-pUL53 core NEC interaction, as demonstrated by the NanoBiT assay system; and (v) the generation of recombinant HCMV ∆UL50-ΣUL53, allowing the assessment of viral replication under conditional expression of the viral core NEC proteins, was used for characterizing viral replication and a mechanistic evaluation of ibrutinib antiviral efficacy. Combined, the results point to a rate-limiting importance of the HCMV core NEC for viral replication and to the option of exploiting this determinant by the targeting of covalently NEC-binding warhead compounds.
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Affiliation(s)
- Julia Tillmanns
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Sigrun Häge
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Eva Maria Borst
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Julia Wardin
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Jan Eickhoff
- Lead Discovery Center GmbH (LDC), 44227 Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH (LDC), 44227 Dortmund, Germany
- The Norwegian College of Fishery Science UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Eileen Socher
- Institute of Anatomy, Functional and Clinical Anatomy, FAU, 91054 Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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28
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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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29
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Orgován Z, Péczka N, Petri L, Ábrányi-Balogh P, Ranđelović I, Tóth S, Szakács G, Nyíri K, Vértessy B, Pálfy G, Vida I, Perczel A, Tóvári J, Keserű GM. Covalent fragment mapping of KRas G12C revealed novel chemotypes with in vivo potency. Eur J Med Chem 2023; 250:115212. [PMID: 36842271 DOI: 10.1016/j.ejmech.2023.115212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
G12C mutant KRas is considered druggable by allele-specific covalent inhibitors due to the nucleophilic character of the oncogenic mutant cysteine at position 12. Discovery of these inhibitors requires the optimization of both covalent and noncovalent interactions. Here, we report covalent fragment screening of our electrophilic fragment library of diverse non-covalent scaffolds equipped with 40 different electrophilic functionalities to identify fragments as suitable starting points targeting Cys12. Screening the library against KRasG12C using Ellman's free thiol assay, followed by protein NMR and cell viability assays, resulted in two potential inhibitor chemotypes. Characterization of these scaffolds in in vitro cellular- and in vivo xenograft models revealed them as promising starting points for covalent drug discovery programs.
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Affiliation(s)
- Zoltán Orgován
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary
| | - Nikolett Péczka
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary; Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary; Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | | | - Szilárd Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Kinga Nyíri
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary
| | - Beáta Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary; MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - István Vida
- Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary; MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary; MTA-ELTE Protein Modelling Research Group, Eötvös Loránd University, Budapest, Hungary
| | - József Tóvári
- Department of Experimental Pharmacology and the National Tumor Biology Laboratory, National Institute of Oncology, Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, and National Drug Discovery and Development Laboratory, Budapest, Hungary; Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
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30
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Dahlin JL, Hua BK, Zucconi BE, Nelson SD, Singh S, Carpenter AE, Shrimp JH, Lima-Fernandes E, Wawer MJ, Chung LPW, Agrawal A, O'Reilly M, Barsyte-Lovejoy D, Szewczyk M, Li F, Lak P, Cuellar M, Cole PA, Meier JL, Thomas T, Baell JB, Brown PJ, Walters MA, Clemons PA, Schreiber SL, Wagner BK. Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nat Commun 2023; 14:1364. [PMID: 36914634 PMCID: PMC10011410 DOI: 10.1038/s41467-023-36829-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Robust, generalizable approaches to identify compounds efficiently with undesirable mechanisms of action in complex cellular assays remain elusive. Such a process would be useful for hit triage during high-throughput screening and, ultimately, predictive toxicology during drug development. Here we generate cell painting and cellular health profiles for 218 prototypical cytotoxic and nuisance compounds in U-2 OS cells in a concentration-response format. A diversity of compounds that cause cellular damage produces bioactive cell painting morphologies, including cytoskeletal poisons, genotoxins, nonspecific electrophiles, and redox-active compounds. Further, we show that lower quality lysine acetyltransferase inhibitors and nonspecific electrophiles can be distinguished from more selective counterparts. We propose that the purposeful inclusion of cytotoxic and nuisance reference compounds such as those profiled in this resource will help with assay optimization and compound prioritization in complex cellular assays like cell painting.
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Grants
- R35 GM127045 NIGMS NIH HHS
- U01 CA272612 NCI NIH HHS
- T32 HL007627 NHLBI NIH HHS
- R37 GM062437 NIGMS NIH HHS
- S10 OD026839 NIH HHS
- R35 GM122481 NIGMS NIH HHS
- U01 DK123717 NIDDK NIH HHS
- Wellcome Trust
- R35 GM122547 NIGMS NIH HHS
- U01 CA217848 NCI NIH HHS
- K99 GM124357 NIGMS NIH HHS
- R35 GM149229 NIGMS NIH HHS
- This study was supported by the Ono Pharma Breakthrough Science Initiative Award (to BKW). Authors acknowledge the following financial support: JLD (NIH NHLBI, T32-HL007627); BKH (National Science Foundation, DGE1144152 and DGE1745303); BEZ (NIH NIGMS, K99-GM124357); SDN (Harvard University’s Graduate Prize Fellowship, Eli Lilly Graduate Fellowship in Chemistry); PA Cole (NIH NIGMS, R37-GM62437); SLS (NIGMS, R35-GM127045); BKW (Ono Pharma Foundation; NIH NIDDK, U01-DK123717); SS (NIH NIGMS, R35-GM122547). The authors gratefully acknowledge the use of the Opera Phenix High-Content/High-Throughput imaging system at the Broad Institute, funded by the NIH S10 grant OD026839. This research was supported in part by the Intramural/Extramural research program of the NCATS, NIH.
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Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Beth E Zucconi
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Mathias J Wawer
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Lawrence P W Chung
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Ayushi Agrawal
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | | | | | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Parnian Lak
- Department of Pharmaceutical Chemistry and Quantitative Biology Institute, University of California San Francisco, San Francisco, CA, USA
| | - Matthew Cuellar
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Tim Thomas
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jonathan B Baell
- Medicinal Chemistry Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA.
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31
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Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [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: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
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Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
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32
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Rodríguez Á, Maneiro M, Lence E, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Quinate-based ligands for irreversible inactivation of the bacterial virulence factor DHQ1 enzyme-A molecular insight. Front Mol Biosci 2023; 10:1111598. [PMID: 36762206 PMCID: PMC9902378 DOI: 10.3389/fmolb.2023.1111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Irreversible inhibition of the enzyme type I dehydroquinase (DHQ1), a promising target for anti-virulence drug development, has been explored by enhancing the electrophilicity of specific positions of the ligand towards covalent lysine modification. For ligand design, we made use of the advantages offered by the intrinsic acid-base properties of the amino substituents introduced in the quinate scaffold, namely compounds 6-7 (R configuration at C3), to generate a potential leaving group, as well as the recognition pattern of the enzyme. The reactivity of the C2-C3 bond (Re face) in the scaffold was also explored using compound 8. The results of the present study show that replacement of the C3 hydroxy group of (-)-quinic acid by a hydroxyamino substituent (compound 6) provides a time-dependent irreversible inhibitor, while compound 7, in which the latter functionality was substituted by an amino group, and the introduction of an oxirane ring at C2-C3 bond, compound 8, do not allow covalent modification of the enzyme. These outcomes were supported by resolution of the crystal structures of DHQ1 from Staphylococcus aureus (Sa-DHQ1) and Salmonella typhi (St-DHQ1) chemically modified by 6 at a resolution of 1.65 and 1.90 Å, respectively, and of St-DHQ1 in the complex with 8 (1.55 Å). The combination of these structural studies with extensive molecular dynamics simulation studies allowed us to understand the molecular basis of the type of inhibition observed. This study is a good example of the importance of achieving the correct geometry between the reactive center of the ligand (electrophile) and the enzyme nucleophile (lysine residue) to allow selective covalent modification. The outcomes obtained with the hydroxyamino derivative 6 also open up new possibilities in the design of irreversible inhibitors based on the use of amino substituents.
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Affiliation(s)
- Ángela Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - José M. Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - Paul Thompson
- Newcastle University Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alastair R. Hawkins
- Newcastle University Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain,*Correspondence: Concepción González-Bello,
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33
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Wu Q, Huang SY. HCovDock: an efficient docking method for modeling covalent protein-ligand interactions. Brief Bioinform 2023; 24:6961470. [PMID: 36573474 DOI: 10.1093/bib/bbac559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/02/2022] [Accepted: 11/17/2022] [Indexed: 12/28/2022] Open
Abstract
Covalent inhibitors have received extensive attentions in the past few decades because of their long residence time, high binding efficiency and strong selectivity. Therefore, it is valuable to develop computational tools like molecular docking for modeling of covalent protein-ligand interactions or screening of potential covalent drugs. Meeting the needs, we have proposed HCovDock, an efficient docking algorithm for covalent protein-ligand interactions by integrating a ligand sampling method of incremental construction and a scoring function with covalent bond-based energy. Tested on a benchmark containing 207 diverse protein-ligand complexes, HCovDock exhibits a significantly better performance than seven other state-of-the-art covalent docking programs (AutoDock, Cov_DOX, CovDock, FITTED, GOLD, ICM-Pro and MOE). With the criterion of ligand root-mean-squared distance < 2.0 Å, HCovDock obtains a high success rate of 70.5% and 93.2% in reproducing experimentally observed structures for top 1 and top 10 predictions. In addition, HCovDock is also validated in virtual screening against 10 receptors of three proteins. HCovDock is computationally efficient and the average running time for docking a ligand is only 5 min with as fast as 1 sec for ligands with one rotatable bond and about 18 min for ligands with 23 rotational bonds. HCovDock can be freely assessed at http://huanglab.phys.hust.edu.cn/hcovdock/.
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Affiliation(s)
- Qilong Wu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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34
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Dueñas ME, Peltier‐Heap RE, Leveridge M, Annan RS, Büttner FH, Trost M. Advances in high-throughput mass spectrometry in drug discovery. EMBO Mol Med 2023; 15:e14850. [PMID: 36515561 PMCID: PMC9832828 DOI: 10.15252/emmm.202114850] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022] Open
Abstract
High-throughput (HT) screening drug discovery, during which thousands or millions of compounds are screened, remains the key methodology for identifying active chemical matter in early drug discovery pipelines. Recent technological developments in mass spectrometry (MS) and automation have revolutionized the application of MS for use in HT screens. These methods allow the targeting of unlabelled biomolecules in HT assays, thereby expanding the breadth of targets for which HT assays can be developed compared to traditional approaches. Moreover, these label-free MS assays are often cheaper, faster, and more physiologically relevant than competing assay technologies. In this review, we will describe current MS techniques used in drug discovery and explain their advantages and disadvantages. We will highlight the power of mass spectrometry in label-free in vitro assays, and its application for setting up multiplexed cellular phenotypic assays, providing an exciting new tool for screening compounds in cell lines, and even primary cells. Finally, we will give an outlook on how technological advances will increase the future use and the capabilities of mass spectrometry in drug discovery.
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Affiliation(s)
- Maria Emilia Dueñas
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel E Peltier‐Heap
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Melanie Leveridge
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Roland S Annan
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Frank H Büttner
- Drug Discovery Sciences, High Throughput BiologyBoehringer Ingelheim Pharma GmbH&CoKGBiberachGermany
| | - Matthias Trost
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
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35
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Abstract
Covalent inhibition has emerged as a promising orthogonal approach for drug discovery, despite the significant challenge in achieving target specificity. To facilitate the structure-based rational design of target-specific covalent modulators, we developed an integrated computational protocol to curate covalent binders from the RCSB Protein Data Bank (PDB). Starting from the macromolecular crystallographic information files (mmCIF) in the PDB archive, covalent bond records, which indicate the side chain modification of amino acid residue by a covalent binder, were collected and cleaned. Then, residue-binder adducts, which are products of chemical reactions between targeted residues and covalent binders, were recovered with the help of the Chemical Component Dictionary in PDB. Finally, several strategies were employed to curate the pre-reaction forms of covalent binders from the adducts. Our curated CovBinderInPDB database contains 7375 covalent modifications in which 2189 unique covalent binders target nine types of amino acid residues (Cys, Lys, Ser, Asp, Glu, His, Met, Thr, and Tyr) from 3555 complex structures of 1170 unique protein chains. This database would set a solid foundation for developing and benchmarking computational strategies for covalent modulator design and is freely accessible at https://yzhang.hpc.nyu.edu/CovBinderInPDB.
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Affiliation(s)
- Xiao-Kang Guo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States, Simons Center for Computational Physical Chemistry, New York University, New York, New York 10003, United States, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China,
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36
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Abstract
Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addition of reactive functional groups to existing ligands can enable potent and selective inhibition of target proteins, as demonstrated by the covalent epidermal growth factor receptor (EGFR) and Bruton's tyrosine kinase (BTK) inhibitors used to treat various cancers. Moreover, the identification of covalent ligands through 'electrophile-first' approaches has also led to the discovery of covalent drugs, such as covalent inhibitors for KRAS(G12C) and SARS-CoV-2 main protease. In particular, the discovery of KRAS(G12C) inhibitors validates the use of covalent screening technologies, which have become more powerful and widespread over the past decade. Chemoproteomics platforms have emerged to complement covalent ligand screening and assist in ligand discovery, selectivity profiling and target identification. This Review showcases covalent drug discovery milestones with emphasis on the lessons learned from these programmes and how an evolving toolbox of covalent drug discovery techniques facilitates success in this field.
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Affiliation(s)
- Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
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37
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Ábrányi-Balogh P, Keeley A, Ferenczy GG, Petri L, Imre T, Grabrijan K, Hrast M, Knez D, Ilaš J, Gobec S, Keserű GM. Next-Generation Heterocyclic Electrophiles as Small-Molecule Covalent MurA Inhibitors. Pharmaceuticals (Basel) 2022; 15:ph15121484. [PMID: 36558935 PMCID: PMC9781958 DOI: 10.3390/ph15121484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Heterocyclic electrophiles as small covalent fragments showed promising inhibitory activity on the antibacterial target MurA (UDP-N-acetylglucosamine 1-carboxyvinyltransferase, EC:2.5.1.7). Here, we report the second generation of heterocyclic electrophiles: the quaternized analogue of the heterocyclic covalent fragment library with improved reactivity and MurA inhibitory potency. Quantum chemical reaction barrier calculations, GSH (L-glutathione) reactivity assay, and thrombin counter screen were also used to demonstrate and explain the improved reactivity and selectivity of the N-methylated heterocycles and to compare the two generations of heterocyclic electrophiles.
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Affiliation(s)
- Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - György G. Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - László Petri
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - Tímea Imre
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
| | - Katarina Grabrijan
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Martina Hrast
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Damijan Knez
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Janez Ilaš
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - György M. Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Correspondence:
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38
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Bolding JE, Martín‐Gago P, Rajabi N, Gamon LF, Hansen TN, Bartling CRO, Strømgaard K, Davies MJ, Olsen CA. Aryl Fluorosulfate Based Inhibitors That Covalently Target the SIRT5 Lysine Deacylase. Angew Chem Int Ed Engl 2022; 61:e202204565. [PMID: 36130196 PMCID: PMC9828517 DOI: 10.1002/anie.202204565] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 01/12/2023]
Abstract
The sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl ϵ-N-carboxyacyllysine posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target have been lacking. Here we report the harnessing of aryl fluorosulfate-based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne-tagged affinity-labeling agents recognize and capture overexpressed SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compound. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will serve as inspiration for future studies investigating SIRT5 and general sirtuin biology in the mitochondria.
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Affiliation(s)
- Julie E. Bolding
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Pablo Martín‐Gago
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Luke F. Gamon
- Department of Biomedical SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenBlegdamsvej 3DK-2200CopenhagenDenmark
| | - Tobias N. Hansen
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Christian R. O. Bartling
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Michael J. Davies
- Department of Biomedical SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenBlegdamsvej 3DK-2200CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
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39
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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: 14] [Impact Index Per Article: 7.0] [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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40
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Bon M, Bilsland A, Bower J, McAulay K. Fragment-based drug discovery-the importance of high-quality molecule libraries. Mol Oncol 2022; 16:3761-3777. [PMID: 35749608 PMCID: PMC9627785 DOI: 10.1002/1878-0261.13277] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/16/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is now established as a complementary approach to high-throughput screening (HTS). Contrary to HTS, where large libraries of drug-like molecules are screened, FBDD screens involve smaller and less complex molecules which, despite a low affinity to protein targets, display more 'atom-efficient' binding interactions than larger molecules. Fragment hits can, therefore, serve as a more efficient start point for subsequent optimisation, particularly for hard-to-drug targets. Since the number of possible molecules increases exponentially with molecular size, small fragment libraries allow for a proportionately greater coverage of their respective 'chemical space' compared with larger HTS libraries comprising larger molecules. However, good library design is essential to ensure optimal chemical and pharmacophore diversity, molecular complexity, and physicochemical characteristics. In this review, we describe our views on fragment library design, and on what constitutes a good fragment from a medicinal and computational chemistry perspective. We highlight emerging chemical and computational technologies in FBDD and discuss strategies for optimising fragment hits. The impact of novel FBDD approaches is already being felt, with the recent approval of the covalent KRASG12C inhibitor sotorasib highlighting the utility of FBDD against targets that were long considered undruggable.
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Affiliation(s)
- Marta Bon
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Alan Bilsland
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Justin Bower
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Kirsten McAulay
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
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41
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Chemical and biology of Sulfur (VI) Fluoride Exchange (SuFEx) Click Chemistry for Drug Discovery. Bioorg Chem 2022; 130:106227. [DOI: 10.1016/j.bioorg.2022.106227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/05/2022] [Accepted: 10/22/2022] [Indexed: 11/19/2022]
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42
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St. Denis JD, Chessari G, Cleasby A, Cons BD, Cowan S, Dalton SE, East C, Murray CW, O’Reilly M, Peakman T, Rapti M, Stow JL. X-ray Screening of an Electrophilic Fragment Library and Application toward the Development of a Novel ERK 1/2 Covalent Inhibitor. J Med Chem 2022; 65:12319-12333. [DOI: 10.1021/acs.jmedchem.2c01044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jeffrey D. St. Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Anne Cleasby
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Benjamin D. Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Suzanna Cowan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Samuel E. Dalton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Charlotte East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Marc O’Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Magdalini Rapti
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Jessie L. Stow
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
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43
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Chan AM, Goodis CC, Pommier EG, Fletcher S. Recent applications of covalent chemistries in protein-protein interaction inhibitors. RSC Med Chem 2022; 13:921-928. [PMID: 36092144 PMCID: PMC9384789 DOI: 10.1039/d2md00112h] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/30/2022] [Indexed: 10/17/2023] Open
Abstract
Protein-protein interactions (PPIs) are large, often featureless domains whose modulations by small-molecules are challenging. Whilst there are some notable successes, such as the BCL-2 inhibitor venetoclax, the requirement for larger ligands to achieve the desired level of potency and selectivity may result in poor "drug-like" properties. Covalent chemistry is presently enjoying a renaissance. In particular, targeted covalent inhibition (TCI), in which a weakly electrophilic "warhead" is installed onto a protein ligand scaffold, is a powerful strategy to develop potent inhibitors of PPIs that are smaller/more drug-like yet have enhanced affinities by virtue of the reinforcing effect on the existing non-covalent interactions by the resulting protein-ligand covalent bond. Furthermore, the covalent bond delivers sustained inhibition, which may translate into significantly reduced therapeutic dosing. Herein, we discuss recent applications of a spectrum of TCIs, as well as covalent screening strategies, in the discovery of more effective inhibitors of PPIs using the HDM2 and BCL-2 protein families as case studies.
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Affiliation(s)
- Alexandria M Chan
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences 20 N. Pine St Baltimore MD 21201 USA
| | - Christopher C Goodis
- University of Maryland School of Pharmacy PharmD Program, 20 N. Pine St Baltimore MD 21201 USA
| | - Elie G Pommier
- University of Maryland School of Pharmacy PharmD Program, 20 N. Pine St Baltimore MD 21201 USA
| | - Steven Fletcher
- University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences 20 N. Pine St Baltimore MD 21201 USA
- University of Maryland Greenebaum Cancer Center 20 S. Greene St Baltimore MD 21201 USA
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44
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Du H, Jiang D, Gao J, Zhang X, Jiang L, Zeng Y, Wu Z, Shen C, Xu L, Cao D, Hou T, Pan P. Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network. Research (Wash D C) 2022; 2022:9873564. [PMID: 35958111 PMCID: PMC9343084 DOI: 10.34133/2022/9873564] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/27/2022] [Indexed: 11/06/2022] Open
Abstract
Covalent ligands have attracted increasing attention due to their unique advantages, such as long residence time, high selectivity, and strong binding affinity. They also show promise for targets where previous efforts to identify noncovalent small molecule inhibitors have failed. However, our limited knowledge of covalent binding sites has hindered the discovery of novel ligands. Therefore, developing in silico methods to identify covalent binding sites is highly desirable. Here, we propose DeepCoSI, the first structure-based deep graph learning model to identify ligandable covalent sites in the protein. By integrating the characterization of the binding pocket and the interactions between each cysteine and the surrounding environment, DeepCoSI achieves state-of-the-art predictive performances. The validation on two external test sets which mimic the real application scenarios shows that DeepCoSI has strong ability to distinguish ligandable sites from the others. Finally, we profiled the entire set of protein structures in the RCSB Protein Data Bank (PDB) with DeepCoSI to evaluate the ligandability of each cysteine for covalent ligand design, and made the predicted data publicly available on website.
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Affiliation(s)
- Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Junbo Gao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Xujun Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Lingxiao Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Yundian Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Zhenxing Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Chao Shen
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Dongsheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410004 Hunan, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, 310058 Zhejiang, China
| | - Peichen Pan
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 Zhejiang, China
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45
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Beerkens BLH, Wang X, Avgeropoulou M, Adistia LN, van Veldhoven JPD, Jespers W, Liu R, Heitman LH, IJzerman AP, van der Es D. Development of subtype-selective covalent ligands for the adenosine A 2B receptor by tuning the reactive group. RSC Med Chem 2022; 13:850-856. [PMID: 35923720 PMCID: PMC9298184 DOI: 10.1039/d2md00132b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/18/2022] [Indexed: 01/15/2024] Open
Abstract
Signalling through the adenosine receptors (ARs), in particular through the adenosine A2B receptor (A2BAR), has been shown to play a role in a variety of pathological conditions, ranging from immune disorders to cancer. Covalent ligands for the A2BAR have the potential to irreversibly block the receptor, as well as inhibit all A2BAR-induced signalling pathways. This will allow a thorough investigation of the pathophysiological role of the receptor. In this study, we synthesized and evaluated a set of potential covalent ligands for the A2BAR. The ligands all contain a core scaffold consisting of a substituted xanthine, varying in type and orientation of electrophilic group (warhead). Here, we find that the right combination of these variables is necessary for a high affinity, irreversible mode of binding and selectivity towards the A2BAR. Altogether, this is the case for sulfonyl fluoride 24 (LUF7982), a covalent ligand that allows for novel ways to interrogate the A2BAR.
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Affiliation(s)
- Bert L H Beerkens
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Xuesong Wang
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Maria Avgeropoulou
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Lisa N Adistia
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Jacobus P D van Veldhoven
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Willem Jespers
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Rongfang Liu
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Daan van der Es
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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46
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Gong S, Hu X, Chen S, Sun B, Wu JL, Li N. Dual roles of drug or its metabolite-protein conjugate: Cutting-edge strategy of drug discovery using shotgun proteomics. Med Res Rev 2022; 42:1704-1734. [PMID: 35638460 DOI: 10.1002/med.21889] [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: 01/07/2022] [Revised: 03/24/2022] [Accepted: 05/04/2022] [Indexed: 11/11/2022]
Abstract
Many drugs can bind directly to proteins or be bioactivated by metabolizing enzymes to form reactive metabolites (RMs) that rapidly bind to proteins to form drug-protein conjugates or metabolite-protein conjugates (DMPCs). The close relationship between DMPCs and idiosyncratic adverse drug reactions (IADRs) has been recognized; drug discovery teams tend to avoid covalent interactions in drug discovery projects. Covalent interactions in DMPCs can provide high potency and long action duration and conquer the intractable targets, inspiring drug design, and development. This forms the dual role feature of DMPCs. Understanding the functional implications of DMPCs in IADR control and therapeutic applications requires precise identification of these conjugates from complex biological samples. While classical biochemical methods have contributed significantly to DMPC detection in the past decades, the low abundance and low coverage of DMPCs have become a bottleneck in this field. An emerging transformation toward shotgun proteomics is on the rise. The evolving shotgun proteomics techniques offer improved reproducibility, throughput, specificity, operability, and standardization. Here, we review recent progress in the systematic discovery of DMPCs using shotgun proteomics. Furthermore, the applications of shotgun proteomics supporting drug development, toxicity mechanism investigation, and drug repurposing processes are also reviewed and prospected.
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Affiliation(s)
- Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Xiaolan Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Shengshuang Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, National Respiratory Medical Center, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau
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47
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Chen P, Sun J, Zhu C, Tang G, Wang W, Xu M, Xiang M, Zhang CJ, Zhang ZM, Gao L, Yao SQ. Cell-Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR-ABL Kinase. Angew Chem Int Ed Engl 2022; 61:e202203878. [PMID: 35438229 DOI: 10.1002/anie.202203878] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Indexed: 12/16/2022]
Abstract
Despite recent interests in developing lysine-targeting covalent inhibitors, no general approach is available to create such compounds. We report herein a general approach to develop cell-active covalent inhibitors of protein kinases by targeting the conserved catalytic lysine residue using key SuFEx and salicylaldehyde-based imine chemistries. We validated the strategy by successfully developing (irreversible and reversible) covalent inhibitors against BCR-ABL kinase. Our lead compounds showed high levels of selectivity in biochemical assays, exhibited nanomolar potency against endogenous ABL kinase in cellular assays, and were active against most drug-resistant ABL mutations. Among them, the salicylaldehyde-containing A5 is the first-ever reversible covalent ABL inhibitor that possessed time-dependent ABL inhibition with prolonged residence time and few cellular off-targets in K562 cells. Bioinformatics further suggested the generality of our strategy against the human kinome.
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Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan, Guangdong, 528200, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and, Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and, Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan, Guangdong, 528200, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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48
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Mons E, Roet S, Kim RQ, Mulder MPC. A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations. Curr Protoc 2022; 2:e419. [PMID: 35671150 DOI: 10.1002/cpz1.419] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Covalent inhibition has become more accepted in the past two decades, as illustrated by the clinical approval of several irreversible inhibitors designed to covalently modify their target. Elucidation of the structure-activity relationship and potency of such inhibitors requires a detailed kinetic evaluation. Here, we elucidate the relationship between the experimental read-out and the underlying inhibitor binding kinetics. Interactive kinetic simulation scripts are employed to highlight the effects of in vitro enzyme activity assay conditions and inhibitor binding mode, thereby showcasing which assumptions and corrections are crucial. Four stepwise protocols to assess the biochemical potency of (ir)reversible covalent enzyme inhibitors targeting a nucleophilic active site residue are included, with accompanying data analysis tailored to the covalent binding mode. Together, this will serve as a guide to make an educated decision regarding the most suitable method to assess covalent inhibition potency. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol I: Progress curve analysis of substrate association competition Basic Data Analysis Protocol 1A: Two-step irreversible covalent inhibition Basic Data Analysis Protocol 1B: One-step irreversible covalent inhibition Basic Data Analysis Protocol 1C: Two-step reversible covalent inhibition Basic Data Analysis Protocol 1D: Two-step irreversible covalent inhibition with substrate depletion Basic Protocol II: Incubation time-dependent potency IC50 (t) Basic Data Analysis Protocol 2: Two-step irreversible covalent inhibition Basic Protocol III: Preincubation time-dependent inhibition without dilution Basic Data Analysis Protocol 3: Preincubation time-dependent inhibition without dilution Basic Data Analysis Protocol 3Ai: Two-step irreversible covalent inhibition Alternative Data Analysis Protocol 3Aii: Two-step irreversible covalent inhibition Basic Data Analysis Protocol 3Bi: One-step irreversible covalent inhibition Alternative Data Analysis Protocol 3Bii: One-step irreversible covalent inhibition Basic Data Analysis Protocol 3C: Two-step reversible covalent inhibition Basic Protocol IV: Preincubation time-dependent inhibition with dilution/competition Basic Data Analysis Protocol 4: Preincubation time-dependent inhibition with dilution Basic Data Analysis Protocol 4Ai: Two-step irreversible covalent inhibition Alternative Data Analysis Protocol 4Aii: Two-step irreversible covalent inhibition Basic Data Analysis Protocol 4Bi: One-step irreversible covalent inhibition Alternative Data Analysis Protocol 4Bii: One-step irreversible covalent inhibition.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.,Current: Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Sander Roet
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim, Norway
| | - Robbert Q Kim
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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49
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Chen P, Sun J, Zhu C, Tang G, Wang W, Xu M, Xiang M, Zhang C, Zhang Z, Gao L, Yao SQ. Cell‐Active, Reversible, and Irreversible Covalent Inhibitors That Selectively Target the Catalytic Lysine of BCR‐ABL Kinase. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Chengjun Zhu
- School of Pharmacy Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan Guangdong 528200 China
| | - Guanghui Tang
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Chong‐Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Zhi‐Min Zhang
- School of Pharmacy Jinan University 601 Huangpu Avenue West Guangzhou 510632 China
- Guangdong Youmei Institute of Intelligent Bio-manufacturing Foshan Guangdong 528200 China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen) Sun Yat-sen University Shenzhen 518107 China
| | - Shao Q. Yao
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
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Qiu Q, Abis G, Mattingly-Peck F, Lynham S, Fraternali F, Conte MR. Allosteric regulation of the soluble epoxide hydrolase by nitro fatty acids using a combined experimental and computational approach. J Mol Biol 2022; 434:167600. [PMID: 35460669 DOI: 10.1016/j.jmb.2022.167600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/31/2022] [Accepted: 04/17/2022] [Indexed: 11/18/2022]
Abstract
The human soluble epoxide hydrolase (hsEH) is a key regulator of epoxy fatty acid (EpFA) metabolism. Inhibition of sEH can maintain endogenous levels of beneficial EpFAs and reduce the levels of their corresponding diol products, thus ameliorating a variety of pathological conditions including cardiovascular, central nervous system and metabolic diseases. The quest for orthosteric drugs that bind directly to the catalytic crevice of hsEH has been prolonged and sustained over the past decades, but the disappointing outcome of clinical trials to date warrants alternative pharmacological approaches. Previously, we have shown that hsEH can be allosterically inhibited by the endogenous electrophilic lipid 15-deoxy-Δ12,14-Prostaglandin-J2, via covalent adduction to two cysteines, C423 and C522. In this study, we explore the properties and behaviour of three electrophilic lipids belonging to the class of the nitro fatty acids, namely 9- and 10-nitrooleate and 10-nitrolinoleate. Biochemical and biophysical investigations revealed that, in addition to C423 and C522, nitro fatty acids can covalently bind to additional nucleophilic residues in hsEH C-terminal domain (CTD), two of which predicted in this study to be latent allosteric sites. Systematic mapping of the protein mutational space and evaluation of possible propagation pathways delineated selected residues, both in the allosteric patches and in other regions of the enzyme, envisaged to play a role on allosteric signalling. The responses elicited by the ligands on the covalent adduction sites supports future fragment-based design studies of new allosteric effectors for hsEH with increased efficacy and selectivity.
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Affiliation(s)
- Qiongju Qiu
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Giancarlo Abis
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Florence Mattingly-Peck
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, The James Black Centre, King's College London, London SE5 9NU, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, UK.
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