1
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Zhang Y, Liu Z, Hirschi M, Brodsky O, Johnson E, Won SJ, Nagata A, Bezwada D, Petroski MD, Majmudar JD, Niessen S, VanArsdale T, Gilbert AM, Hayward MM, Stewart AE, Nager AR, Melillo B, Cravatt BF. An allosteric cyclin E-CDK2 site mapped by paralog hopping with covalent probes. Nat Chem Biol 2024:10.1038/s41589-024-01738-7. [PMID: 39294320 DOI: 10.1038/s41589-024-01738-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 08/20/2024] [Indexed: 09/20/2024]
Abstract
More than half of the ~20,000 protein-encoding human genes have paralogs. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to subsets of paralogous proteins. Here we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs lacking the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we substituted the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-CCNE1-N112C interaction into in vitro NanoBRET (bioluminescence resonance energy transfer) and in cellulo activity-based protein profiling assays capable of identifying compounds that reversibly inhibit both the N112C mutant and wild-type CCNE1:CDK2 (cyclin-dependent kinase 2) complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings, thus, show how electrophile-cysteine interactions mapped by chemical proteomics can extend the understanding of protein ligandability beyond covalent chemistry.
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Affiliation(s)
- Yuanjin Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Zhonglin Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Marscha Hirschi
- Medicine Design, Pfizer Research and Development, Pfizer, Inc., La Jolla, CA, USA
| | - Oleg Brodsky
- Medicine Design, Pfizer Research and Development, Pfizer, Inc., La Jolla, CA, USA
| | - Eric Johnson
- Medicine Design, Pfizer Research and Development, Pfizer, Inc., La Jolla, CA, USA
| | - Sang Joon Won
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Asako Nagata
- Medicine Design, Pfizer Research and Development, Pfizer, Inc., La Jolla, CA, USA
| | - Divya Bezwada
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Jaimeen D Majmudar
- Discovery Sciences, Pfizer Research and Development, Pfizer, Inc., Cambridge, MA, USA
| | - Sherry Niessen
- Oncology Research and Development, Pfizer, Inc., La Jolla, CA, USA
- Belharra Therapeutics, San Diego, CA, USA
| | - Todd VanArsdale
- Oncology Research and Development, Pfizer, Inc., La Jolla, CA, USA
| | - Adam M Gilbert
- Discovery Sciences, Pfizer Research and Development, Pfizer, Inc., Groton, CT, USA
| | - Matthew M Hayward
- Discovery Sciences, Pfizer Research and Development, Pfizer, Inc., Groton, CT, USA
- Magnet Biomedicine, Boston, MA, USA
| | - Al E Stewart
- Medicine Design, Pfizer Research and Development, Pfizer, Inc., La Jolla, CA, USA
| | - Andrew R Nager
- Oncology Research and Development, Pfizer, Inc., La Jolla, CA, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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2
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Duan D, Guo X, Tian J, Li M, Jin X, Wang Z, Wang L, Yan Y, Xiao J, Song P, Wang X. Targeting thioredoxin reductase by eupalinilide B promotes apoptosis of colorectal cancer cells in vitro and in vivo. Chem Biol Interact 2024; 399:111137. [PMID: 38977166 DOI: 10.1016/j.cbi.2024.111137] [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: 03/27/2024] [Revised: 06/21/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Aberrant activation of thioredoxin reductase (TrxR) is correlated with tumor occurrence and progression, suggesting that TrxR inhibitors can be used as antitumor agents. In this study, we evaluated the anticancer efficacy of eupalinilides B on colorectal cancer cells. Eupalinilides B primarily targeted the conserved selenocysteine 498 residues in TrxR. Besides, it inhibited the enzyme activity in an irreversible manner. After eupalinilides B was used to pharmacologically inhibit TrxR, reactive oxygen species accumulated, and the intracellular redox balance was broken, finally causing oxidative stress-induced tumor cell apoptosis. Significantly, eupalinilides B treatment inhibited in vivo tumor growth. Targeting TrxR by eupalinilides B reveals the new mechanism underlying eupalinilides B and provides insight in developing eupalinilides B as the candidate antitumor chemotherapeutic agent for the treatment of cancer.
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Affiliation(s)
- Dongzhu Duan
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, China
| | - Xiangyu Guo
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, China
| | - Jingjing Tian
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, China
| | - Mi Li
- School of Pharmacy and Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, 730000, China
| | - Xiaojie Jin
- School of Pharmacy and Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, 730000, China
| | - Zihua Wang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, China.
| | - Le Wang
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, China
| | - Yunyun Yan
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, China
| | - Jian Xiao
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, China.
| | - Peng Song
- Affiliated Hospital of Gansu University of Chinese Medicine and Key Laboratory of Prevention and Treatment for Chronic Diseases by TCM, Gansu Province, Lanzhou, 730000, China.
| | - Xiaoling Wang
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, 721013, China.
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3
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Minotti G. Cardiovascular toxicity of Bruton tyrosine kinase inhibitors: forget about selectivity but watch the clock. Blood Adv 2024; 8:3810-3812. [PMID: 38696711 PMCID: PMC11371468 DOI: 10.1182/bloodadvances.2024013348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024] Open
Affiliation(s)
- Giorgio Minotti
- Units of Drug Sciences and Clinical Pharmacology, University and Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
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4
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Raouf YS. Covalent Inhibitors: To Infinity and Beyond. J Med Chem 2024; 67:10513-10516. [PMID: 38913822 DOI: 10.1021/acs.jmedchem.4c01308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Affiliation(s)
- Yasir S Raouf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain 15551, UAE
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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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Schwarz M, Kurkunov M, Wittlinger F, Rudalska R, Wang G, Schwalm MP, Rasch A, Wagner B, Laufer SA, Knapp S, Dauch D, Gehringer M. Development of Highly Potent and Selective Covalent FGFR4 Inhibitors Based on S NAr Electrophiles. J Med Chem 2024; 67:6549-6569. [PMID: 38604131 DOI: 10.1021/acs.jmedchem.3c02483] [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: 04/13/2024]
Abstract
Fibroblast growth factor receptor 4 (FGFR4) is thought to be a driver in several cancer types, most notably in hepatocellular carcinoma. One way to achieve high potency and isoform selectivity for FGFR4 is covalently targeting a rare cysteine (C552) in the hinge region of its kinase domain that is not present in other FGFR family members (FGFR1-3). Typically, this cysteine is addressed via classical acrylamide electrophiles. We demonstrate that noncanonical covalent "warheads" based on nucleophilic aromatic substitution (SNAr) chemistry can be employed in a rational manner to generate highly potent and (isoform-)selective FGFR4 inhibitors with a low intrinsic reactivity. Key compounds showed low to subnanomolar potency, efficient covalent inactivation kinetics, and excellent selectivity against the other FGFRs, the kinases with an equivalent cysteine, and a representative subset of the kinome. Moreover, these compounds achieved nanomolar potencies in cellular assays and demonstrated good microsomal stability, highlighting the potential of SNAr-based approaches in covalent inhibitor design.
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Affiliation(s)
- Moritz Schwarz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Maksym Kurkunov
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Florian Wittlinger
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Ramona Rudalska
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Department of Medical Oncology and Pneumology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Guiqun Wang
- German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Str. 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Martin Peter Schwalm
- German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Str. 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Alexander Rasch
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Benedikt Wagner
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Stefan Knapp
- German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Str. 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Daniel Dauch
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- Department of Medical Oncology and Pneumology, University Hospital Tübingen, 72076 Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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7
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Serafim RAM, Gehringer M, Borsari C. Targeted Covalent Inhibitors in Drug Discovery, Chemical Biology and Beyond. Pharmaceuticals (Basel) 2024; 17:206. [PMID: 38399421 PMCID: PMC10891537 DOI: 10.3390/ph17020206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Covalent inhibitors have experienced a revival in medicinal chemistry and chemical biology in recent decades [...].
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Affiliation(s)
- Ricardo A. M. Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided & Functionally Instructed Tumor Therapies’, University of Tübingen, 72076 Tübingen, Germany
| | - Chiara Borsari
- Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy
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8
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Cheke RS, Kharkar PS. Covalent inhibitors: An ambitious approach for the discovery of newer oncotherapeutics. Drug Dev Res 2024; 85:e22132. [PMID: 38054744 DOI: 10.1002/ddr.22132] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/04/2023] [Accepted: 10/29/2023] [Indexed: 12/07/2023]
Abstract
Covalent inhibitors have been used to treat several diseases for over a century. However, strategic approaches for the rational design of covalent drugs have taken a definitive shape in recent times. Since the first appearance of covalent inhibitors in the late 18th century, the field has grown tremendously and around 30% of marketed drugs are covalent inhibitors especially, for oncology indications. However, the off-target toxicity and safety concerns can be significant issues related to the covalent drugs. Covalent kinase inhibitor (CKI) targeted oncotherapeutics has advanced dramatically over the last two decades since the discovery of afatinib (Gilotrif®), an EGFR inhibitor. Since then, US FDA has approved 10 CKIs for diverse cancer targets. The present review broadly summarizes the ongoing development in the discovery of newer CKIs from 2016 till the end of 2022. We believe that these efforts will assist the modern medicinal chemist actively working in the field of CKI discovery for varied indications.
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Affiliation(s)
- Rameshwar S Cheke
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
| | - Prashant S Kharkar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, India
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9
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Zhang Y, Liu Z, Hirschi M, Brodsky O, Johnson E, Won SJ, Nagata A, Petroski MD, Majmudar JD, Niessen S, VanArsdale T, Gilbert AM, Hayward MM, Stewart AE, Nager AR, Melillo B, Cravatt B. Expanding the ligandable proteome by paralog hopping with covalent probes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576274. [PMID: 38293178 PMCID: PMC10827202 DOI: 10.1101/2024.01.18.576274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
More than half of the ~20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.
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Affiliation(s)
- Yuanjin Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Zhonglin Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Marsha Hirschi
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Oleg Brodsky
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Eric Johnson
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Sang Joon Won
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Asako Nagata
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | | | - Jaimeen D Majmudar
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Cambridge, MA 02139, USA
| | - Sherry Niessen
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
- Current address: Belharra Therapeutics, 3985 Sorrento Valley Blvd suite c, San Diego, CA 92121
| | - Todd VanArsdale
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Adam M Gilbert
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
| | - Matthew M Hayward
- Discovery Sciences, Pfizer Research and Development, Pfizer Inc., Groton, CT 06340, USA
- Current address: Magnet Biomedicine, 321 Harrison Ave., Suite 600, Boston, MA 02118, USA
| | - Al E Stewart
- Medicine Design, Pfizer Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Andrew R Nager
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Benjamin Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037 USA
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10
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Jauslin WT, Schild M, Schaefer T, Borsari C, Orbegozo C, Bissegger L, Zhanybekova S, Ritz D, Schmidt A, Wymann M, Gillingham D. A high affinity pan-PI3K binding module supports selective targeted protein degradation of PI3Kα. Chem Sci 2024; 15:683-691. [PMID: 38179525 PMCID: PMC10763047 DOI: 10.1039/d3sc04629j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/01/2023] [Indexed: 01/06/2024] Open
Abstract
Class I phosphoinositide 3-kinases (PI3Ks) control cellular growth, but are also essential in insulin signaling and glucose homeostasis. Pan-PI3K inhibitors thus generate substantial adverse effects, a reality that has plagued drug development against this target class. We present here evidence that a high affinity binding module with the capacity to target all class I PI3K isoforms can facilitate selective degradation of the most frequently mutated class I isoform, PI3Kα, when incorporated into a cereblon-targeted (CRBN) degrader. A systematic proteomics study guided the fine tuning of molecular features to optimize degrader selectivity and potency. Our work resulted in the creation of WJ112-14, a PI3Kα-specific nanomolar degrader that should serve as an important research tool for studying PI3K biology. Given the toxicities observed in the clinic with unselective PI3Kα inhibitors, the results here offer a new approach toward selectively targeting this frequently mutated oncogenic driver.
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Affiliation(s)
| | - Matthias Schild
- Department of Chemistry, University of Basel 4056 Basel Switzerland
| | - Thorsten Schaefer
- Department of Biomedicine, University of Basel 4031 Basel Switzerland
| | - Chiara Borsari
- Department of Biomedicine, University of Basel 4031 Basel Switzerland
| | - Clara Orbegozo
- Department of Biomedicine, University of Basel 4031 Basel Switzerland
| | - Lukas Bissegger
- Department of Biomedicine, University of Basel 4031 Basel Switzerland
| | | | - Danilo Ritz
- Proteomics Core Facility, Biozentrum, University of Basel 4056 Basel Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel 4056 Basel Switzerland
| | - Matthias Wymann
- Department of Biomedicine, University of Basel 4031 Basel Switzerland
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11
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Guo X, Wang Y, An Y, Liu Z, Liu J, Chen J, Zhan MM, Liang M, Hou Z, Wan C, Yin F, Wang R, Li Z. Development of Lysine Crotonyl-Mimic Probe to Covalently Identify H3K27Cr Interacting Proteins. Chemistry 2023; 29:e202301624. [PMID: 37587551 DOI: 10.1002/chem.202301624] [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: 05/22/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023]
Abstract
Histone lysine crotonylation (Kcr) is one newly discovered acylation modification and regulates numerous pathophysiological processes. The binding affinity between Kcr and its interacting proteins is generally weak, which makes it difficult to effectively identify Kcr-interacting partners. Changing the amide of crotonyl to an ester increased reactivity with proximal cysteines and retained specificity for Kcr antibody. The probe "H3g27Cr" was designed by incorporating the ester functionality into a H3K27 peptide. Using this probe, multiple Kcr-interacting partners including STAT3 were successfully identified, and this has not been reported previously. Further experiments suggested that STAT3 possibly could form complexes with Histone deacetylase HDACs to downregulate the acetylation and crotonylation of Histone H3K27. Our unique design provided intriguing tools to further explore Kcr-interacting proteins and elucidate their working mechanisms.
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Affiliation(s)
- Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Yuhao An
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zhihong Liu
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Jianbo Liu
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Jiaxin Chen
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Mei-Miao Zhan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Mingcha Liang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
| | - Feng Yin
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Rui Wang
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, P.R. China
- Pingshan translational medicine center, Shenzhen Bay Laboratory, Shenzhen, 518118, P.R. China
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12
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Zhou Q, Liu X, Neri D, Li W, Favalli N, Bassi G, Yang S, Yang D, Vogt PK, Wang MW. Structural insights into the interaction of three Y-shaped ligands with PI3Kα. Proc Natl Acad Sci U S A 2023; 120:e2304071120. [PMID: 37585458 PMCID: PMC10450665 DOI: 10.1073/pnas.2304071120] [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: 03/10/2023] [Accepted: 07/19/2023] [Indexed: 08/18/2023] Open
Abstract
Class IA phosphoinositide 3-kinase alpha (PI3Kα) is an important drug target because it is one of the most frequently mutated proteins in human cancers. However, small molecule inhibitors currently on the market or under development have safety concerns due to a lack of selectivity. Therefore, other chemical scaffolds or unique mechanisms of catalytic kinase inhibition are needed. Here, we report the cryo-electron microscopy structures of wild-type PI3Kα, the dimer of p110α and p85α, in complex with three Y-shaped ligands [cpd16 (compound 16), cpd17 (compound 17), and cpd18 (compound 18)] of different affinities and no inhibitory effect on the kinase activity. Unlike ATP-competitive inhibitors, cpd17 adopts a Y-shaped conformation with one arm inserted into a binding pocket formed by R770 and W780 and the other arm lodged in the ATP-binding pocket at an angle that is different from that of the ATP phosphate tail. Such a special interaction induces a conformation of PI3Kα resembling that of the unliganded protein. These observations were confirmed with two isomers (cpd16 and cpd18). Further analysis of these Y-shaped ligands revealed the structural basis of differential binding affinities caused by stereo- or regiochemical modifications. Our results may offer a different direction toward the design of therapeutic agents against PI3Kα.
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Affiliation(s)
- Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Xiao Liu
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich8093, Switzerland
| | - Wenxin Li
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich8093, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich8093, Switzerland
| | - Su Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Peter K. Vogt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
| | - Ming-Wei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai200032, China
- Research Center for Deepsea Bioresources, Sanya572025, China
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo113-0033, Japan
- School of Pharmacy, Hainan Medical College, Haikou570228, China
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13
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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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14
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Galbiati A, Bova S, Pacchiana R, Borsari C, Persico M, Zana A, Bruno S, Donadelli M, Fattorusso C, Conti P. Discovery of a spirocyclic 3-bromo-4,5-dihydroisoxazole covalent inhibitor of hGAPDH with antiproliferative activity against pancreatic cancer cells. Eur J Med Chem 2023; 254:115286. [PMID: 37058971 DOI: 10.1016/j.ejmech.2023.115286] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/16/2023]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a key glycolytic enzyme, plays a crucial role in the energy metabolism of cancer cells and has been proposed as a valuable target for the development of anticancer agents. Among a series of 5-substituted 3-bromo-4,5-dihydroisoxazole (BDHI) derivatives, we identified the spirocyclic compound 11, which is able to covalently inactivate recombinant human GAPDH (hGAPDH) with a faster reactivity than koningic acid, one of the most potent hGAPDH inhibitors known to date. Computational studies confirmed that conformational rigidification is crucial to stabilize the interaction of the inhibitor with the binding site, thus favoring the subsequent covalent bond formation. Investigation of intrinsic warhead reactivity at different pH disclosed the negligible reactivity of 11 with free thiols, highlighting its ability to selectively react with the activated cysteine of hGAPDH with respect to other sulfhydryl groups. Compound 11 strongly reduced cancer cell growth in four different pancreatic cancer cell lines and its antiproliferative activity correlated well with the intracellular inhibition of hGAPDH. Overall, our results qualify 11 as a potent hGAPDH covalent inhibitor with a moderate drug-like reactivity that could be further exploited to develop anticancer agents.
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Affiliation(s)
- Andrea Galbiati
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy
| | - Stefania Bova
- Department of Medicine and Surgery, University of Parma, 43125, Parma, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, 37134, Verona, Italy
| | - Chiara Borsari
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy; Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Marco Persico
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Aureliano Zana
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy
| | - Stefano Bruno
- Food and Drug Department, University of Parma, 43124, Parma, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, 37134, Verona, Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli, Italy
| | - Paola Conti
- Department of Pharmaceutical Sciences, University of Milan, Via Mangiagalli 25, 20133, Milano, Italy.
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15
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Dai Q, Sun Q, Ouyang X, Liu J, Jin L, Liu A, He B, Fan T, Jiang Y. Antitumor Activity of s-Triazine Derivatives: A Systematic Review. Molecules 2023; 28:molecules28114278. [PMID: 37298753 DOI: 10.3390/molecules28114278] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
1,3,5-triazine derivatives, also called s-triazines, are a series of containing-nitrogen heterocyclic compounds that play an important role in anticancer drug design and development. To date, three s-triazine derivatives, including altretamine, gedatolisib, and enasidenib, have already been approved for refractory ovarian cancer, metastatic breast cancer, and leukemia therapy, respectively, demonstrating that the s-triazine core is a useful scaffold for the discovery of novel anticancer drugs. In this review, we mainly focus on s-triazines targeting topoisomerases, tyrosine kinases, phosphoinositide 3-kinases, NADP+-dependent isocitrate dehydrogenases, and cyclin-dependent kinases in diverse signaling pathways, which have been extensively studied. The medicinal chemistry of s-triazine derivatives as anticancer agents was summarized, including discovery, structure optimization, and biological applications. This review will provide a reference to inspire new and original discoveries.
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Affiliation(s)
- Qiuzi Dai
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Qinsheng Sun
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Xiaorong Ouyang
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Jinyang Liu
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Liye Jin
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Ahao Liu
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Binsheng He
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Tingting Fan
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
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16
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein-Drug Adducts. Pharmaceuticals (Basel) 2023; 16:547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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; (E.M.)
- 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; (E.M.)
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
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17
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Feng X, Du M, Li S, Zhang Y, Ding J, Wang J, Wang Y, Liu P. Hydroxysafflor yellow A regulates lymphangiogenesis and inflammation via the inhibition of PI3K on regulating AKT/mTOR and NF-κB pathway in macrophages to reduce atherosclerosis in ApoE-/- mice. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 112:154684. [PMID: 36738477 DOI: 10.1016/j.phymed.2023.154684] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/10/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Macrophage-mediated inflammatory infiltration and pathological lymphangiogenesis around atherosclerotic plaques are newly highlighted treatment targets of atherosclerosis. Although the effect of Hydroxysafflor yellow A(HSYA) on atherosclerosis was clear, few studies focus on the regulation of HSYA on such mechanisms. PURPOSE This study aimed to uncover the key site of HSYA on improving atherosclerosis by regulating macrophage-induced inflammation and lymphangiogenesis. STUDY DESIGN This study was designed to explore the new mechanism of HSYA on alleviating atherosclerosis in vitro and in vivo. METHODS We determined the expression of vascular endothelial growth factor C(VEGF-C) in Raw264.7 cells and high-fat diet fed ApoE knockout (ApoE-/-) mice. Raw264.7 cells were treated with HSYA under the stimulation of LPS and ox-LDL. HFD induced ApoE-/- mice were given different concentrations of HSYA-saline solution by tail vein injection and ATV-saline suspension by gavage. C57/B6j mice fed with chow diet were used for the control group. H&E, oil red O and immunofluorescence staining analysis were used for visualizing the pathological changes. The biological impact of HSYA was evaluated by body weight, lipid metabolism, inflammation levels, and corresponding function indexes of kidney and liver. RT-qPCR and western blot methods were conducted to determine the expression of the inflammation and lymphangiogenesis factors. Molecular docking and microscale thermophoresis analysis were used to verify the combination of HSYA and PI3K. RESULTS In vivo, HSYA reduced the plaque formation, hepatic steatosis and inflammation-related lymphangiogenesis (IAL). It also changed the serum levels of inflammation (VEGF-C, TNF-α, IL-6, VCAM1, MCP1), lipid indexes (LDL, CHOL, TRIG) and relevant lymphangiogenesis (VEGF-C and LYVE-1) and inflammation (VCAM-1 and IL-6) signals in the aorta. In vitro, HSYA regulated Akt/mTOR and NF-κB activation by the inhibition of PI3K in macrophages. CONCLUSION HSYA affects inflammation and inflammation-associated lymphangiogenesis via suppressing PI3K to affect AKT/mTOR and NF-B pathway activation in macrophages, showing a comprehensive protective effect on atherosclerosis.
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Affiliation(s)
- Xiaoteng Feng
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Min Du
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Sijin Li
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifan Zhang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jie Ding
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiarou Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiru Wang
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ping Liu
- Department of Cardiology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
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18
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Somsen B, Schellekens RJ, Verhoef CJ, Arkin MR, Ottmann C, Cossar PJ, Brunsveld L. Reversible Dual-Covalent Molecular Locking of the 14-3-3/ERRγ Protein-Protein Interaction as a Molecular Glue Drug Discovery Approach. J Am Chem Soc 2023; 145:6741-6752. [PMID: 36926879 PMCID: PMC10064330 DOI: 10.1021/jacs.2c12781] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Indexed: 03/18/2023]
Abstract
Molecules that stabilize protein-protein interactions (PPIs) are invaluable as tool compounds for biophysics and (structural) biology, and as starting points for molecular glue drug discovery. However, identifying initial starting points for PPI stabilizing matter is highly challenging, and chemical optimization is labor-intensive. Inspired by chemical crosslinking and reversible covalent fragment-based drug discovery, we developed an approach that we term "molecular locks" to rapidly access molecular glue-like tool compounds. These dual-covalent small molecules reversibly react with a nucleophilic amino acid on each of the partner proteins to dynamically crosslink the protein complex. The PPI between the hub protein 14-3-3 and estrogen-related receptor γ (ERRγ) was used as a pharmacologically relevant case study. Based on a focused library of dual-reactive small molecules, a molecular glue tool compound was rapidly developed. Biochemical assays and X-ray crystallographic studies validated the ternary covalent complex formation and overall PPI stabilization via dynamic covalent crosslinking. The molecular lock approach is highly selective for the specific 14-3-3/ERRγ complex, over other 14-3-3 complexes. This selectivity is driven by the interplay of molecular reactivity and molecular recognition of the composite PPI binding interface. The long lifetime of the dual-covalent locks enabled the selective stabilization of the 14-3-3/ERRγ complex even in the presence of several other competing 14-3-3 clients with higher intrinsic binding affinities. The molecular lock approach enables systematic, selective, and potent stabilization of protein complexes to support molecular glue drug discovery.
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Affiliation(s)
- Bente
A. Somsen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Rick J.C. Schellekens
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Carlo J.A. Verhoef
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California, San Francisco, California 94143, United States
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter J. Cossar
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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19
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Karges J, Cohen SM. Rhenium(V) Complexes as Cysteine-Targeting Coordinate Covalent Warheads. J Med Chem 2023; 66:3088-3105. [PMID: 36752718 PMCID: PMC9969397 DOI: 10.1021/acs.jmedchem.2c02074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Interest in covalent enzyme inhibitors as therapeutic agents has seen a recent resurgence. Covalent enzyme inhibitors typically possess an organic functional group that reacts with a key feature of the target enzyme, often a nucleophilic cysteine residue. Herein, the application of small, modular ReV complexes as inorganic cysteine-targeting warheads is described. These metal complexes were found to react with cysteine residues rapidly and selectively. To demonstrate the utility of these ReV complexes, their reactivity with SARS-CoV-2-associated cysteine proteases is presented, including the SARS-CoV-2 main protease and papain-like protease and human enzymes cathepsin B and L. As all of these proteins are cysteine proteases, these enzymes were found to be inhibited by the ReV complexes through the formation of adducts. These findings suggest that these ReV complexes could be used as a new class of warheads for targeting surface accessible cysteine residues in disease-relevant target proteins.
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20
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De Pascale M, Bissegger L, Tarantelli C, Beaufils F, Prescimone A, Mohamed Seid Hedad H, Kayali O, Orbegozo C, Raguž L, Schaefer T, Hebeisen P, Bertoni F, Wymann MP, Borsari C. Investigation of morpholine isosters for the development of a potent, selective and metabolically stable mTOR kinase inhibitor. Eur J Med Chem 2023; 248:115038. [PMID: 36634458 DOI: 10.1016/j.ejmech.2022.115038] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/17/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
Upregulation of mechanistic target of rapamycin (mTOR) signaling drives various types of cancers and neurological diseases. Rapamycin and its analogues (rapalogs) are first generation mTOR inhibitors, and selectively block mTOR complex 1 (TORC1) by an allosteric mechanism. In contrast, second generation ATP-binding site inhibitors of mTOR kinase (TORKi) target both TORC1 and TORC2. Here, we explore 3,6-dihydro-2H-pyran (DHP) and tetrahydro-2H-pyran (THP) as isosteres of the morpholine moiety to unlock a novel chemical space for TORKi generation. A library of DHP- and THP-substituted triazines was prepared, and molecular modelling provided a rational for a structure activity relationship study. Finally, compound 11b [5-(4-(3-oxa-8-azabicyclo[3.2.1]octan-8-yl)-6-(tetrahydro-2H-pyran-4-yl)-1,3,5-triazin-2-yl)-4-(difluoromethyl)pyridin-2-amine] was selected due its potency and selectivity for mTOR kinase over the structurally related class I phosphoinositide 3-kinases (PI3Ks) isoforms. 11b displayed high metabolic stability towards CYP1A1 degradation, which is of advantage in drug development. After oral administration to male Sprague Dawley rats, 11b reached high concentrations both in plasma and brain, revealing an excellent oral bioavailability. In a metabolic stability assay using human hepatocytes, 11b was more stable than PQR620, the first-in-class brain penetrant TORKi. Compound 11b also displayed dose-dependent anti-proliferative activity in splenic marginal zone lymphoma (SMZL) cell lines as single agent and when combined with BCL2 inhibition (venetoclax). Our results identify the THP-substituted triazine core as a novel scaffold for the development of metabolically stable TORKi for the treatment of chronic diseases and cancers driven by mTOR deregulation and requiring drug distribution also to the central nervous system.
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Affiliation(s)
- Martina De Pascale
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Lukas Bissegger
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Florent Beaufils
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Alessandro Prescimone
- University of Basel, Department of Chemistry, Mattenstrasse 24a, 4058, Basel, Switzerland
| | | | - Omar Kayali
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Via Francesco Chiesa 5, 6500, Bellinzona, Switzerland
| | - Clara Orbegozo
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Luka Raguž
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Thorsten Schaefer
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Paul Hebeisen
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Via Francesco Chiesa 5, 6500, Bellinzona, Switzerland; Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Matthias P Wymann
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland.
| | - Chiara Borsari
- University of Basel, Department of Biomedicine, Mattenstrasse 28, 4058, Basel, Switzerland.
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21
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Wan C, Hou Z, Yang D, Zhou Z, Xu H, Wang Y, Dai C, Liang M, Meng J, Chen J, Yin F, Wang R, Li Z. The thiol-sulfoxonium ylide photo-click reaction for bioconjugation. Chem Sci 2023; 14:604-612. [PMID: 36741507 PMCID: PMC9847666 DOI: 10.1039/d2sc05650j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/01/2022] [Indexed: 12/04/2022] Open
Abstract
Visible-light-mediated methods were heavily studied as a useful tool for cysteine-selective bio-conjugation; however, many current methods suffer from bio-incompatible reaction conditions and slow kinetics. To address these challenges, herein, we report a transition metal-free thiol-sulfoxonium ylide photo-click reaction that enables bioconjugation under bio-compatible conditions. The reaction is highly cysteine-selective and generally finished within minutes with naturally occurring riboflavin derivatives as organic photocatalysts. The catalysts and substrates are readily accessible and bench stable and have satisfactory water solubility. As a proof-of-concept study, the reaction was smoothly applied in chemo-proteomic analysis, which provides efficient tools to explore the druggable content of the human proteome.
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Affiliation(s)
- Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
| | - Dongyan Yang
- College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering Guangzhou 510225 P. R. China
| | - Ziyuan Zhou
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen 518116 P. R. China
| | - Hongkun Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
| | - Chuan Dai
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
| | - Mingchan Liang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Jun Meng
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College Shenzhen 518116 P. R. China
| | - Jiean Chen
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School Shenzhen 518055 P. R. China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory Shenzhen 518118 P. R. China
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22
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Ramos-Llorca A, Decraecker L, Cacheux VMY, Zeiburlina I, De bruyn M, Battut L, Moreno-Cinos C, Ceradini D, Espinosa E, Dietrich G, Berg M, De Meester I, Van Der Veken P, Boeckxstaens G, Lambeir AM, Denadai-Souza A, Augustyns K. Chemically diverse activity-based probes with unexpected inhibitory mechanisms targeting trypsin-like serine proteases. Front Chem 2023; 10:1089959. [PMID: 36688031 PMCID: PMC9849758 DOI: 10.3389/fchem.2022.1089959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Activity-based probes (ABP) are molecules that bind covalently to the active form of an enzyme family, making them an attractive tool for target and biomarker identification and drug discovery. The present study describes the synthesis and biochemical characterization of novel activity-based probes targeting trypsin-like serine proteases. We developed an extensive library of activity-based probes with "clickable" affinity tags and a diaryl phosphonate warhead. A wide diversity was achieved by including natural amino acid analogs as well as basic polar residues as side chains. A detailed enzymatic characterization was performed in a panel of trypsin-like serine proteases. Their inhibitory potencies and kinetic profile were examined, and their IC50 values, mechanism of inhibition, and kinetic constants were determined. The activity-based probes with a benzyl guanidine side chain showed the highest inhibitory effects in the panel. Surprisingly, some of the high-affinity probes presented a reversible inhibitory mechanism. On the other hand, probes with different side chains exhibited the expected irreversible mechanism. For the first time, we demonstrate that not only irreversible probes but also reversible probes can tightly label recombinant proteases and proteases released from human mast cells. Even under denaturing SDS-PAGE conditions, reversible slow-tight-binding probes can label proteases due to the formation of high-affinity complexes and slow dissociation rates. This unexpected finding will transform the view on the required irreversible nature of activity-based probes. The diversity of this library of activity-based probes combined with a detailed enzyme kinetic characterization will advance their applications in proteomic studies and drug discovery.
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Affiliation(s)
- Alba Ramos-Llorca
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Lisse Decraecker
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Valérie M. Y. Cacheux
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Irena Zeiburlina
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Michelle De bruyn
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Louise Battut
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Eric Espinosa
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Gilles Dietrich
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Maya Berg
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Guy Boeckxstaens
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Alexandre Denadai-Souza
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
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23
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Huang J, Chen L, Wu J, Ai D, Zhang JQ, Chen TG, Wang L. Targeting the PI3K/AKT/mTOR Signaling Pathway in the Treatment of Human Diseases: Current Status, Trends, and Solutions. J Med Chem 2022; 65:16033-16061. [PMID: 36503229 DOI: 10.1021/acs.jmedchem.2c01070] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway is one of the most important intracellular pathways involved in cell proliferation, growth, differentiation, and survival. Therefore, this route is a prospective biological target for treating various human diseases, such as tumors, neurodegenerative diseases, pulmonary fibrosis, and diabetes. An increasing number of clinical studies emphasize the necessity of developing novel molecules targeting the PI3K/AKT/mTOR pathway. This review focuses on recent advances in ATP-competitive inhibitors, allosteric inhibitors, covalent inhibitors, and proteolysis-targeting chimeras against the PI3K/AKT/mTOR pathway, and highlights possible solutions for overcoming the toxicities and acquired drug resistance of currently available drugs. We also provide recommendations for the future design and development of promising drugs targeting this pathway.
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Affiliation(s)
- Jindi Huang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Liye Chen
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jiangxia Wu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Daiqiao Ai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ji-Quan Zhang
- College of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Tie-Gen Chen
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Room 109, Building C, SSIP Healthcare and Medicine Demonstration Zone, Zhongshan Tsuihang New District, Zhongshan, Guangdong 528400, China
| | - Ling Wang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, Joint International Research Laboratory of Synthetic Biology and Medicine, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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24
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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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25
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Systematic Exploration of Privileged Warheads for Covalent Kinase Drug Discovery. Pharmaceuticals (Basel) 2022; 15:ph15111322. [PMID: 36355497 PMCID: PMC9695834 DOI: 10.3390/ph15111322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Kinase-targeted drug discovery for cancer therapy has advanced significantly in the last three decades. Currently, diverse kinase inhibitors or degraders have been reported, such as allosteric inhibitors, covalent inhibitors, macrocyclic inhibitors, and PROTAC degraders. Out of these, covalent kinase inhibitors (CKIs) have been attracting attention due to their enhanced selectivity and exceptionally strong affinity. Eight covalent kinase drugs have been FDA-approved thus far. Here, we review current developments in CKIs. We explore the characteristics of the CKIs: the features of nucleophilic amino acids and the preferences of electrophilic warheads. We provide systematic insights into privileged warheads for repurposing to other kinase targets. Finally, we discuss trends in CKI development across the whole proteome.
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26
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Lv D, Ji Y, Zhang Q, Shi Z, Chen T, Zhang C, Wang X, Ren T, Gao Z, Zhong C. Mailuoshutong pill for varicocele-associated male infertility—Phytochemical characterisation and multitarget mechanism. Front Pharmacol 2022; 13:961011. [PMID: 36160417 PMCID: PMC9500298 DOI: 10.3389/fphar.2022.961011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/26/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Varicocele (VC) is a relatively common and treatable cause of male infertility. Mailuoshutong pill (MLST), a traditional Chinese patent medicine, is widely used for treating varicose vein disease, but the underlying mechanism of MLST on varicocele-associated male infertility is unclear. Objective: To reveal the phytochemical characterisation and multitarget mechanism of MLST on varicocele-associated male infertility. Methods: The components in MLST were determined using UHPLC-MS/MS. Through network analysis, we constructed the “Drug-Components-Targets-Disease” network and predicted the potential biological functions and signaling pathways of MLST. Finally, the therapeutic effects and potential mechanisms of MLST were discovered by pharmacological experiments. Results: By network analysis, the “Drug-Components-Targets-Disease” network was constructed, 62 components such as apigenin, limonin, kaempferol, and obacunoic acid may be the main active components of MLST for varicocele-associated male infertility, 28 targets such as VEGFA, PIK3CA, AKT1, and MTOR are considered as hub targets, signaling pathways such as HIF-1, Estrogen, PI3K/Akt, and mTOR may be key pathways for MLST against varicocele-associated male infertility. Through pharmacological experiments, we found that MLST ameliorated VC-induced testicular atrophy. Further histomorphology showed that MLST reduced VC-induced damage to testicular spermatogonia and seminiferous tubule, while MLST reduced ROS and MDA levels and increased antioxidant enzymes (GSH, GSH-Px, SOD, and CAT) levels. TUNEL staining and immunofluorescence showed that MLST reduced VC-induced apoptosis in testicular tissue, decreased BAX, and increased BCL2. Western blot results showed that MLST decreased the phosphorylation of PI3K, AKT, and mTOR proteins, and decreased the expression of HIF1α. Conclusion: The phytochemical characterisation and multitarget mechanism of MLST on varicocele-associated male infertility were discovered using network analysis and pharmacological experiments. We verified that MLST can inhibit the activation of the PI3K/Akt/mTOR signaling pathway, reduce the expression of HIF1α, and further attenuate VC-induced oxidative stress and apoptosis in the testis. These findings provide evidence for the therapeutic role of MLST in varicocele-associated male infertility.
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Affiliation(s)
- Dongfang Lv
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yun Ji
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qian Zhang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhuozhuo Shi
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tengfei Chen
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chao Zhang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiangyun Wang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Taotao Ren
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhaowang Gao
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chongfu Zhong
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
- *Correspondence: Chongfu Zhong,
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27
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Sõrmus T, Lavogina D, Teearu A, Enkvist E, Uri A, Viht K. Construction of Covalent Bisubstrate Inhibitor of Protein Kinase Reacting with Cysteine Residue at Substrate-Binding Site. J Med Chem 2022; 65:10975-10991. [PMID: 35960538 DOI: 10.1021/acs.jmedchem.2c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent clinical success with targeted covalent inhibitors points to new possibilities for development of protein kinase (PK)-targeted drugs by exploiting reactive cysteine residues in and around the ATP-binding site. However, more than 300 human PKs lack cysteine residues in the ATP-binding site. Here, we report the first covalent bisubstrate PK inhibitor whose electrophilic warhead reaches outside the ATP-binding site and reacts with a distant cysteine residue. A series of covalent inhibitors and their reversible counterparts were synthesized and characterized. The most potent reversible inhibitor possessed picomolar affinity and its cysteine-reactive counterpart revealed high value of kinact/KI ratio (6.2 × 107 M-1 s-1) for the reaction with the catalytic subunit of cAMP-dependent PK (PKAc). Under optimized conditions, fluorescent dye-labeled covalent inhibitors demonstrated PKA-selectivity in the cell lysate and reacted with several proteins inside live cells, including PKAc. The disclosed compounds serve as leads for targeting PKs possessing an analogously positioned cysteine residue.
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Affiliation(s)
- Tanel Sõrmus
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Darja Lavogina
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Anu Teearu
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Erki Enkvist
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Asko Uri
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
| | - Kaido Viht
- Institute of Chemistry, University of Tartu, 14A Ravila St., 50411 Tartu, Estonia
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28
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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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