1
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Yuan B, Feng Y, Ma M, Duan W, Wu Y, Liu J, Zhao HY, Yang Z, Zhang SQ, Xin M. Lysine-Targeted Covalent Inhibitors of PI3Kδ Synthesis and Screening by In Situ Interaction Upgradation. J Med Chem 2024; 67:20076-20099. [PMID: 39561981 DOI: 10.1021/acs.jmedchem.4c01284] [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: 11/21/2024]
Abstract
Targeting the lysine residue of protein kinases to develop covalent inhibitors is an emerging hotspot. Herein, we have reported an approach to develop lysine-targeted covalent inhibitors of PI3Kδ by in situ interaction upgradation of the H-bonding to covalent bonding. Several warhead groups were introduced and screened in situ, leading to lysine-targeted covalent inhibitors bearing aromatic esters with high bioactivity and PI3Kδ selectivity. Compound A11 bearing phenolic ester was finally optimized to show a long duration of action in SU-DHL-6 cells by multiple assays. Docking simulation and further protein mass spectrometry confirmed that A11 bound to PI3Kδ by covalent-bonding interactions with Lys779. Furthermore, A11 exhibited potently antitumor efficacy without obvious toxicity in the SU-DHL-6 and Pfeiffer xenograft mouse models. This study identified A11 to be a much more effective antitumor agent in vitro and in vivo as a lysine-targeted covalent inhibitor, and it also provided a practical approach for the development of lysine-targeted covalent inhibitors.
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Affiliation(s)
- Bo Yuan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Yifan Feng
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Mengyan Ma
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Weiming Duan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Yujie Wu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Jiaxin Liu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Hong-Yi Zhao
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Zhe Yang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - San-Qi Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
| | - Minhang Xin
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P. R. China
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2
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Zhou M, Li S, Tan Y, Huang W, Li Y, Yuan X, Li Z. Global Profiling Lysine Reactivity and Ligandability with Oxidant-Triggered Bioconjugation Chemistry. Angew Chem Int Ed Engl 2024:e202418473. [PMID: 39543955 DOI: 10.1002/anie.202418473] [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: 09/25/2024] [Revised: 11/14/2024] [Accepted: 11/14/2024] [Indexed: 11/17/2024]
Abstract
Due to the high abundance and diverse functions of lysine residues, both in the interior and on the surface of proteins, the development of new methods to characterize their reactivity and ligandability could significantly expand the pool of druggable targets. To date, only a limited number of aminophilic electrophiles have been assessed for interactions with the lysine proteome, resulting in a substantial fraction remaining inaccessible to current probes. Here, to the best of our knowledge, we report the first oxidant-triggered bioconjugation platform for in-depth profiling of lysines. We quantified over 7000 covalently modifiable lysine residues, which significantly expands the coverage of ligandable lysines in the whole proteome. Chemical proteomics enabled the mapping of more than 100 endogenous kinases, thus providing a comprehensive landscape of ligandable catalytic lysines within the kinome. Moreover, we identified a suite of new ligandable lysines such as K60 of ENO1 and K31 of PPIA, offering insights for exploring new functional and targetable residues. These findings could provide valuable clues for the development of targeted covalent inhibitors (TCIs).
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Affiliation(s)
- Mengya Zhou
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632, Guangzhou, China
| | - Shengrong Li
- Guangdong Second Provincial General Hospital, Postdoctoral Station of Traditional Chinese Medicine, Jinan University, 510632, Guangzhou, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632, Guangzhou, China
| | - Weizhen Huang
- The First Huizhou Affiliated Hospital of Guangdong Medical University, 516001, Huizhou, China
| | - Yifang Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632, Guangzhou, China
| | - Xia Yuan
- The First Huizhou Affiliated Hospital of Guangdong Medical University, 516001, Huizhou, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, 510632, Guangzhou, China
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3
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Paterson LC, Humphreys PG, Kelly HA, Kerr WJ. Collaborative GSK-University of Strathclyde doctoral research and training programmes: Transforming approaches to industry-academia engagement. Drug Discov Today 2024; 29:104162. [PMID: 39245346 DOI: 10.1016/j.drudis.2024.104162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/23/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
A global biopharma company, GSK, and the University of Strathclyde have developed an expansive and transformative research and training partnership originating in chemistry-aligned disciplines, with subsequent extensive expansion across further areas of the company. This has opened unique approaches for the delivery of collaborative research innovations while also enhancing the professional development and learning of GSK personnel, in addition to other embedded researchers and collaborating scientists, on a pathway towards more rapid and efficient discovery of new medicines.
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Affiliation(s)
- Laura C Paterson
- University of Strathclyde, Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, UK
| | | | - Henry A Kelly
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK.
| | - William J Kerr
- University of Strathclyde, Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, UK.
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4
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Weaver J, Craven GB, Tram L, Chen H, Taunton J. Aminomethyl Salicylaldehydes Lock onto a Surface Lysine by Forming an Extended Intramolecular Hydrogen Bond Network. J Am Chem Soc 2024; 146:24233-24237. [PMID: 39177126 DOI: 10.1021/jacs.4c04314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
The development of electrophilic ligands that rapidly modify specific lysine residues remains a major challenge. Salicylaldehyde-based inhibitors have been reported to form stable imine adducts with the catalytic lysine of protein kinases. However, the targeted lysine in these examples is buried in a hydrophobic environment. A key unanswered question is whether this strategy can be applied to a lysine on the surface of a protein, where rapid hydrolysis of the resulting salicylaldimine is more likely. Here, we describe a series of aminomethyl-substituted salicylaldehydes that target a fully solvated lysine on the surface of the ATPase domain of Hsp90. By systematically varying the orientation of the salicylaldehyde, we discovered ligands with long residence times, the best of which engages Hsp90 in a quasi-irreversible manner. Crystallographic analysis revealed a daisy-chain network of intramolecular hydrogen bonds in which the salicylaldimine is locked into position by the adjacent piperidine linker. This study highlights the potential of aminomethyl salicylaldehydes to generate conformationally stabilized, hydrolysis-resistant imines, even when the targeted lysine is far from the ligand binding site and is exposed to bulk solvent.
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Affiliation(s)
- Jacqueline Weaver
- Chemistry and Chemical Biology Program, University of California─San Francisco, San Francisco, California 94143, United States
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California─San Francisco, San Francisco, California 94158, United States
| | - Linh Tram
- Chemistry and Chemical Biology Program, University of California─San Francisco, San Francisco, California 94143, United States
| | - Hao Chen
- Department of Cellular and Molecular Pharmacology, University of California─San Francisco, San Francisco, California 94158, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California─San Francisco, San Francisco, California 94158, United States
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5
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Tang G, Wang X, Huang H, Xu M, Ma X, Miao F, Lu X, Zhang CJ, Gao L, Zhang ZM, Yao SQ. Small Molecule-Induced Post-Translational Acetylation of Catalytic Lysine of Kinases in Mammalian Cells. J Am Chem Soc 2024; 146:23978-23988. [PMID: 39162335 DOI: 10.1021/jacs.4c07181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Reversible lysine acetylation is an important post-translational modification (PTM). This process in cells is typically carried out enzymatically by lysine acetyltransferases and deacetylases. The catalytic lysine in the human kinome is highly conserved and ligandable. Small-molecule strategies that enable post-translational acetylation of the catalytic lysine on kinases in a target-selective manner therefore provide tremendous potential in kinase biology. Herein, we report the first small molecule-induced chemical strategy capable of global acetylation of the catalytic lysine on kinases from mammalian cells. By surveying various lysine-acetylating agents installed on a promiscuous kinase-binding scaffold, Ac4 was identified and shown to effectively acetylate the catalytic lysine of >100 different protein kinases from live Jurkat/K562 cells. In order to demonstrate that this strategy was capable of target-selective and reversible chemical acetylation of protein kinases, we further developed six acetylating compounds on the basis of VX-680 (a noncovalent inhibitor of AURKA). Among them, Ac13/Ac14, while displaying excellent in vitro potency and sustained cellular activity against AURKA, showed robust acetylation of its catalytic lysine (K162) in a target-selective manner, leading to irreversible inhibition of endogenous kinase activity. The reversibility of this chemical acetylation was confirmed on Ac14-treated recombinant AURKA protein, followed by deacetylation with SIRT3 (a lysine deacetylase). Finally, the reversible Ac13-induced acetylation of endogenous AURKA was demonstrated in SIRT3-transfected HCT116 cells. By disclosing the first cell-active acetylating compounds capable of both global and target-selective post-translational acetylation of the catalytic lysine on kinases, our strategy could provide a useful chemical tool in kinase biology and drug discovery.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xuan Wang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518000, China
- 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
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xingyu Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Fengfei Miao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xiaoyun Lu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518000, 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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6
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Li H, Wen X, Ren Y, Fan Z, Zhang J, He G, Fu L. Targeting PI3K family with small-molecule inhibitors in cancer therapy: current clinical status and future directions. Mol Cancer 2024; 23:164. [PMID: 39127670 DOI: 10.1186/s12943-024-02072-1] [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: 06/15/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The Phosphatidylinositol-3-kinase (PI3K) family is well-known to comprise three classes of intracellular enzymes. Class I PI3Ks primarily function in signaling by responding to cell surface receptor stimulation, while class II and III are more involved in membrane transport. Under normal physiological conditions, the PI3K signaling network orchestrates cell growth, division, migration and survival. Aberrant activation of the PI3K signaling pathway disrupts cellular activity and metabolism, often marking the onset of cancer. Currently, the Food and Drug Administration (FDA) has approved the clinical use of five class I PI3K inhibitors. These small-molecule inhibitors, which exhibit varying selectivity for different class I PI3K family members, are primarily used in the treatment of breast cancer and hematologic malignancies. Therefore, the development of novel class I PI3K inhibitors has been a prominent research focus in the field of oncology, aiming to enhance potential therapeutic selectivity and effectiveness. In this review, we summarize the specific structures of PI3Ks and their functional roles in cancer progression. Additionally, we critically evaluate small molecule inhibitors that target class I PI3K, with a particular focus on their clinical applications in cancer treatment. Moreover, we aim to analyze therapeutic approaches for different types of cancers marked by aberrant PI3K activation and to identify potential molecular targets amenable to intervention with small-molecule inhibitors. Ultimately, we propose future directions for the development of therapeutic strategies that optimize cancer treatment outcomes by modulating the PI3K family.
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Affiliation(s)
- Hongyao Li
- Institute of Precision Drug Innovation and Cancer Center, the Second Hospital of Dalian Medical University, Dalian, 116023, China
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan University, Chengdu, 610041, China
| | - Xiang Wen
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan University, Chengdu, 610041, China
| | - Yueting Ren
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan University, Chengdu, 610041, China
- Department of Brain Science, Faculty of Medicine, Imperial College, London, SW72AZ, UK
| | - Zhichao Fan
- Institute of Precision Drug Innovation and Cancer Center, the Second Hospital of Dalian Medical University, Dalian, 116023, China
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan University, Chengdu, 610041, China
| | - Jin Zhang
- School of Pharmaceutical Sciences of Medical School, Shenzhen University, Shenzhen, 518000, China.
| | - Gu He
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Leilei Fu
- Institute of Precision Drug Innovation and Cancer Center, the Second Hospital of Dalian Medical University, Dalian, 116023, China.
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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7
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Ünsal Ö, Bacaksiz ZS, Khamraev V, Montanari V, Beinborn M, Kumar K. Prolonged Activation of the GLP-1 Receptor via Covalent Capture. ACS Chem Biol 2024; 19:1453-1465. [PMID: 38935975 DOI: 10.1021/acschembio.4c00039] [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: 06/29/2024]
Abstract
The incretin gut hormone glucagon-like peptide-1 (GLP-1) has become a household name because of its ability to induce glucose-dependent insulin release with accompanying weight loss in patients. Indeed, derivatives of the peptide exert numerous pleiotropic actions that favorably affect other metabolic functions, and consequently, such compounds are being considered as treatments for a variety of ailments. The ability of native GLP-1 to function as a clinical drug is severely limited because of its short half-life in vivo. All of the beneficial effects of GLP-1 come from its agonism at the cognate receptor, GLP-1R. In our quest for long-lived activation of the receptor, we hypothesized that an agonist that had the ability to covalently cross-link with GLP-1R would prove useful. We here report the structure-guided design of peptide analogues containing an electrophilic warhead that could be covalently captured by a resident native nucleophile on the receptor. The compounds were evaluated using washout experiments, and resistance to such washing serves as an index of prolonged activation and covalent capture, which we use to tabulate longevity and robust long-lived GLP-1R agonism. The addition of SulF (cross-linkable warhead), an N-terminal trifluoroethyl group (for protease protection), and a C18 diacid lipid (protractor) all contributed to the increased wash resistance of GLP-1. The most effective compound based on the wash resistance metric, C2K26DAC18_K34SulF, has all three elements outlined and may serve as a blueprint and a proof-of-concept scaffold for the design of clinically useful molecules.
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Affiliation(s)
- Özge Ünsal
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Z Selin Bacaksiz
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Vladislav Khamraev
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Vittorio Montanari
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Martin Beinborn
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
- Molecular Pharmacology Research Center, Tufts Medical Center, Boston, Massachusetts 02111, United States
| | - Krishna Kumar
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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8
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Wang X, Sun J, Huang H, Tang G, Chen P, Xiang M, Li L, Zhang ZM, Gao L, Yao SQ. Kinase Inhibition via Small Molecule-Induced Intramolecular Protein Cross-Linking. Angew Chem Int Ed Engl 2024; 63:e202404195. [PMID: 38695161 DOI: 10.1002/anie.202404195] [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: 02/29/2024] [Indexed: 07/02/2024]
Abstract
Remarkable progress has been made in the development of cysteine-targeted covalent inhibitors. In kinase drug discovery, covalent inhibitors capable of targeting other nucleophilic residues (i.e. lysine, or K) have emerged in recent years. Besides a highly conserved catalytic lysine, almost all human protein kinases possess an equally conserved glutamate/aspartate (e.g. E/D) that forms a K-E/D salt bridge within the enzyme's active site. Electrophilic ynamides were previously used as effective peptide coupling reagents and to develop E/D-targeting covalent protein inhibitors/probes. In the present study, we report the first ynamide-based small-molecule inhibitors capable of inducing intramolecular cross-linking of various protein kinases, leading to subsequent irreversible inhibition of kinase activity. Our strategy took advantage of the close distance between the highly conserved catalytic K and E/D residues in a targeted kinase, thus providing a conceptually general approach to achieve irreversible kinase inhibition with high specificity and desirable cellular potency. Finally, this ynamide-facilitated, ligand-induced mechanism leading to intramolecular kinase cross-linking and inhibition was unequivocally established by using recombinant ABL kinase as a representative.
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Affiliation(s)
- Xuan Wang
- 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
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, 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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9
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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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10
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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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11
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Zhao Y, Duan K, Fan Y, Li S, Huang L, Tu Z, Sun H, Cook GM, Yang J, Sun P, Tan Y, Ding K, Li Z. Catalyst-free late-stage functionalization to assemble α-acyloxyenamide electrophiles for selectively profiling conserved lysine residues. Commun Chem 2024; 7:31. [PMID: 38355988 PMCID: PMC10866925 DOI: 10.1038/s42004-024-01107-4] [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: 11/19/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Covalent probes coupled with chemical proteomics represent a powerful method for investigating small molecule and protein interactions. However, the creation of a reactive warhead within various ligands to form covalent probes has been a major obstacle. Herein, we report a convenient and robust process to assemble a unique electrophile, an α-acyloxyenamide, through a one-step late-stage coupling reaction. This procedure demonstrates remarkable tolerance towards other functional groups and facilitates ligand-directed labeling in proteins of interest. The reactive group has been successfully incorporated into a clinical drug targeting the EGFR L858R mutant, erlotinib, and a pan-kinase inhibitor. The resulting probes have been shown to be able to covalently engage a lysine residue proximal to the ATP-binding pocket of the EGFR L858R mutant. A series of active sites, and Mg2+, ATP-binding sites of kinases, such as K33 of CDK1, CDK2, CDK5 were detected. This is the first report of engaging these conserved catalytic lysine residues in kinases with covalent inhibition. Further application of this methodology to natural products has demonstrated its success in profiling ligandable conserved lysine residues in whole proteome. These findings offer insights for the development of new targeted covalent inhibitors (TCIs).
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Affiliation(s)
- Yuanyuan Zhao
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Kang Duan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Youlong Fan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shengrong Li
- Guangdong Second Provincial General Hospital, Postdoctoral Station of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, China
| | - Liyan Huang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengchao Tu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 TatChee Avenue, Kowloon, Hong Kong, 999077, China
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Jing Yang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, China
| | - Pinghua Sun
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China.
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12
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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13
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Kawano M, Murakawa S, Higashiguchi K, Matsuda K, Tamura T, Hamachi I. Lysine-Reactive N-Acyl- N-aryl Sulfonamide Warheads: Improved Reaction Properties and Application in the Covalent Inhibition of an Ibrutinib-Resistant BTK Mutant. J Am Chem Soc 2023; 145:26202-26212. [PMID: 37987622 DOI: 10.1021/jacs.3c08740] [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: 11/22/2023]
Abstract
The covalent inhibition of a target protein has gained widespread attention in the field of drug discovery. Most of the current covalent drugs utilize the high reactivity of cysteines toward modest electrophiles. However, there is a growing need for warheads that can target lysine residues to expand the range of covalently druggable proteins and to deal with emerging proteins with mutations resistant to cysteine-targeted covalent drugs. We have recently developed an N-acyl-N-alkyl sulfonamide (NASA) as a lysine-targeted electrophile. Despite its successful application, this NASA warhead suffered from instability in physiological environments, such as serum-containing medium, because of its high intrinsic reactivity. In this study, we sought to modify the structure of the NASA warhead and found that N-acyl-N-aryl sulfonamides (ArNASAs) are promising electrophiles for use in a lysine-targeted covalent inhibition strategy. We prepared a focused library of ArNASA derivatives with diverse structures and reactivity and identified several warhead candidates with suppressed hydrolysis-mediated inactivation and reduced nonspecific reactions with off-target proteins, without sacrificing the reactivity toward the target. These reaction properties enabled the improved covalent inhibition of intracellular heat shock protein 90 (HSP90) in the presence of serum and the development of the first irreversible inhibitor for ibrutinib-resistant Bruton's tyrosine kinase (BTK) bearing the C481S mutation. This study clearly demonstrated the use of a set of ArNASA warheads to create highly potent covalent drugs and highlighted the importance of enriching the current arsenal of lysine-reactive warheads.
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Affiliation(s)
- Masaharu Kawano
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Syunsuke Murakawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Higashiguchi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Matsuda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8103, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO (Exploratory Research for Advanced Technology, JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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14
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Cosgrove B, Grant EK, Bertrand S, Down KD, Somers DO, P Evans J, Tomkinson NCO, Barker MD. Covalent targeting of non-cysteine residues in PI4KIIIβ. RSC Chem Biol 2023; 4:1111-1122. [PMID: 38033723 PMCID: PMC10685791 DOI: 10.1039/d3cb00142c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 12/02/2023] Open
Abstract
The synthesis and characterisation of fluorosulfate covalent inhibitors of the lipid kinase PI4KIIIβ is described. The conserved lysine residue located within the ATP binding site was targeted, and optimised compounds based upon reversible inhibitors with good activity and physicochemical profile showed strong reversible interactions and slow onset times for the covalent inhibition, resulting in an excellent selectivity profile for the lipid kinase target. X-Ray crystallography demonstrated a distal tyrosine residue could also be targeted using a fluorosulfate strategy. Combination of this knowledge showed that a dual covalent inhibitor could be developed which reveals potential in addressing the challenges associated with drug resistant mutations.
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Affiliation(s)
- Brett Cosgrove
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
- Department of Pure and Applied Chemistry, University of Strathclyde Glasgow G1 1XL UK
| | - Emma K Grant
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Sophie Bertrand
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Kenneth D Down
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - Don O Somers
- Structural and Biophysical Science, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | - John P Evans
- Screening, Profiling and Mechanistic Biology, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
| | | | - Michael D Barker
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre Stevenage SG1 2NY UK
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15
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Tang G, Wang W, Wang X, Ding K, Ngan SC, Chen JY, Sze SK, Gao L, Yuan P, Lu X, Yao SQ. Cell-active, irreversible covalent inhibitors that selectively target the catalytic lysine of EGFR by using fluorosulfate-based SuFEx chemistry. Eur J Med Chem 2023; 259:115671. [PMID: 37499291 DOI: 10.1016/j.ejmech.2023.115671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/09/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
EGFR signaling is involved in multiple cellular processes including cell proliferation, differentiation and development, making this protein kinase one of the most valuable drug targets for the treatment of non-small cell lung carcinomas (NSCLC). Herein, we describe the design and synthesis of a series of potential covalent inhibitors targeting the catalytically conserved lysine (K745) of EGFR on the basis of Erlotinib, an FDA-approved first-generation EGFR drug. Different amine-reactive electrophiles were introduced at positions on the Erlotinib scaffold proximal to K745 in EGFR. The optimized compound 26 (as well as its close analog 30), possessing a novel arylfluorosulfate group (ArOSO2F), showed excellent in vitro potency (as low as 0.19 nM in independent IC50 determination) and selectivity against EGFR and many of its drug-resistant mutants. Both intact protein mass spectrometry (MS) and site-mapping analysis revealed that compound 26 covalently bound to EGFR at K745 through the formation of a sulfamate. In addition, compound 26 displayed good anti-proliferative potency against EGFR-overexpressing HCC827 cells by inhibiting endogenous EGFR autophosphorylation. The pharmacokinetic studies of compound 26 demonstrated the druggable potential of other ArOSO2F-containing compounds. Finally, competitive activity-based protein profiling (ABPP), cellular thermal shift assay (CETSA), as well as cellular wash-out experiments, all showed compound 26 to be the first cell-active, fluorosulfate-based targeted covalent inhibitor (TCI) of protein kinases capable of covalently engaging the catalytically conserved lysine of its target in live mammalian cells.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China; State Key Laboratory of Bioorganic & Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Jiao-Yu Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Siu Kwan Sze
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China
| | - Peiyan Yuan
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518000, China.
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, 510632, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore.
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16
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Chen Y, Craven GB, Kamber RA, Cuesta A, Zhersh S, Moroz YS, Bassik MC, Taunton J. Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes. Nat Chem 2023; 15:1616-1625. [PMID: 37460812 DOI: 10.1038/s41557-023-01281-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/23/2023] [Indexed: 11/05/2023]
Abstract
Advances in chemoproteomic technology have revealed covalent interactions between small molecules and protein nucleophiles, primarily cysteine, on a proteome-wide scale. Most chemoproteomic screening approaches are indirect, relying on competition between electrophilic fragments and a minimalist electrophilic probe with inherently limited proteome coverage. Here we develop a chemoproteomic platform for direct electrophile-site identification based on enantiomeric pairs of clickable arylsulfonyl fluoride probes. Using stereoselective site modification as a proxy for ligandability in intact cells, we identify 634 tyrosines and lysines within functionally diverse protein sites, liganded by structurally diverse probes. Among multiple validated sites, we discover a chiral probe that modifies Y228 in the MYC binding site of the epigenetic regulator WDR5, as revealed by a high-resolution crystal structure. A distinct chiral probe stimulates tumour cell phagocytosis by covalently modifying Y387 in the recently discovered immuno-oncology target APMAP. Our work provides a deep resource of ligandable tyrosines and lysines for the development of covalent chemical probes.
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Affiliation(s)
- Ying Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Roarke A Kamber
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Yurii S Moroz
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
- Chemspace LLC, Kyiv, Ukraine
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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17
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Wang W, Wang X, Tang G, Zhu C, Xiang M, Xiao Q, Zhang ZM, Gao L, Yao SQ. Multitarget inhibitors/probes that target LRRK2 and AURORA A kinases noncovalently and covalently. Chem Commun (Camb) 2023; 59:10789-10792. [PMID: 37594149 DOI: 10.1039/d3cc03530a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Herein, we report a salicylaldehyde-based, reversible covalent inhibitor (A2) that possesses moderate cellular activity against AURKA with a prolonged residence time and shows significant non-covalent inhibition towards LRRK2. Our results indicated that this multitarget kinase inhibitor may be used as the starting point for future development of more potent, selective and dual-targeting covalent kinase inhibitors against AURKA and LRRK2 for mitophagy.
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Affiliation(s)
- Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518000, China.
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore.
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18
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Cirillo D, Diceglie M, Nazaré M. Isoform-selective targeting of PI3K: time to consider new opportunities? Trends Pharmacol Sci 2023; 44:601-621. [PMID: 37438206 DOI: 10.1016/j.tips.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/14/2023]
Abstract
Phosphoinositide-3-kinases (PI3Ks) are central to several cellular signaling pathways in human physiology and are potential pharmacological targets for many pathologies including cancer, thrombosis, and pulmonary diseases. Tremendous efforts to develop isoform-selective inhibitors have culminated in the approval of several drugs, validating PI3K as a tractable and therapeutically relevant target. Although successful therapeutic validation has focused on isoform-selective class I orthosteric inhibitors, recent clinical findings have indicated challenges regarding poor drug tolerance owing to sustained on-target inhibition. Hence, additional approaches are warranted to increase the clinical benefits of specific clinical treatment options, which may involve the employment of so far underexploited targeting modalities or the development of inhibitors for currently underexplored PI3K class II isoforms. We review recent key discoveries in the development of isoform-selective inhibitors, focusing particularly on PI3K class II isoforms, and highlight the emerging importance of developing a broader arsenal of pharmacological tools.
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Affiliation(s)
- Davide Cirillo
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany
| | - Marta Diceglie
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Berlin, Germany.
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19
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Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH. How many kinases are druggable? A review of our current understanding. Biochem J 2023; 480:1331-1363. [PMID: 37642371 PMCID: PMC10586788 DOI: 10.1042/bcj20220217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
There are over 500 human kinases ranging from very well-studied to almost completely ignored. Kinases are tractable and implicated in many diseases, making them ideal targets for medicinal chemistry campaigns, but is it possible to discover a drug for each individual kinase? For every human kinase, we gathered data on their citation count, availability of chemical probes, approved and investigational drugs, PDB structures, and biochemical and cellular assays. Analysis of these factors highlights which kinase groups have a wealth of information available, and which groups still have room for progress. The data suggest a disproportionate focus on the more well characterized kinases while much of the kinome remains comparatively understudied. It is noteworthy that tool compounds for understudied kinases have already been developed, and there is still untapped potential for further development in this chemical space. Finally, this review discusses many of the different strategies employed to generate selectivity between kinases. Given the large volume of information available and the progress made over the past 20 years when it comes to drugging kinases, we believe it is possible to develop a tool compound for every human kinase. We hope this review will prove to be both a useful resource as well as inspire the discovery of a tool for every kinase.
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Affiliation(s)
- Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Han Wee Ong
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Mohammad Anwar Hossain
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - Zachary W. Davis-Gilbert
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, U.S.A
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20
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Zhu L, Chang X, Zhang S, Bai X, Finko AV, Xu X, Bian J, Liu X, Huang H. Enhancing the affinity of novel GLS1 allosteric inhibitors by targeting key residue Lys320. Future Med Chem 2023; 15:1393-1414. [PMID: 37610850 DOI: 10.4155/fmc-2023-0114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
Aim: A series of novel GLS1 irreversible allosteric inhibitors targeting Lys320 might have robust enzyme inhibitory activity and potent antitumor activity. Materials & methods: Novel GLS1 allosteric inhibitors targeting Lys320 were synthesized and their anticancer activity was assessed. Moreover, GLS1 protein was used as a model system to analyze the reactivity of these electrophilic groups in GLS1 irreversible allosteric inhibitors with other amino acids, including tyrosine, histidine, serine and threonine, using biochemical and biophysical assays. Results: AC16 exhibited robust GLS1 inhibitory activity, antiproliferative effect in vitro, good plasma stability and potential covalent addition with GLS1 K320. Conclusion: This study opens a novel avenue for the design of robust irreversible GLS1 inhibitors targeting the allosteric site K320.
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Affiliation(s)
- Li Zhu
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
| | - Xiujin Chang
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Shengpeng Zhang
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
| | - Xiumei Bai
- Department of Chemistry, Lomonosov Moscow State University (MSU), Moscow, 119991, Russia
| | - Alexander V Finko
- Department of Chemistry, Lomonosov Moscow State University (MSU), Moscow, 119991, Russia
| | - Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, PR China
| | - Xiaoping Liu
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
| | - Huidan Huang
- Center of Drug Screening & Evaluation, Wannan Medical College, Wuhu, Anhui, 241000, PR China
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21
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Lee SB, Yu J, Kim H, Kim KW, Jeong JW, Kim YL, Park SJ, Koo TS, Lee C, Hong KB, Choi S. Novel Strategy To Inhibit Transthyretin Amyloidosis via the Synergetic Effect of Chemoselective Acylation and Noncovalent Inhibitor Release. J Med Chem 2023; 66:2893-2903. [PMID: 36749109 DOI: 10.1021/acs.jmedchem.2c01926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strategies for developing targeted covalent inhibitors (TCIs), which have the advantages of a prolonged duration of action and selectivity toward a drug target, have attracted great interest in drug discovery. Herein, we report chemoselective covalent inhibitors that specifically target lysine ε-amine groups that conjugate with an endogenous protein to prevent disease-causing protein misfolding and aggregation. These TCIs are unique because the benzoyl group is preferentially conjugated to Lys15 at the top of the T4 binding site within transthyretin (TTR) while simultaneously releasing a potent noncovalent TTR kinetic stabilizer. The potency of these covalent inhibitors is superior to tafamidis, the only FDA-approved drug for the treatment of hereditary TTR amyloidosis. In addition to investigations into the covalent modification of TTR via reverse-phase high-performance liquid chromatography, direct methods are performed to confirm and visualize the presumed covalent interaction via mass spectrometry and X-ray crystallography.
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Affiliation(s)
- Seok Beom Lee
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jaeni Yu
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Hyunwoo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kun Woo Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Jong Woo Jeong
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Yun Lan Kim
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, Republic of Korea
| | - Tae-Sung Koo
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ki Bum Hong
- New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Sungwook Choi
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejon 34134, Republic of Korea
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22
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Gilbert K, Vuorinen A, Aatkar A, Pogány P, Pettinger J, Grant EK, Kirkpatrick JM, Rittinger K, House D, Burley GA, Bush JT. Profiling Sulfur(VI) Fluorides as Reactive Functionalities for Chemical Biology Tools and Expansion of the Ligandable Proteome. ACS Chem Biol 2023; 18:285-295. [PMID: 36649130 PMCID: PMC9942091 DOI: 10.1021/acschembio.2c00633] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023]
Abstract
Here, we report a comprehensive profiling of sulfur(VI) fluorides (SVI-Fs) as reactive groups for chemical biology applications. SVI-Fs are reactive functionalities that modify lysine, tyrosine, histidine, and serine sidechains. A panel of SVI-Fs were studied with respect to hydrolytic stability and reactivity with nucleophilic amino acid sidechains. The use of SVI-Fs to covalently modify carbonic anhydrase II (CAII) and a range of kinases was then investigated. Finally, the SVI-F panel was used in live cell chemoproteomic workflows, identifying novel protein targets based on the type of SVI-F used. This work highlights how SVI-F reactivity can be used as a tool to expand the liganded proteome.
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Affiliation(s)
- Katharine
E. Gilbert
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Aini Vuorinen
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Arron Aatkar
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Peter Pogány
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | - Jonathan Pettinger
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Emma K. Grant
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | | | - Katrin Rittinger
- The
Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, United Kingdom
| | - David House
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Glenn A. Burley
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Jacob T. Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
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23
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Al Hasan M, Sabirianov M, Redwine G, Goettsch K, Yang SX, Zhong HA. Binding and selectivity studies of phosphatidylinositol 3-kinase (PI3K) inhibitors. J Mol Graph Model 2023; 121:108433. [PMID: 36812742 DOI: 10.1016/j.jmgm.2023.108433] [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: 11/21/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
Overexpression of the Phosphatidylinositol 3-kinase (PI3K) proteins have been observed in cancer cells. Targeting the phosphatidylinositol 3-kinase (PI3K) signaling transduction pathway by inhibition of the PI3K substrate recognition sites has been proved to be an effective approach to block cancer progression. Many PI3K inhibitors have been developed. Seven drugs have been approved by the US FDA with a mechanism of targeting the phosphatidylinositol 3-kinase/protein kinase-B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway. In this study, we used docking tools to investigate selective binding of ligands toward four different subtypes of PI3Ks (PI3Kα, PI3Kβ, PI3Kγ and PI3Kδ). The affinity predicted from both the Glide dock and the Movable-Type (MT)-based free energy calculations agreed well with the experimental data. The validation of our predicted methods with a large dataset of 147 ligands showed very small mean errors. We identified residues that may dictate the subtype-specific binding. Particularly, residues Asp964, Ser806, Lys890 and Thr886 of PI3Kγ might be utilized for PI3Kγ-selective inhibitor design. Residues Val828, Trp760, Glu826 and Tyr813 may be important for PI3Kδ-selective inhibitor binding.
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Affiliation(s)
- Mohammad Al Hasan
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Matthew Sabirianov
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Grace Redwine
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Kaitlin Goettsch
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA
| | - Stephen X Yang
- Westlake High School, 100 Lakeview Canyon Rd, Thousand Oaks, CA, 91362, USA
| | - Haizhen A Zhong
- DSC 309, Department of Chemistry, The University of Nebraska at Omaha, 6001 Dodge Street, Omaha, NE, 68182, USA.
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24
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Chen P, Tang G, Zhu C, Sun J, Wang X, Xiang M, Huang H, Wang W, Li L, Zhang ZM, Gao L, Yao SQ. 2-Ethynylbenzaldehyde-Based, Lysine-Targeting Irreversible Covalent Inhibitors for Protein Kinases and Nonkinases. J Am Chem Soc 2023; 145:3844-3849. [PMID: 36774655 DOI: 10.1021/jacs.2c11595] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Lysine-targeting irreversible covalent inhibitors have attracted growing interests in recent years, especially in the fields of kinase research. Despite encouraging progress, few chemistries are available to develop inhibitors that are exclusively lysine-targeting, selective, and cell-active. We report herein a 2-ethynylbenzaldehyde (EBA)-based, lysine-targeting strategy to generate potent and selective small-molecule inhibitors of ABL kinase by selectively targeting the conserved catalytic lysine in the enzyme. We showed the resulting compounds were cell-active, capable of covalently engaging endogenous ABL kinase in K562 cells with long-residence time and few off-targets. We further validated the generality of this strategy by developing EBA-based irreversible inhibitors against EGFR (a kinase) and Mcl-1 (a nonkinase) that covalently reacted with the catalytic and noncatalytic lysine within each target.
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Affiliation(s)
- Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Jie Sun
- 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
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen 361005, 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, Shenzhen 518107, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
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25
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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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26
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Fındık V, Varınca Gerçik BT, Sinek Ö, Erdem SS, Ruiz-López MF. Mechanistic Investigation of Lysine-Targeted Covalent Inhibition of PI3Kδ via ONIOM QM:QM Computations. J Chem Inf Model 2022; 62:6775-6787. [PMID: 35980989 DOI: 10.1021/acs.jcim.2c00569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) enzymes are important drug targets, especially in oncology, and several inhibitors are currently under investigation in clinical trials for the treatment of lymphocytic leukemia, follicular lymphoma, breast, thyroid, colorectal, and lung cancer. Targeted covalent inhibitors hold significant promise for drug discovery research especially for kinases. Targeting the lysine residues attracts attention as a new strategy in designing targeted covalent inhibitors, since the lysine residue provides several advantages over the traditional cysteine residue. Recently, new highly selective covalent inhibitors of PI3Kδ with activated ester warheads, targeting the conserved Lys779 residue, were reported. Based on the observed kinetics, a covalent inhibition mechanism was proposed, but the atomistic details of the reaction are still not understood. Therefore, in the present work, we have conducted quantum chemical ONIOM M06-2X/6-31+G(d,p):PM6 calculations on the active site cluster structure of PI3Kδ to elucidate the microscopic details of the mechanism of the aminolysis reaction between Lys779 and the ester inhibitors. Our calculations clearly discriminate the noncovalent methyl ester inhibitor and the covalent inhibitors with activated phenolic esters. For the representative p-NO2, p-F, p-H, and p-OCH3 phenolic esters, the Gibbs free energy profiles of alternative mechanistic paths through either Asp782 or Asp911 demonstrate the modulatory role of active site aspartate residues. The most plausible path alters depending on the electron-withdrawing/donating nature of the p-substituted phenolate leaving group. Inhibitors with sufficiently strong electron-withdrawing group prefer direct dissociation of the leaving group from the tetrahedral zwitterion intermediate, while the ones with electron-donating group favor the formation of a neutral tetrahedral intermediate prior to the dissociation. The relative Gibbs free energy barriers of p-NO2 < p-F < p-H < p-OCH3 substituted phenyl esters display the same qualitative trend as the experimentally measured kinact/KI values. Our results provide in depth insight into the mechanism, which can pave the way for optimizing the inhibitor efficiency.
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Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, 54000, Nancy, France.,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | | | - Öykü Sinek
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
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27
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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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28
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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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29
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Extended Applications of Small-Molecule Covalent Inhibitors toward Novel Therapeutic Targets. Pharmaceuticals (Basel) 2022; 15:ph15121478. [PMID: 36558928 PMCID: PMC9786830 DOI: 10.3390/ph15121478] [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: 11/04/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Recently, small-molecule covalent inhibitors have been accepted as a practical tool for targeting previously "undruggable" proteins. The high target selectivity of modern covalent inhibitors is now alleviating toxicity concerns regarding the covalent modifications of proteins. However, despite the tremendous clinical success of current covalent inhibitors, there are still unmet medical needs that covalent inhibitors have not yet addressed. This review categorized representative covalent inhibitors based on their mechanism of covalent inhibition: conventional covalent inhibitors, targeted covalent inhibitors (TCIs), and expanded TCIs. By reviewing both Food and Drug Administration (FDA)-approved drugs and drug candidates from recent literature, we provide insight into the future direction of covalent inhibitor development.
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30
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Yang T, Cuesta A, Wan X, Craven GB, Hirakawa B, Khamphavong P, May JR, Kath JC, Lapek JD, Niessen S, Burlingame AL, Carelli JD, Taunton J. Reversible lysine-targeted probes reveal residence time-based kinase selectivity. Nat Chem Biol 2022; 18:934-941. [PMID: 35590003 PMCID: PMC9970282 DOI: 10.1038/s41589-022-01019-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022]
Abstract
The expansion of the target landscape of covalent inhibitors requires the engagement of nucleophiles beyond cysteine. Although the conserved catalytic lysine in protein kinases is an attractive candidate for a covalent approach, selectivity remains an obvious challenge. Moreover, few covalent inhibitors have been shown to engage the kinase catalytic lysine in animals. We hypothesized that reversible, lysine-targeted inhibitors could provide sustained kinase engagement in vivo, with selectivity driven in part by differences in residence time. By strategically linking benzaldehydes to a promiscuous kinase binding scaffold, we developed chemoproteomic probes that reversibly and covalently engage >200 protein kinases in cells and mice. Probe-kinase residence time was dramatically enhanced by a hydroxyl group ortho to the aldehyde. Remarkably, only a few kinases, including Aurora A, showed sustained, quasi-irreversible occupancy in vivo, the structural basis for which was revealed by X-ray crystallography. We anticipate broad application of salicylaldehyde-based probes to proteins that lack a druggable cysteine.
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Affiliation(s)
- Tangpo Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Xiaobo Wan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States,Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Gregory B. Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Brad Hirakawa
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Penney Khamphavong
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Jeffrey R. May
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - John C. Kath
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - John D. Lapek
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Sherry Niessen
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jordan D. Carelli
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
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31
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Sun H, Xi M, Jin Q, Zhu Z, Zhang Y, Jia G, Zhu G, Sun M, Zhang H, Ren X, Zhang Y, Xu Z, Huang H, Shen J, Li B, Ge G, Chen K, Zhu W. Chemo- and Site-Selective Lysine Modification of Peptides and Proteins under Native Conditions Using the Water-Soluble Zolinium. J Med Chem 2022; 65:11840-11853. [DOI: 10.1021/acs.jmedchem.2c00937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiguo Sun
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mengyu Xi
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qiang Jin
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yani Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guihua Jia
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guanghao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Mengru Sun
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Hongwei Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Xuelian Ren
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yong Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - He Huang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingshan Shen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Li
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, No. 38 Xue Yuan Road, Haidian District, Beijing 100191, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Kaixian Chen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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32
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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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33
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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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34
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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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35
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The emerging role of mass spectrometry-based proteomics in drug discovery. Nat Rev Drug Discov 2022; 21:637-654. [PMID: 35351998 DOI: 10.1038/s41573-022-00409-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Proteins are the main targets of most drugs; however, system-wide methods to monitor protein activity and function are still underused in drug discovery. Novel biochemical approaches, in combination with recent developments in mass spectrometry-based proteomics instrumentation and data analysis pipelines, have now enabled the dissection of disease phenotypes and their modulation by bioactive molecules at unprecedented resolution and dimensionality. In this Review, we describe proteomics and chemoproteomics approaches for target identification and validation, as well as for identification of safety hazards. We discuss innovative strategies in early-stage drug discovery in which proteomics approaches generate unique insights, such as targeted protein degradation and the use of reactive fragments, and provide guidance for experimental strategies crucial for success.
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36
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Daniels MH, Malojcic G, Clugston SL, Williams B, Coeffet-Le Gal M, Pan-Zhou XR, Venkatachalan S, Harmange JC, Ledeboer M. Discovery and Optimization of Highly Selective Inhibitors of CDK5. J Med Chem 2022; 65:3575-3596. [PMID: 35143203 DOI: 10.1021/acs.jmedchem.1c02069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most prevalent monogenic human disease, but to date, only one therapy (tolvaptan) is approved to treat kidney cysts in ADPKD patients. Cyclin-dependent kinase 5 (CDK5), an atypical member of the cyclin-dependent kinase family, has been implicated as a target for treating ADPKD. However, no compounds have been disclosed to date that selectively inhibit CDK5 while sparing the broader CDK family members. Herein, we report the discovery of CDK5 inhibitors, including GFB-12811, that are highly selective over the other tested kinases. In cellular assays, our compounds demonstrate CDK5 target engagement while avoiding anti-proliferative effects associated with inhibiting other CDKs. In addition, we show that the compounds in this series exhibit promising in vivo PK profiles, enabling their use as tool compounds for interrogating the role of CDK5 in ADPKD and other diseases.
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Affiliation(s)
- Matthew H Daniels
- Goldfinch Bio, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Goran Malojcic
- Goldfinch Bio, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Susan L Clugston
- Goldfinch Bio, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Brett Williams
- Goldfinch Bio, 215 First Street, Cambridge, Massachusetts 02142, United States
| | | | - Xin-Ru Pan-Zhou
- Goldfinch Bio, 215 First Street, Cambridge, Massachusetts 02142, United States
| | | | | | - Mark Ledeboer
- Goldfinch Bio, 215 First Street, Cambridge, Massachusetts 02142, United States
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37
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Wang B, Wu H, Hu C, Wang H, Liu J, Wang W, Liu Q. An overview of kinase downregulators and recent advances in discovery approaches. Signal Transduct Target Ther 2021; 6:423. [PMID: 34924565 PMCID: PMC8685278 DOI: 10.1038/s41392-021-00826-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Since the clinical approval of imatinib, the discovery of protein kinase downregulators entered a prosperous age. However, challenges still exist in the discovery of kinase downregulator drugs, such as the high failure rate during development, side effects, and drug-resistance problems. With the progress made through multidisciplinary efforts, an increasing number of new approaches have been applied to solve the above problems during the discovery process of kinase downregulators. In terms of in vitro and in vivo drug evaluation, progress was also made in cellular and animal model platforms for better and more clinically relevant drug assessment. Here, we review the advances in drug design strategies, drug property evaluation technologies, and efficacy evaluation models and technologies. Finally, we discuss the challenges and perspectives in the development of kinase downregulator drugs.
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Affiliation(s)
- Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Haizhen Wang
- Hefei PreceDo pharmaceuticals Co., Ltd, Hefei, Anhui, 230088, People's Republic of China
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
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38
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Ferlenghi F, Scalvini L, Vacondio F, Castelli R, Bozza N, Marseglia G, Rivara S, Lodola A, La Monica S, Minari R, Petronini PG, Alfieri R, Tiseo M, Mor M. A sulfonyl fluoride derivative inhibits EGFR L858R/T790M/C797S by covalent modification of the catalytic lysine. Eur J Med Chem 2021; 225:113786. [PMID: 34464874 DOI: 10.1016/j.ejmech.2021.113786] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
The emergence of the C797S mutation in EGFR is a frequent mechanism of resistance to osimertinib in the treatment of non-small cell lung cancer (NSCLC). In the present work, we report the design, synthesis and biochemical characterization of UPR1444 (compound 11), a new sulfonyl fluoride derivative which potently and irreversibly inhibits EGFRL858R/T790M/C797S through the formation of a sulfonamide bond with the catalytic residue Lys745. Enzymatic assays show that compound 11 displayed an inhibitory activity on EGFRWT comparable to that of osimertinib, and it resulted more selective than the sulfonyl fluoride probe XO44, recently reported to inhibit a significant part of the kinome. Neither compound 11 nor XO44 inhibited EGFRdel19/T790M/C797S triple mutant. When tested in Ba/F3 cells expressing EGFRL858R/T790M/C797S, compound 11 resulted significantly more potent than osimertinib at inhibiting both EGFR autophosphorylation and proliferation, even if the inhibition of EGFR autophosphorylation by compound 11 in Ba/F3 cells was not long lasting.
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Affiliation(s)
| | - Laura Scalvini
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Nicole Bozza
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Silvia Rivara
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Alessio Lodola
- Department of Food and Drug, University of Parma, Parma, Italy.
| | - Silvia La Monica
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Roberta Minari
- Medical Oncology, University Hospital of Parma, Parma, Italy
| | | | - Roberta Alfieri
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Marcello Tiseo
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology, University Hospital of Parma, Parma, Italy
| | - Marco Mor
- Department of Food and Drug, University of Parma, Parma, Italy
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39
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Fındık V, Ruiz-López MF, Erdem SS. Mechanistic insights into lysine-targeting covalent inhibition through a theoretical study of ester aminolysis. Org Biomol Chem 2021; 19:9996-10004. [PMID: 34755747 DOI: 10.1039/d1ob01963e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Development of targeted covalent inhibitors in drug design has a broad and important interest and many efforts are currently being made in this direction. Targeted covalent inhibitors have special relevance in oncology due to the possibilities they offer to overcome the problems of acquired resistance. In recent experiments, lysine-targeting has been envisaged for the irreversible inhibition of the heterodimeric lipid kinase phosphoinositide 3-kinase delta (PI3Kδ). Activated esters have been evaluated and shown to be promising inhibitors of this enzyme, but the reaction mechanisms display specificities that are not yet fully understood. In the present work, we have carried out a theoretical study of the aminolysis reaction of model esters in aqueous solution to gain insights into the corresponding biological processes. We have found that phenolic esters bearing electron-withdrawing groups are particularly reactive. The predicted mechanism involves the formation of a tetrahedral zwitterionic intermediate, which dissociates into an alkoxide and a protonated amide, this charge separation being the driving force for the subsequent proton transfer and final product formation. Structure-reactivity relationships are reported and shown to be a useful tool for evaluating potential inhibitor candidates.
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Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-les-Nancy, France. .,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey.
| | - Manuel F Ruiz-López
- LPCT, UMR 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-les-Nancy, France.
| | - Safiye Sag Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey.
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40
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Fournier JCL, Evans JP, Zappacosta F, Thomas DA, Patel VK, White GV, Campos S, Tomkinson NCO. Acetylation of the Catalytic Lysine Inhibits Kinase Activity in PI3Kδ. ACS Chem Biol 2021; 16:1644-1653. [PMID: 34397208 DOI: 10.1021/acschembio.1c00225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Covalent inhibition is a powerful strategy to develop potent and selective small molecule kinase inhibitors. Targeting the conserved catalytic lysine is an attractive method for selective kinase inactivation. We have developed novel, selective inhibitors of phosphoinositide 3-kinase δ (PI3Kδ) which acylate the catalytic lysine, Lys779, using activated esters as the reactive electrophiles. The acylating agents were prepared by adding the activated ester motif to a known selective dihydroisobenzofuran PI3Kδ inhibitor. Three esters were designed, including an acetate ester which was the smallest lysine modification evaluated in this work. Covalent binding to the enzyme was characterized by intact protein mass spectrometry of the PI3Kδ-ester adducts. An enzymatic digest coupled with tandem mass spectrometry identified Lys779 as the covalent binding site, and a biochemical activity assay confirmed that PI3Kδ inhibition was a direct result of covalent lysine acylation. These results indicate that a simple chemical modification such as lysine acetylation is sufficient to inhibit kinase activity. The selectivity of the compounds was evaluated against lipid kinases in cell lysates using a chemoproteomic binding assay. Due to the conserved nature of the catalytic lysine across the kinome, we believe the covalent inhibition strategy presented here could be applicable to a broad range of clinically relevant targets.
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Affiliation(s)
- Julie C. L. Fournier
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John P. Evans
- Arctoris, 120E Olympic Avenue, Milton Park, Oxford, OX14 4SA, United Kingdom
| | | | - Daniel A. Thomas
- Arctoris, 120E Olympic Avenue, Milton Park, Oxford, OX14 4SA, United Kingdom
| | - Vipulkumar K. Patel
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Gemma V. White
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Sebastien Campos
- Pharmaron, West Hill Innovation Park, Hertford Road, Hoddesdon, Hertfordshire EN11 9FH, United Kingdom
| | - Nicholas C. O. Tomkinson
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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41
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Quach D, Tang G, Anantharajan J, Baburajendran N, Poulsen A, Wee JLK, Retna P, Li R, Liu B, Tee DHY, Kwek PZ, Joy JK, Yang W, Zhang C, Foo K, Keller TH, Yao SQ. Strategic Design of Catalytic Lysine‐Targeting Reversible Covalent BCR‐ABL Inhibitors**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- David Quach
- NUS Graduate School for Integrative Sciences and Engineering 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02 Singapore 119077 Singapore
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Guanghui Tang
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - John L. K. Wee
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Priya Retna
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Rong Li
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Boping Liu
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Doris H. Y. Tee
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Perlyn Z. Kwek
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Joma K. Joy
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Wan‐Qi Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Chong‐Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100050 China
| | - Klement Foo
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Thomas H. Keller
- Experimental Drug Development Centre 10 Biopolis Road, Chromos, #05-01 Singapore 138670 Singapore
| | - Shao Q. Yao
- NUS Graduate School for Integrative Sciences and Engineering 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02 Singapore 119077 Singapore
- Department of Chemistry National University of Singapore Singapore 117543 Singapore
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42
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Quach D, Tang G, Anantharajan J, Baburajendran N, Poulsen A, Wee JLK, Retna P, Li R, Liu B, Tee DHY, Kwek PZ, Joy JK, Yang WQ, Zhang CJ, Foo K, Keller TH, Yao SQ. Strategic Design of Catalytic Lysine-Targeting Reversible Covalent BCR-ABL Inhibitors*. Angew Chem Int Ed Engl 2021; 60:17131-17137. [PMID: 34008286 DOI: 10.1002/anie.202105383] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors have re-emerged as validated drugs to overcome acquired resistance in cancer treatment. Herein, by using a carbonyl boronic acid (CBA) warhead, we report the structure-based design of BCR-ABL inhibitors via reversible covalent targeting of the catalytic lysine with improved potency against both wild-type and mutant ABL kinases, especially ABLT315I bearing the gatekeeper residue mutation. We show the evolutionarily conserved lysine can be targeted selectively, and the selectivity depends largely on molecular recognition of the non-covalent pharmacophore in this class of inhibitors, probably due to the moderate reactivity of the warhead. We report the first co-crystal structures of covalent inhibitor-ABL kinase domain complexes, providing insights into the interaction of this warhead with the catalytic lysine. We also employed label-free mass spectrometry to evaluate off-targets of our compounds at proteome-wide level in different mammalian cells.
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Affiliation(s)
- David Quach
- NUS Graduate School for Integrative Sciences and Engineering, 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02, Singapore, 119077, Singapore.,Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Anders Poulsen
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - John L K Wee
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Priya Retna
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Rong Li
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Boping Liu
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Doris H Y Tee
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Perlyn Z Kwek
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Joma K Joy
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Wan-Qi Yang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines and Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100050, China
| | - Klement Foo
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Thomas H Keller
- Experimental Drug Development Centre, 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Shao Q Yao
- NUS Graduate School for Integrative Sciences and Engineering, 21 Lower Kent Ridge, University Hall, Tan China Tuan Wing, #04-02, Singapore, 119077, Singapore.,Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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43
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Yang C, Xu C, Li Z, Chen Y, Wu T, Hong H, Lu M, Jia Y, Yang Y, Liu X, Deng M, Chen Z, Li Q, Ling Y, Zhou Y. Bioisosteric replacements of the indole moiety for the development of a potent and selective PI3Kδ inhibitor: Design, synthesis and biological evaluation. Eur J Med Chem 2021; 223:113661. [PMID: 34237636 DOI: 10.1016/j.ejmech.2021.113661] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/18/2022]
Abstract
Based on indole scaffold, a potent and selective phosphoinositide 3-kinase delta (PI3Kδ) inhibitor, namely FD223, was developed by the bioisosteric replacement drug discovery approach and studied for the treatment of acute myeloid leukemia (AML). In vitro studies revealed that FD223 displays high potency (IC50 = 1 nM) and selectivity (29-51 fold over other PI3K isoforms) against PI3Kδ, and exhibits efficient inhibition of the proliferation of AML cell lines (MOLM-16, HL-60, EOL-1 and KG-1) by suppressing p-AKT Ser473 thus causing G1 phase arrest during the cell cycle. Further given the favorable pharmacokinetic (PK) profiles of FD223, in vivo studies were evaluated using xenograft model in nude mice, confirming its significant antitumor efficacy meanwhile with no observable toxicity. All these results are comparable to the positive group of Idelalisib (CAL-101), indicating that FD223 has potential for further development as a promising PI3Kδ inhibitor for the treatment of leukemia such as AML.
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Affiliation(s)
- Chengbin Yang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Chenyue Xu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Zhipeng Li
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yi Chen
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Tianze Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Hui Hong
- Lyrae Therapeutics, L.L.C., Shanghai, 200438, China
| | - Mingzhu Lu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yu Jia
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Yongtai Yang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xiaofeng Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Mingli Deng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Zhenxia Chen
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Qingquan Li
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Yun Ling
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China; Zhuhai-Fudan Innovation Institute, Zhuhai, Guangdong, 519000, China.
| | - Yaming Zhou
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai, 200433, China.
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Wolter M, Valenti D, Cossar PJ, Hristeva S, Levy LM, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. An Exploration of Chemical Properties Required for Cooperative Stabilization of the 14-3-3 Interaction with NF-κB-Utilizing a Reversible Covalent Tethering Approach. J Med Chem 2021; 64:8423-8436. [PMID: 34076416 PMCID: PMC8237268 DOI: 10.1021/acs.jmedchem.1c00401] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Protein–protein
modulation has emerged as a proven approach
to drug discovery. While significant progress has been gained in developing
protein–protein interaction (PPI) inhibitors, the orthogonal
approach of PPI stabilization lacks established methodologies for
drug design. Here, we report the systematic ″bottom-up″
development of a reversible covalent PPI stabilizer. An imine bond
was employed to anchor the stabilizer at the interface of the 14-3-3/p65
complex, leading to a molecular glue that elicited an 81-fold increase
in complex stabilization. Utilizing protein crystallography and biophysical
assays, we deconvoluted how chemical properties of a stabilizer translate
to structural changes in the ternary 14-3-3/p65/molecular glue complex.
Furthermore, we explore how this leads to high cooperativity and increased
stability of the complex.
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Affiliation(s)
- Madita Wolter
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Dario Valenti
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands.,Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Peter J Cossar
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Stanimira Hristeva
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Laura M Levy
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Thorsten Genski
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Torsten Hoffmann
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Dimitrios Tzalis
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227 Dortmund, Germany
| | - Christian Ottmann
- Department of Biomedical Engineering, Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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Roskoski R. Properties of FDA-approved small molecule phosphatidylinositol 3-kinase inhibitors prescribed for the treatment of malignancies. Pharmacol Res 2021; 168:105579. [PMID: 33774181 DOI: 10.1016/j.phrs.2021.105579] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
The discovery of the phosphatidylinositol 3-kinase (PI 3-kinase) pathway was a major advance in understanding eukaryotic signal transduction. The high frequency of PI 3-kinase pathway mutations in many cancers stimulated the development of drugs targeting these oncogenic mutants. The PI 3-kinases are divided into three classes and Class I PI 3-kinases, which catalyze the phosphorylation of phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2) to generate phosphatidylinositol-3,4,5-trisphosphate (PIP3), are the main subject of this review. The class I PI 3-kinases are made up of p110α, p110β, p110δ, and p110γ catalytic subunits. These catalytic subunits are constitutively bound to regulatory subunits (p85α, p85β, p55γ, p101, and p87 proteins). The p85/p55 regulatory subunits heterodimerize with p110α or p110δ thereby forming complexes that are regulated chiefly by receptor protein-tyrosine kinases. The p101 and p87 subunits heterodimerize with p110γ to form complexes that are regulated mainly by G protein-coupled receptors (GPCRs). Complexes containing the p110β subunit are activated by receptor protein-tyrosine kinases as well as GPCRs. Following the generation of PIP3, the AKT and mTOR protein-serine/threonine kinases are activated leading to cell growth, proliferation, and survival. Like protein kinases, the PI 3-kinase domains consist of a bilobed structure connected by a hinge-linker segment. ATP and most PI 3-kinase and protein kinase inhibitors form hydrogen bonds with hinge residues. The small and large lobes of PI 3-kinases and protein kinases have a very similar three-dimensional structure called the protein kinase fold. Both PI 3-kinases and eukaryotic protein kinases possess an activation segment that begins with a DFG triad (Asp-Phe-Gly); the activation segment of protein kinases usually ends with an APE (Ala-Pro-Glu) signature while that of PI 3-kinases ends with a PFxLT (Pro-Phe-Xxx-Leu-Thr) signature. Dormant PI 3-kinases have a collapsed activation loop and active PI 3-kinases have an extended activation loop. The distance between the α-carbon atom of the DFG-D residue at the beginning of the activation loop and that of the PFxLT-F residue at the end of the activation loop in dormant PI 3-kinases is about 13 Å; this distance in active PI 3-kinases is about 18 Å. The protein kinase catalytic loop has an HRD (His-Arg-Asp) signature while that of the PI 3-kinases reverses the order with a DRH triad. Alpelisib is an orally effective FDA-approved PI 3-kinase-α inhibitor used for the treatment of breast cancer. Copanlisib, duvelisib, idelalisib, and umbralisib are PI 3-kinase-δ inhibitors that are approved for the third-line treatment of follicular lymphomas and other hematological disorders. Copanlisib is also a potent inhibitor of PI 3-kinase-α. Of the five approved drugs, all are orally bioavailable except copanlisib. Idelalisib interacts with the active conformation of PI 3-kinase-δ and is classified as a type I inhibitor. Alpelisib and copanlisib interact with inactive PI 3-kinase-α and PI 3-kinase-γ, respectively, and are classified as a type I½ antagonists. Except for umbralisib with a molecular weight of 571.5, all five drugs conform to the Lipinski rule of five for oral effectiveness. Copanlisib, however, must be given intravenously. Alpelisib and copanlisib inhibit PI 3-kinase-α, which is involved in insulin signaling, and both drugs promote insulin-resistance and produce hyperglycemia. The five FDA-approved PI 3-kinase inhibitors produce significant on-target toxicities, more so than many approved protein kinase antagonists. The development of PI 3-kinase inhibitors with fewer toxicities is an important long-term therapeutic goal.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 3754 Brevard Road, Suite 116, Box 19, Horse Shoe, NC 28742-8814, United States.
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46
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Research advances on selective phosphatidylinositol 3 kinase δ (PI3Kδ) inhibitors. Bioorg Med Chem Lett 2020; 30:127457. [PMID: 32755681 DOI: 10.1016/j.bmcl.2020.127457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022]
Abstract
PI3Kδ in B cells mediates antigen receptor signaling and promote neutrophil chemotaxis. The activation of PI3Kδ can cause mast cell maturation and degranulation, myeloid cell dysfunction, and cytokine release. As a key signal molecule, PI3Kδ interacts with the lipid binding domain of a variety of cellular proteins as a secondary messenger, ultimately affecting a series of significant cellular pathways in disease pathology. Therefore, many research organizations and pharmaceutical companies have studied it to develop effectively selective PI3Kδ inhibitors as therapeutics. This review summarizes research advances in varying chemical classes of selective PI3Kδ inhibitors and the structure-activity relationship, and it mainly focuses on the propeller- versus flat-type class of inhibitors.
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47
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Avoiding or Co-Opting ATP Inhibition: Overview of Type III, IV, V, and VI Kinase Inhibitors. NEXT GENERATION KINASE INHIBITORS 2020. [PMCID: PMC7359047 DOI: 10.1007/978-3-030-48283-1_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
As described in the previous chapter, most kinase inhibitors that have been developed for use in the clinic act by blocking ATP binding; however, there is growing interest in identifying compounds that target kinase activities and functions without interfering with the conserved features of the ATP-binding site. This chapter will highlight alternative approaches that exploit unique kinase structural features that are being targeted to identify more selective and potent inhibitors. The figure below, adapted from (Sammons et al., Molecular Carcinogenesis 58:1551–1570, 2019), provides a graphical description of the various approaches to manipulate kinase activity. In addition to the type I and II inhibitors, type III kinase inhibitors have been identified to target sites adjacent to the ATP-binding site in the catalytic domain. New information on kinase structure and substrate-binding sites has enabled the identification of type IV kinase inhibitor compounds that target regions outside the catalytic domain. The combination of targeting unique allosteric sites outside the catalytic domain with ATP-targeted compounds has yielded a number of novel bivalent type V kinase inhibitors. Finally, emerging interest in the development of irreversible compounds that form selective covalent interactions with key amino acids involved in kinase functions comprise the class of type VI kinase inhibitors.
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48
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Wei L, Wen W, Rao L, Huang Y, Lei M, Liu K, Hu S, Song R, Ren Y, Wan J. Cov_FB3D: A De Novo Covalent Drug Design Protocol Integrating the BA-SAMP Strategy and Machine-Learning-Based Synthetic Tractability Evaluation. J Chem Inf Model 2020; 60:4388-4402. [PMID: 32233478 DOI: 10.1021/acs.jcim.9b01197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
De novo drug design actively seeks to use sets of chemical rules for the fast and efficient identification of structurally new chemotypes with the desired set of biological properties. Fragment-based de novo design tools have been successfully applied in the discovery of noncovalent inhibitors. Nevertheless, these tools are rarely applied in the field of covalent inhibitor design. Herein, we present a new protocol, called Cov_FB3D, which involves the in silico assembly of potential novel covalent inhibitors by identifying the active fragments in the covalently binding site of the target protein. In this protocol, we propose a BA-SAMP strategy, which combines the noncovalent moiety score with the X-Score as the molecular mechanism (MM) level, and the covalent candidate score with the PM7 as the QM level. The synthetic accessibility of each suggested compound could be further evaluated with machine-learning-based synthetic complexity evaluation (SCScore). An in-depth test of this protocol against the crystal structures of 15 covalent complexes consisting of BTK inhibitors, KRAS inhibitors, EGFR inhibitors, EphB1 inhibitors, MAGL inhibitors, and MAPK inhibitors revealed that most of these inhibitors could be de novo reproduced from the fragments by Cov_FB3D. The binding modes of most generated reference poses could accurately reproduce the known binding mode of most of the reference covalent adduct in the binding site (RMSD ≤ 2 Å). In particular, most of these inhibitors were ranked in the top 2%, using the BA-SAMP strategy. Notably, the novel human ALDOA inhibitor (T1) with potent inhibitory activity (0.34 ± 0.03 μM) and greater synthetic accessibility was successfully de novo designed by this protocol. The positive results confirm the abilities of Cov_FB3D protocol.
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Affiliation(s)
- Lin Wei
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Wuqiang Wen
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Li Rao
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yunyuan Huang
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Mengting Lei
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Kai Liu
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, 530200, People's Republic of China
| | - Saiya Hu
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Rongrong Song
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yanliang Ren
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jian Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
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49
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White G, Prior C, Mills SJ, Baker K, Whitfield H, Riley AM, Oganesyan VS, Potter BVL, Brearley CA. Regioisomeric Family of Novel Fluorescent Substrates for SHIP2. ACS Med Chem Lett 2020; 11:309-315. [PMID: 32184962 PMCID: PMC7073872 DOI: 10.1021/acsmedchemlett.9b00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/18/2019] [Indexed: 12/27/2022] Open
Abstract
SHIP2 (SH2-domain containing inositol 5-phosphatase type 2) is a canonical 5-phosphatase, which, through its catalytic action on PtdInsP3, regulates the PI3K/Akt pathway and metabolic action of insulin. It is a drug target, but there is limited evidence of inhibition of SHIP2 by small molecules in the literature. With the goal to investigate inhibition, we report a homologous family of synthetic, chromophoric benzene phosphate substrates of SHIP2 that display the headgroup regiochemical hallmarks of the physiological inositide substrates that have proved difficult to crystallize with 5-phosphatases. Using time-dependent density functional theory (TD-DFT), we explore the intrinsic fluorescence of these novel substrates and show how fluorescence can be used to assay enzyme activity. The TD-DFT approach promises to inform rational design of enhanced active site probes for the broadest family of inositide-binding/metabolizing proteins, while maintaining the regiochemical properties of bona fide inositide substrates.
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Affiliation(s)
- Gaye White
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Christopher Prior
- School of Chemistry, UEA, Norwich Research Park, Norwich NR47TJ, U.K
| | - Stephen J. Mills
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Kendall Baker
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Hayley Whitfield
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Andrew M. Riley
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | | | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K
| | - Charles A. Brearley
- School of Biological Sciences, UEA, Norwich Research Park, Norwich NR4 7TJ, U.K
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50
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Dalton SE, Campos S. Covalent Small Molecules as Enabling Platforms for Drug Discovery. Chembiochem 2020; 21:1080-1100. [DOI: 10.1002/cbic.201900674] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel E. Dalton
- Astex Pharmaceuticals 436 Cambridge Science Park Milton Road Cambridge CB4 0QA UK
| | - Sebastien Campos
- PharmaronDrug Discovery Services Europe Hertford Road Hoddesdon Hertfordshire EN11 9BU UK
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