1
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Pei BB, Wang J, Ji J, Chen Q, Wang CQ, Feng C. Radical Decarboxylation-Initiated S H2' Reaction of β,β-Difluoroenol Sulfonates: Access to α,α-Difluoroketones. Org Lett 2024. [PMID: 38796776 DOI: 10.1021/acs.orglett.4c01555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2024]
Abstract
Reported herein is a novel radical decarboxylation-initiated SH2' reaction of β,β-difluoroenol sulfonates. This transformation is characterized by mild reaction conditions, a broad substrate scope, and late-stage modification of drug molecules, providing general and mechanistically distinct access to bioactive and synthetically versatile α,α-difluoroketones. Preliminary mechanistic studies demonstrate that this reaction proceeds through a succession of silver-mediated decarboxylative radical generation and radical-addition-induced β-elimination of the sulfonyl radical.
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Affiliation(s)
- Bing-Bing Pei
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis (IAS), School of Chemistry and Molecular Engineering, State Key Laboratory of Material-Oriented Chemical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, Jiangsu 211816, China
| | - Jiali Wang
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis (IAS), School of Chemistry and Molecular Engineering, State Key Laboratory of Material-Oriented Chemical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, Jiangsu 211816, China
| | - Jiuyang Ji
- Capital Construction Office, Nanjing Tech University, 30 South Puzhu Road, Nanjing, Jiangsu 211816, China
| | - Qing Chen
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis (IAS), School of Chemistry and Molecular Engineering, State Key Laboratory of Material-Oriented Chemical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, Jiangsu 211816, China
| | - Cheng-Qiang Wang
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis (IAS), School of Chemistry and Molecular Engineering, State Key Laboratory of Material-Oriented Chemical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, Jiangsu 211816, China
| | - Chao Feng
- Technical Institute of Fluorochemistry (TIF), Institute of Advanced Synthesis (IAS), School of Chemistry and Molecular Engineering, State Key Laboratory of Material-Oriented Chemical Engineering, Nanjing Tech University, 30 South Puzhu Road, Nanjing, Jiangsu 211816, China
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2
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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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3
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Falke S, Lieske J, Herrmann A, Loboda J, Karničar K, Günther S, Reinke PYA, Ewert W, Usenik A, Lindič N, Sekirnik A, Dretnik K, Tsuge H, Turk V, Chapman HN, Hinrichs W, Ebert G, Turk D, Meents A. Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors. J Med Chem 2024; 67:7048-7067. [PMID: 38630165 PMCID: PMC11089505 DOI: 10.1021/acs.jmedchem.3c02351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/15/2024]
Abstract
Emerging RNA viruses, including SARS-CoV-2, continue to be a major threat. Cell entry of SARS-CoV-2 particles via the endosomal pathway involves cysteine cathepsins. Due to ubiquitous expression, cathepsin L (CatL) is considered a promising drug target in the context of different viral and lysosome-related diseases. We characterized the anti-SARS-CoV-2 activity of a set of carbonyl- and succinyl epoxide-based inhibitors, which were previously identified as inhibitors of cathepsins or related cysteine proteases. Calpain inhibitor XII, MG-101, and CatL inhibitor IV possess antiviral activity in the very low nanomolar EC50 range in Vero E6 cells and inhibit CatL in the picomolar Ki range. We show a relevant off-target effect of CatL inhibition by the coronavirus main protease α-ketoamide inhibitor 13b. Crystal structures of CatL in complex with 14 compounds at resolutions better than 2 Å present a solid basis for structure-guided understanding and optimization of CatL inhibitors toward protease drug development.
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Affiliation(s)
- Sven Falke
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Julia Lieske
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Alexander Herrmann
- Institute
of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Munich, Germany
| | - Jure Loboda
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Katarina Karničar
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Sebastian Günther
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Patrick Y. A. Reinke
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Wiebke Ewert
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
| | - Aleksandra Usenik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Nataša Lindič
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Andreja Sekirnik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Klemen Dretnik
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- The
Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Hideaki Tsuge
- Faculty of
Life Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Vito Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henry N. Chapman
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
- Hamburg
Centre for Ultrafast Imaging, Universität
Hamburg, Luruper Chaussee
149, 22761 Hamburg, Germany
- Department
of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Winfried Hinrichs
- Institute
of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Gregor Ebert
- Institute
of Virology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Munich, Germany
- Institute
of Virology, Technical University of Munich, Trogerstraße 30, 81675 Munich, Germany
| | - Dušan Turk
- Department
of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre
of Excellence for Integrated Approaches in Chemistry and Biology of
Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Alke Meents
- Center
for Free-Electron Laser Science CFEL, Deutsches
Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany
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4
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Liu F, Zhou T, Zhang S, Li Y, Chen Y, Miao Z, Wang X, Yang G, Li Q, Zhang L, Liu Y. Cathepsin B: The dawn of tumor therapy. Eur J Med Chem 2024; 269:116329. [PMID: 38508117 DOI: 10.1016/j.ejmech.2024.116329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Cathepsin B (CTSB) is a key lysosomal protease that plays a crucial role in the development of cancer. This article elucidates the relationship between CTSB and cancer from the perspectives of its structure, function, and role in tumor growth, migration, invasion, metastasis, angiogenesis and autophagy. Further, we summarized the research progress of cancer treatment related drugs targeting CTSB, as well as the potential and advantages of Traditional Chinese medicine in treating tumors by regulating the expression of CTSB.
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Affiliation(s)
- Fuxian Liu
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Ting Zhou
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China; Experimental & Training Teaching Centers, Gansu University of Chinese Medicine, Lanzhou, China
| | - Shangzu Zhang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Yangyang Li
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Yan Chen
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Zhiming Miao
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xin Wang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Gengqiang Yang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Qiyang Li
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China
| | - Liying Zhang
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China.
| | - Yongqi Liu
- Provincial-Level Key Laboratory for Molecular Medicine of Major Diseases and the Prevention and Treatment with Traditional Chinese Medicine Research in Gansu Colleges and Universities, Gansu University of Chinese Medicine, Lanzhou, China; College of Basic Medicine, Gansu University of Chinese Medicine, Lanzhou, China; Key Laboratory of Dunhuang Medicine and Transformation at Provincial and Ministerial Level, Gansu University of Chinese Medicine, Lanzhou, China.
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5
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González JEH, Salas-Sarduy E, Alvarez LH, Valiente PA, Arni RK, Pascutti PG. Three Decades of Targeting Falcipains to Develop Antiplasmodial Agents: What have we Learned and What can be Done Next? Curr Med Chem 2024; 31:2234-2263. [PMID: 37711130 DOI: 10.2174/0929867331666230913165219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/06/2023] [Accepted: 07/25/2023] [Indexed: 09/16/2023]
Abstract
Malaria is a devastating infectious disease that affects large swathes of human populations across the planet's tropical regions. It is caused by parasites of the genus Plasmodium, with Plasmodium falciparum being responsible for the most lethal form of the disease. During the intraerythrocytic stage in the human hosts, malaria parasites multiply and degrade hemoglobin (Hb) using a battery of proteases, which include two cysteine proteases, falcipains 2 and 3 (FP-2 and FP-3). Due to their role as major hemoglobinases, FP-2 and FP-3 have been targeted in studies aiming to discover new antimalarials and numerous inhibitors with activity against these enzymes, and parasites in culture have been identified. Nonetheless, cross-inhibition of human cysteine cathepsins remains a serious hurdle to overcome for these compounds to be used clinically. In this article, we have reviewed key functional and structural properties of FP-2/3 and described different compound series reported as inhibitors of these proteases during decades of active research in the field. Special attention is also paid to the wide range of computer-aided drug design (CADD) techniques successfully applied to discover new active compounds. Finally, we provide guidelines that, in our understanding, will help advance the rational discovery of new FP-2/3 inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE/UNESP, São José do Rio Preto, SP, Brazil
- Department of Pharmaceutical Sciences, UZA II, University of Vienna, Vienna, 1090, Austria
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, CONICET, San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnología (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | | | - Pedro Alberto Valiente
- Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Canada
| | | | - Pedro Geraldo Pascutti
- Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, RJ, Brazil
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6
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Verma K, Lahariya AK, Verma G, Kumari M, Gupta D, Maurya N, Verma AK, Mani A, Schneider KA, Bharti PK. Screening of potential antiplasmodial agents targeting cysteine protease-Falcipain 2: a computational pipeline. J Biomol Struct Dyn 2023; 41:8121-8164. [PMID: 36218071 DOI: 10.1080/07391102.2022.2130984] [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: 07/13/2022] [Accepted: 09/24/2022] [Indexed: 10/17/2022]
Abstract
The spread of antimalarial drug resistance is a substantial challenge in achieving global malaria elimination. Consequently, the identification of novel therapeutic candidates is a global health priority. Malaria parasite necessitates hemoglobin degradation for its survival, which is mediated by Falcipain 2 (FP2), a promising antimalarial target. In particular, FP2 is a key enzyme in the erythrocytic stage of the parasite's life cycle. Here, we report the screening of approved drugs listed in DrugBank using a computational pipeline that includes drug-likeness, toxicity assessments, oral toxicity evaluation, oral bioavailability, docking analysis, maximum common substructure (MCS) and molecular dynamics (MD) Simulations analysis to identify capable FP2 inhibitors, which are hence potential antiplasmodial agents. A total of 45 drugs were identified, which have positive drug-likeness, no toxic features and good bioavailability. Among these, six drugs showed good binding affinity towards FP2 compared to E64, an epoxide known to inhibit FP2. Notably, two of them, Cefalotin and Cefoxitin, shared the highest MCS with E64, which suggests that they possess similar biological activity as E64. In an investigation using MD for 100 ns, Cefalotin and Cefoxitin showed adequate protein compactness as well as satisfactory complex stability. Overall, these computational approach findings can be applied for designing and developing specific inhibitors or new antimalarial agents for the treatment of malaria infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanika Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Ayush Kumar Lahariya
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Garima Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- School of Studies in Microbiology, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Monika Kumari
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Biotechnology, St. Aloysius' (Autonomous) College, Affiliated to Rani Durgawati University, Jabalpur, Madhya Pradesh, Jabalpur, India
| | - Divanshi Gupta
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Biological Sciences, Rani Durgawati University, Jabalpur, Madhya Pradesh, India
| | - Neha Maurya
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, India
| | - Anil Kumar Verma
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj, India
| | | | - Praveen Kumar Bharti
- Division of Vector-Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
- Department of Parasite Host Biology, National Institute of Malaria Research, Delhi, India
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7
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Hartley B, Bassiouni W, Schulz R, Julien O. The roles of intracellular proteolysis in cardiac ischemia-reperfusion injury. Basic Res Cardiol 2023; 118:38. [PMID: 37768438 DOI: 10.1007/s00395-023-01007-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Ischemic heart disease remains a leading cause of human mortality worldwide. One form of ischemic heart disease is ischemia-reperfusion injury caused by the reintroduction of blood supply to ischemic cardiac muscle. The short and long-term damage that occurs due to ischemia-reperfusion injury is partly due to the proteolysis of diverse protein substrates inside and outside of cardiomyocytes. Ischemia-reperfusion activates several diverse intracellular proteases, including, but not limited to, matrix metalloproteinases, calpains, cathepsins, and caspases. This review will focus on the biological roles, intracellular localization, proteolytic targets, and inhibitors of these proteases in cardiomyocytes following ischemia-reperfusion injury. Recognition of the intracellular function of each of these proteases includes defining their activation, proteolytic targets, and their inhibitors during myocardial ischemia-reperfusion injury. This review is a step toward a better understanding of protease activation and involvement in ischemic heart disease and developing new therapeutic strategies for its treatment.
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Affiliation(s)
- Bridgette Hartley
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Wesam Bassiouni
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
| | - Richard Schulz
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada.
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada.
- Mazankowski Alberta Heart Institute, University of Alberta, Edmonton, AB, Canada.
- Women and Children's Health Research Institute, University of Alberta, Edmonton, AB, Canada.
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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8
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Columbus I, Ghindes-Azaria L, Herzog IM, Blum E, Parvari G, Eichen Y, Cohen Y, Gershonov E, Drug E, Saphier S, Elias S, Smolkin B, Zafrani Y. Species-specific lipophilicities of fluorinated diketones in complex equilibria systems and their potential as multifaceted reversible covalent warheads. Commun Chem 2023; 6:197. [PMID: 37715018 PMCID: PMC10504258 DOI: 10.1038/s42004-023-01004-2] [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: 06/28/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
Combined molecular, physicochemical and chemical properties of electrophilic warheads can be applied to create covalent drugs with diverse facets. Here we study these properties in fluorinated diketones (FDKs) and their multicomponent equilibrium systems in the presence of protic nucleophiles, revealing the potential of the CF2(CO)2 group to act as a multifaceted warhead for reversible covalent drugs. The equilibria compositions of various FDKs in water/octanol contain up to nine species. A simultaneous direct species-specific 19F-NMR-based log P determination of these complex equilibria systems was achieved and revealed in some cases lipophilic to hydrophilic shifts, indicating possible adaptation to different environments. This was also demonstrated in 19F-MAS-NMR-based water-membrane partitioning measurements. An interpretation of the results is suggested by the aid of a DFT study and 19F-DOSY-NMR spectroscopy. In dilute solutions, a model FDK reacted with protected cysteine to form two hemi-thioketal regioisomers, indicating possible flexible regio-reactivity of CF2(CO)2 warheads toward cysteine residues.
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Affiliation(s)
- Ishay Columbus
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Lee Ghindes-Azaria
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ido Michael Herzog
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eliav Blum
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Galit Parvari
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa, Israel
| | - Yoav Eichen
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa, Israel
| | - Yoram Cohen
- School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | - Eytan Gershonov
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eyal Drug
- Department of Analytic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sigal Saphier
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel.
| | - Shlomi Elias
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Boris Smolkin
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Yossi Zafrani
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel.
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9
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Citarella A, Dimasi A, Moi D, Passarella D, Scala A, Piperno A, Micale N. Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives. Biomolecules 2023; 13:1339. [PMID: 37759739 PMCID: PMC10647625 DOI: 10.3390/biom13091339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The main protease (Mpro) plays a pivotal role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is considered a highly conserved viral target. Disruption of the catalytic activity of Mpro produces a detrimental effect on the course of the infection, making this target one of the most attractive for the treatment of COVID-19. The current success of the SARS-CoV-2 Mpro inhibitor Nirmatrelvir, the first oral drug for the treatment of severe forms of COVID-19, has further focused the attention of researchers on this important viral target, making the search for new Mpro inhibitors a thriving and exciting field for the development of antiviral drugs active against SARS-CoV-2 and related coronaviruses.
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Affiliation(s)
- Andrea Citarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Alessandro Dimasi
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Davide Moi
- Department of Chemical and Geological Sciences, University of Cagliari, S.P. 8 CA, 09042 Cagliari, Italy;
| | - Daniele Passarella
- Department of Chemistry, University of Milan, Via Golgi 19, 20133 Milano, Italy; (A.D.); (D.P.)
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres 31, 98166 Messina, Italy; (A.S.); (A.P.)
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10
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Xu J, Li Y, Zhu X, Lv S, Xu Y, Cheng T, Liu G, Liu R. Pyridinium-Masked Enol as a Precursor for Constructing Alpha-Fluoromethyl Ketones. Org Lett 2023; 25:6211-6216. [PMID: 37584477 DOI: 10.1021/acs.orglett.3c02419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
We present herein a pyridinium-masked enol as a versatile platform to produce ketones bearing tri-, di-, and monofluoromethyl in the presence of [Ir(dF(Me)ppy)]2(dtbbpy)]PF6 under blue light (455 nm) irradiation. By simply changing the F-source, α-trifluoromethyl ketones, α-difluoromethyl ketones, and α-monofluoromethyl ketones could be easily prepared in moderate to excellent yields in one step, making it a practical tool for the synthesis of fluorine-containing ketones. In addition, the pyridinium-masked enol could also be extended to the synthesis of sulfonyl ketones. The findings of the present protocol contribute to the arsenal of fluorine chemistry and might have potential applications in the pharmaceutical and agrochemical industries.
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Affiliation(s)
- Jijun Xu
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
| | - Yi Li
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
| | - Xuanyu Zhu
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
| | - Shisong Lv
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
| | - Yiming Xu
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
| | - Tanyu Cheng
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
| | - Guohua Liu
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
| | - Rui Liu
- Joint Laboratory of International Cooperation of Resource Chemistry of Ministry of Education, Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai 201418, China
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11
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Algar‐Lizana S, Bonache MÁ, González‐Muñiz R. SARS-CoV-2 main protease inhibitors: What is moving in the field of peptides and peptidomimetics? J Pept Sci 2022; 29:e3467. [PMID: 36479966 PMCID: PMC9877768 DOI: 10.1002/psc.3467] [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: 10/14/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still affecting people worldwide. Despite the good degree of immunological protection achieved through vaccination, there are still severe cases that require effective antivirals. In this sense, two specific pharmaceutical preparations have been marketed already, the RdRp polymerase inhibitor molnupiravir and the main viral protease inhibitor nirmatrelvir (commercialized as Paxlovid, a combination with ritonavir). Nirmatrelvir is a peptidomimetic acting as orally available, covalent, and reversible inhibitor of SARS-CoV-2 main viral protease. The success of this compound has revitalized the search for new peptide and peptidomimetic protease inhibitors. This highlight collects some selected examples among those recently published in the field of SARS-CoV-2.
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12
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Novel Class of Proteasome Inhibitors: In Silico and In Vitro Evaluation of Diverse Chloro(trifluoromethyl)aziridines. Int J Mol Sci 2022; 23:ijms232012363. [PMID: 36293216 PMCID: PMC9603864 DOI: 10.3390/ijms232012363] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is the major proteolytic system in the cytosol and nucleus of all eukaryotic cells. The role of proteasome inhibitors (PIs) as critical agents for regulating cancer cell death has been established. Aziridine derivatives are well-known alkylating agents employed against cancer. However, to the best of our knowledge, aziridine derivatives showing inhibitory activity towards proteasome have never been described before. Herein we report a new class of selective and nonPIs bearing an aziridine ring as a core structure. In vitro cell-based assays (two leukemia cell lines) also displayed anti-proliferative activity for some compounds. In silico studies indicated non-covalent binding mode and drug-likeness for these derivatives. Taken together, these results are promising for developing more potent PIs.
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13
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Hu F, Wang L, Hu Y, Wang D, Wang W, Jiang J, Li N, Yin P. A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe. Brief Bioinform 2021; 22:bbab301. [PMID: 34368837 PMCID: PMC8385923 DOI: 10.1093/bib/bbab301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/11/2021] [Accepted: 07/15/2021] [Indexed: 01/03/2023] Open
Abstract
The identification of protein-ligand interaction plays a key role in biochemical research and drug discovery. Although deep learning has recently shown great promise in discovering new drugs, there remains a gap between deep learning-based and experimental approaches. Here, we propose a novel framework, named AIMEE, integrating AI model and enzymological experiments, to identify inhibitors against 3CL protease of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2), which has taken a significant toll on people across the globe. From a bioactive chemical library, we have conducted two rounds of experiments and identified six novel inhibitors with a hit rate of 29.41%, and four of them showed an IC50 value <3 μM. Moreover, we explored the interpretability of the central model in AIMEE, mapping the deep learning extracted features to the domain knowledge of chemical properties. Based on this knowledge, a commercially available compound was selected and was proven to be an activity-based probe of 3CLpro. This work highlights the great potential of combining deep learning models and biochemical experiments for intelligent iteration and for expanding the boundaries of drug discovery. The code and data are available at https://github.com/SIAT-code/AIMEE.
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Affiliation(s)
- Fan Hu
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lei Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yishen Hu
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Dongqi Wang
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Weijie Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianbing Jiang
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, 518055, China
| | - Nan Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Peng Yin
- Guangdong-Hong Kong-Macao Joint Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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14
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Li J, Zhu Y, Liu B, Tang F, Zheng X, Huang W. An Atom-Economic Inverse Solid-Phase Peptide Synthesis Using Bn or BcM Esters of Amino Acids. Org Lett 2021; 23:7571-7574. [PMID: 34533312 DOI: 10.1021/acs.orglett.1c02769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An atom-economic N-to-C-directed solid-phase peptide synthesis is reported that uses benzyl (Bn) or (benzhydryl-carbamoyl)-methyl (BcM) esters of amino acids as the building blocks, which facilitate efficient hydrazinolysis, convenient conversion to acyl azide, and robust amidation with the next amino acid ester. This method is free of coupling reagents and free of protection on the side-chain OH, CO2H, CONH2, etc., therefore exhibiting a significantly improved atom economy compared to those of BOC- or Fmoc-based C-to-N-directed approaches.
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Affiliation(s)
- Jian Li
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 310024, China.,CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yue Zhu
- CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,Group of Lead Compound, Department of Pharmacy, Hengyang Medicinal School, University of South China, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang, Hunan 421001, China
| | - Bo Liu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 310024, China.,CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Feng Tang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 310024, China.,CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xing Zheng
- Group of Lead Compound, Department of Pharmacy, Hengyang Medicinal School, University of South China, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang, Hunan 421001, China
| | - Wei Huang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, Hangzhou 310024, China.,CAS Key Laboratory of Receptor Research, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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15
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Joshi D, Milligan JC, Zeisner TU, O'Reilly N, Diffley JFX, Papageorgiou G. An improved method for the incorporation of fluoromethyl ketones into solid phase peptide synthesis techniques. RSC Adv 2021; 11:20457-20464. [PMID: 34178310 PMCID: PMC8185805 DOI: 10.1039/d1ra03046a] [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] [Indexed: 11/21/2022] Open
Abstract
An improved and expedient technique for the synthesis of peptidyl-fluoromethyl ketones is described. The methodology is based on prior coupling of an aspartate fluoromethyl ketone to a linker and mounting it onto resin-bound methylbenzhydrylamine hydrochloride. Subsequently, by utilising standard Fmoc peptide procedures, a number of short Z-protected peptides were synthesised and assessed as possible inhibitors of the main protease from SARS-CoV-2 (3CLpro). An improved and expedient technique for the synthesis of peptidyl-fluoromethyl ketones is described.![]()
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Affiliation(s)
- Dhira Joshi
- Peptide Chemistry STP, The Francis Crick Institute 1 Midland Road London NW1 1AT UK +44 (0)203 796 2359
| | - Jennifer C Milligan
- Chromosome Replication Laboratory, The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Theresa U Zeisner
- Cell Cycle Laboratory, The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - Nicola O'Reilly
- Peptide Chemistry STP, The Francis Crick Institute 1 Midland Road London NW1 1AT UK +44 (0)203 796 2359
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute 1 Midland Road London NW1 1AT UK
| | - George Papageorgiou
- Peptide Chemistry STP, The Francis Crick Institute 1 Midland Road London NW1 1AT UK +44 (0)203 796 2359
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16
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Citarella A, Scala A, Piperno A, Micale N. SARS-CoV-2 M pro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors. Biomolecules 2021; 11:607. [PMID: 33921886 PMCID: PMC8073203 DOI: 10.3390/biom11040607] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
The uncontrolled spread of the COVID-19 pandemic caused by the new coronavirus SARS-CoV-2 during 2020-2021 is one of the most devastating events in the history, with remarkable impacts on the health, economic systems, and habits of the entire world population. While some effective vaccines are nowadays approved and extensively administered, the long-term efficacy and safety of this line of intervention is constantly under debate as coronaviruses rapidly mutate and several SARS-CoV-2 variants have been already identified worldwide. Then, the WHO's main recommendations to prevent severe clinical complications by COVID-19 are still essentially based on social distancing and limitation of human interactions, therefore the identification of new target-based drugs became a priority. Several strategies have been proposed to counteract such viral infection, including the repurposing of FDA already approved for the treatment of HIV, HCV, and EBOLA, inter alia. Among the evaluated compounds, inhibitors of the main protease of the coronavirus (Mpro) are becoming more and more promising candidates. Mpro holds a pivotal role during the onset of the infection and its function is intimately related with the beginning of viral replication. The interruption of its catalytic activity could represent a relevant strategy for the development of anti-coronavirus drugs. SARS-CoV-2 Mpro is a peculiar cysteine protease of the coronavirus family, responsible for the replication and infectivity of the parasite. This review offers a detailed analysis of the repurposed drugs and the newly synthesized molecules developed to date for the treatment of COVID-19 which share the common feature of targeting SARS-CoV-2 Mpro, as well as a brief overview of the main enzymatic and cell-based assays to efficaciously screen such compounds.
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Affiliation(s)
| | | | | | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy; (A.C.); (A.S.); (A.P.)
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17
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Pseudo-Dipeptide Bearing α,α-Difluoromethyl Ketone Moiety as Electrophilic Warhead with Activity against Coronaviruses. Int J Mol Sci 2021; 22:ijms22031398. [PMID: 33573283 PMCID: PMC7866854 DOI: 10.3390/ijms22031398] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/26/2021] [Indexed: 12/18/2022] Open
Abstract
The synthesis of α-fluorinated methyl ketones has always been challenging. New methods based on the homologation chemistry via nucleophilic halocarbenoid transfer, carried out recently in our labs, allowed us to design and synthesize a target-directed dipeptidyl α,α-difluoromethyl ketone (DFMK) 8 as a potential antiviral agent with activity against human coronaviruses. The ability of the newly synthesized compound to inhibit viral replication was evaluated by a viral cytopathic effect (CPE)-based assay performed on MCR5 cells infected with one of the four human coronaviruses associated with respiratory distress, i.e., hCoV-229E, showing antiproliferative activity in the micromolar range (EC50 = 12.9 ± 1.22 µM), with a very low cytotoxicity profile (CC50 = 170 ± 3.79 µM, 307 ± 11.63 µM, and 174 ± 7.6 µM for A549, human embryonic lung fibroblasts (HELFs), and MRC5 cells, respectively). Docking and molecular dynamics simulations studies indicated that 8 efficaciously binds to the intended target hCoV-229E main protease (Mpro). Moreover, due to the high similarity between hCoV-229E Mpro and SARS-CoV-2 Mpro, we also performed the in silico analysis towards the second target, which showed results comparable to those obtained for hCoV-229E Mpro and promising in terms of energy of binding and docking pose.
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18
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Current Synthetic Routes to Peptidyl Mono-Fluoromethyl Ketones (FMKs) and Their Applications. Molecules 2020; 25:molecules25235601. [PMID: 33260551 PMCID: PMC7730879 DOI: 10.3390/molecules25235601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 11/17/2022] Open
Abstract
Peptidyl mono-fluoromethyl ketones (FMKs) are a class of biologically active molecules that show potential as both protease inhibitors for the treatment of a range of diseases and as chemical probes for the interrogation of cellular processes. This review describes the current solid- and solution-phase routes employed for the synthesis of peptidyl mono-FMKs. In addition, it provides a brief overview of some of the key applications of FMKs in the fields of chemical biology and medicinal chemistry.
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