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Nemčovičová I, Lopušná K, Štibrániová I, Benedetti F, Berti F, Felluga F, Drioli S, Vidali M, Katrlík J, Pažitná L, Holazová A, Blahutová J, Lenhartová S, Sláviková M, Klempa B, Ondrejovič M, Chmelová D, Legerská B, Miertuš S, Klacsová M, Uhríková D, Kerti L, Frecer V. Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis. J Enzyme Inhib Med Chem 2024; 39:2301772. [PMID: 38221792 PMCID: PMC10791089 DOI: 10.1080/14756366.2024.2301772] [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: 07/29/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024] Open
Abstract
The viral genome of the SARS-CoV-2 coronavirus, the aetiologic agent of COVID-19, encodes structural, non-structural, and accessory proteins. Most of these components undergo rapid genetic variations, though to a lesser extent the essential viral proteases. Consequently, the protease and/or deubiquitinase activities of the cysteine proteases Mpro and PLpro became attractive targets for the design of antiviral agents. Here, we develop and evaluate new bis(benzylidene)cyclohexanones (BBC) and identify potential antiviral compounds. Three compounds were found to be effective in reducing the SARS-CoV-2 load, with EC50 values in the low micromolar concentration range. However, these compounds also exhibited inhibitory activity IC50 against PLpro at approximately 10-fold higher micromolar concentrations. Although originally developed as PLpro inhibitors, the comparison between IC50 and EC50 of BBC indicates that the mechanism of their in vitro antiviral activity is probably not directly related to inhibition of viral cysteine proteases. In conclusion, our study has identified new potential noncytotoxic antiviral compounds suitable for in vivo testing and further improvement.
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Affiliation(s)
- Ivana Nemčovičová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Katarína Lopušná
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Iveta Štibrániová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Fabio Benedetti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Federico Berti
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Fulvia Felluga
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Sara Drioli
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Mattia Vidali
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Alena Holazová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jana Blahutová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Simona Lenhartová
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Monika Sláviková
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miroslav Ondrejovič
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Daniela Chmelová
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Barbora Legerská
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Stanislav Miertuš
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
- ICARST n.o, Bratislava, Slovakia
| | - Mária Klacsová
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Daniela Uhríková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Lukáš Kerti
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
| | - Vladimír Frecer
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Bratislava, Slovakia
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2
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Ibrahim PEGF, Zuccotto F, Zachariae U, Gilbert I, Bodkin M. Accurate prediction of dynamic protein-ligand binding using P-score ranking. J Comput Chem 2024; 45:1762-1778. [PMID: 38647338 DOI: 10.1002/jcc.27370] [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: 10/20/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
Abstract
Protein-ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein-ligand system, solvent-mediated interactions, and associated entropy changes. In addition, scoring functions are only weakly accurate due to the short time required for calculating enthalpic and entropic binding interactions. The workflow described here attempts to address these limitations by combining supervised molecular dynamics with dynamical averaging quantum mechanics fragment molecular orbital. This combination significantly increased the ability to predict the experimental binding structure of protein-ligand complexes independent from the starting position of the ligands or the binding site conformation. We found that the predictive power could be enhanced by combining the residence time and interaction energies as descriptors in a novel scoring function named the P-score. This is illustrated using six different protein-ligand targets as case studies.
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Affiliation(s)
- Peter E G F Ibrahim
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Fabio Zuccotto
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Ulrich Zachariae
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Ian Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
| | - Mike Bodkin
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee, UK
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3
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Zhang W, Xiao L, Li D, Hu Y, Yu W. New Strategies for Responding to SARS-CoV-2: The Present and Future of Dual-Target Drugs. J Med Chem 2024. [PMID: 38967785 DOI: 10.1021/acs.jmedchem.4c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
The 2019 coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of deaths, posing a serious threat to public health and safety. Rapid mutations of SARS-CoV-2 and complex interactions among multiple targets during infection pose a risk of expiry for small molecule inhibitors. This suggests that the traditional concept of "one bug, one drug" could be ineffective in dealing with the coronavirus. The dual-target drug strategy is expected to be the key to ending coronavirus infections. However, the lack of design method and improper combination of dual-targets poses obstacle to the discovery of new dual-target drugs. In this Perspective, we summarized the profiles concerning drug design methods, structure-activity relationships, and pharmacological parameters of dual-target drugs for the treatment of COVID-19. Importantly, we underscored how target combination and rational drug design illuminate the development of dual-target drugs for SARS-CoV-2.
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Affiliation(s)
- Wenyi Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Lecheng Xiao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Hu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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4
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Hamed A, Abdel-Razek AS, Abdelwahab AB, El Taweel A, GabAllah M, Sewald N, Shaaban M. Diverse bioactive secondary metabolites from Aspergillus terreus: antimicrobial, anticancer, and anti-SARS-CoV-2 activity studies. Z NATURFORSCH C 2024; 0:znc-2024-0083. [PMID: 38916050 DOI: 10.1515/znc-2024-0083] [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: 04/09/2024] [Accepted: 06/09/2024] [Indexed: 06/26/2024]
Abstract
Owing to its high interest as prolific source of diverse bioactive compounds referred in our previous research work, we have scaled-up the fermentation of the marine Aspergillus terreus LGO13 on a liquid culture medium to isolate and identify the very minor/further promising bioactive secondary metabolites and to study their antibacterial, cytotoxic, and antiviral properties. Twenty-three known bioactive metabolites, including the recently discovered microbial natural product N-benzoyl-tryptophan (1), were obtained herein. Their structures were determined using HR-ESI-MS 1D/2D NMR spectroscopy and data from the literature. The biological properties of the microbial extract and the resulting compounds were examined using a set of microorganisms, cervix carcinoma KB-3-1, nonsmall cell lung cancer (NSCLC) A549, and coronavirus (SARS-CoV-2), respectively. Molecular docking (MD) simulations were used to investigate the potential targets of the separated metabolites as anti-SARS-CoV-2 drugs. According to the current study, a viral protein that may be the target of anticovid drugs is a papain-like protease (PLpro), and chaetominine (2) appears to be a viable choice against this protein. We evaluated the antiviral efficacy of chaetominine (2), fumitremorgin C (6), and azaspirofuran A (9) against SARS-CoV-2 based on MD data. Chaetominine (2) and azaspirofuran A (9) displayed intermediate selectivity indices (SI = 6.6 and 3.2, respectively), while fumitremorgin C (6) displayed a high selectivity index (SI = 19.77). These findings show that fumitremorgin C has promising antiviral action against SARS-CoV-2.
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Affiliation(s)
- Abdelaaty Hamed
- Chemistry Department, Faculty of Science, Al-Azhar University, Nasr City-Cairo 11884, Egypt
| | - Ahmed S Abdel-Razek
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Institute of Genetic Engineering and Biotechnology Research, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
| | - Ahmed B Abdelwahab
- Temisis Therapeutics, 19 avenue de la Forêt de Haye, 54500 Vandœuvre-lès-Nancy, France
| | - Ahmed El Taweel
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt
| | - Mohamed GabAllah
- Center of Scientific Excellence for Influenza Virus, Environmental Research Division, National Research Centre, Giza 12622, Egypt
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Institute of Genetic Engineering and Biotechnology Research, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
| | - Mohamed Shaaban
- Organic and Bioorganic Chemistry, Faculty of Chemistry, Bielefeld University, D-33501 Bielefeld, Germany
- Microbial Chemistry Department, Institute of Genetic Engineering and Biotechnology Research, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, El-Buhouth St. 33, Dokki-Cairo 12622, Egypt
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5
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Patel DK, Kumar H, Sobhia ME. Exploring the binding dynamics of covalent inhibitors within active site of PL pro in SARS-CoV-2. Comput Biol Chem 2024; 112:108132. [PMID: 38959551 DOI: 10.1016/j.compbiolchem.2024.108132] [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: 02/27/2024] [Revised: 06/03/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
In the global fight against the COVID-19 pandemic caused by the highly transmissible SARS-CoV-2 virus, the search for potent medications is paramount. With a focused investigation on the SARS-CoV-2 papain-like protease (PLpro) as a promising therapeutic target due to its pivotal role in viral replication and immune modulation, the catalytic triad of PLpro comprising Cys111, His272, and Asp286, highlights Cys111 as an intriguing nucleophilic center for potential covalent bonds with ligands. The detailed analysis of the binding site unveils crucial interactions with both hydrophobic and polar residues, demonstrating the structural insights of the cavity and deepening our understanding of its molecular landscape. The sequence of PLpro among variants of concern (Alpha, Beta, Gamma, Delta and Omicron) and the recent variant of interest, JN.1, remains conserved with no mutations at the active site. Moreover, a thorough exploration of apo, non-covalently bound, and covalently bound PLpro conformations exposes significant conformational changes in loop regions, offering invaluable insights into the intricate dynamics of ligand-protein complex formation. Employing strategic in silico medication repurposing, this study swiftly identifies potential molecules for target inhibition. Within the domain of covalent docking studies and molecular dynamics, using reported inhibitors and clinically tested molecules elucidate the formation of stable covalent bonds with the cysteine residue, laying a robust foundation for potential therapeutic applications. These details not only deepen our comprehension of PLpro inhibition but also play a pivotal role in shaping the dynamic landscape of COVID-19 treatment strategies.
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Affiliation(s)
- Deepesh Kumar Patel
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Mohali, Punjab 160062, India.
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6
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Zhu Y, Meng J, Feng B, Zhao Y, Zang Y, Lu L, Su M, Yang Q, Zhang Q, Feng L, Zhao J, Shao M, Ma Y, Yang X, Yang H, Li J, Jiang X, Rao Z. De novo design of SARS-CoV-2 main protease inhibitors with characteristic binding modes. Structure 2024:S0969-2126(24)00217-X. [PMID: 38925121 DOI: 10.1016/j.str.2024.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/09/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which spreads rapidly all over the world. The main protease (Mpro) is significant to the replication and transcription of viruses, making it an attractive drug target against coronaviruses. Here, we introduce a series of novel inhibitors which are designed de novo through structure-based drug design approach that have great potential to inhibit SARS-CoV-2 Mproin vitro. High-resolution structures show that these inhibitors form covalent bonds with the catalytic cysteine through the novel dibromomethyl ketone (DBMK) as a reactive warhead. At the same time, the designed phenyl group beside the DBMK warhead inserts into the cleft between H41 and C145 through π-π stacking interaction, splitting the catalytic dyad and disrupting proton transfer. This unique binding model provides novel clues for the cysteine protease inhibitor development of SARS-CoV-2 as well as other pathogens.
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Affiliation(s)
- Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Jiaolong Meng
- State Key Laboratory of Molecular & Process Engineering, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Bo Feng
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yao Zhao
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China.
| | - Yi Zang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Lingang Laboratory, Shanghai 200031, China
| | - Lingling Lu
- State Key Laboratory of Molecular & Process Engineering, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Mingbo Su
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qi Yang
- Guangzhou National Laboratory, Guangzhou, Guangdong 510005, China
| | - Qi Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lu Feng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, Nankai University, and Tianjin Key Laboratory of Protein Sciences, Tianjin 300071, China
| | - Jinyi Zhao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Maolin Shao
- Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100091, China
| | - Yuanyuan Ma
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jia Li
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China.
| | - Xuefeng Jiang
- State Key Laboratory of Molecular & Process Engineering, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Response, College of Life Sciences, Nankai University, and Tianjin Key Laboratory of Protein Sciences, Tianjin 300071, China; Laboratory of Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100091, China.
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7
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van Vliet VJE, De Silva A, Mark BL, Kikkert M. Viral deubiquitinating proteases and the promising strategies of their inhibition. Virus Res 2024; 344:199368. [PMID: 38588924 PMCID: PMC11025011 DOI: 10.1016/j.virusres.2024.199368] [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: 11/30/2023] [Revised: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Several viruses are now known to code for deubiquitinating proteases in their genomes. Ubiquitination is an essential post-translational modification of cellular substrates involved in many processes in the cell, including in innate immune signalling. This post-translational modification is regulated by the ubiquitin conjugation machinery, as well as various host deubiquitinating enzymes. The conjugation of ubiquitin chains to several innate immune related factors is often needed to induce downstream signalling, shaping the antiviral response. Viral deubiquitinating proteins, besides often having a primary function in the viral replication cycle by cleaving the viral polyprotein, are also able to cleave ubiquitin chains from such host substrates, in that way exerting a function in innate immune evasion. The presence of viral deubiquitinating enzymes has been firmly established for numerous animal-infecting viruses, such as some well-researched and clinically important nidoviruses, and their presence has now been confirmed in several plant viruses as well. Viral proteases in general have long been highlighted as promising drug targets, with a current focus on small molecule inhibitors. In this review, we will discuss the range of viral deubiquitinating proteases known to date, summarise the various avenues explored to inhibit such proteases and discuss novel strategies and models intended to inhibit and study these specific viral enzymes.
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Affiliation(s)
- Vera J E van Vliet
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands; The Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Anuradha De Silva
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, South Holland, the Netherlands.
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8
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Hou M, Hou W, Qin M, Wang Q, Zhou L. Photo-sensitive peptide inducing targeted cross-linking in a one-step and reagent-, enzyme- and antibody-free detection of SARS-Cov-2 marker protein. Bioelectrochemistry 2024; 157:108672. [PMID: 38428185 DOI: 10.1016/j.bioelechem.2024.108672] [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: 05/18/2023] [Revised: 02/17/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Modern biosensing technology plays a crucial role in combating the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). However, the associated assays remain costly, considering their extensive daily use. In response, we developed a simplified one-step SARS-CoV-2 protease assay that reduces both time and financial expenses. This approach eliminates the need for extra reagents, enzymes, or antibodies. The simplification involves a photo-sensitive Bengal red-tagged substrate peptide, allowing specific cross-linking upon protease-substrate recognition. This process forms a di-tyrosine product with a distinctive fluorescence signal readout, enabling the detection of SARS-CoV-2 in patient serum samples. This method anticipates a major reduction in assay costs in the near future.
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Affiliation(s)
- Meihui Hou
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan Xinzhuang, Jinan 250022, China
| | - Wenmin Hou
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan Xinzhuang, Jinan 250022, China
| | - Mingyu Qin
- Medical College, Soochow University, 333 East Road of Ganjiang, Suzhou 215026, China
| | - Qun Wang
- Yuhuangding Hospital, 20 East Road of Yuhuangding, Yantai 264000, China
| | - Lei Zhou
- School of Biological Science and Technology, University of Jinan, 336 West Road of Nan Xinzhuang, Jinan 250022, China.
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9
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Ho WY, Shen ZH, Chen Y, Chen TH, Lu X, Fu YS. Therapeutic implications of quercetin and its derived-products in COVID-19 protection and prophylactic. Heliyon 2024; 10:e30080. [PMID: 38765079 PMCID: PMC11098804 DOI: 10.1016/j.heliyon.2024.e30080] [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: 12/01/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, which has triggered a global pandemic of the coronavirus infectious disease 2019 (COVID-19). Outbreaks of emerging infectious diseases continue to challenge human health worldwide. The virus conquers human cells through the angiotensin-converting enzyme 2 receptor-driven pathway by mostly targeting the human respiratory tract. Quercetin is a natural flavonoid widely represented in the plant kingdom. Cumulative evidence has demonstrated that quercetin and its derivatives have various pharmacological properties including anti-cancer, anti-hypertension, anti-hyperlipidemia, anti-hyperglycemia, anti-microbial, antiviral, neuroprotective, and cardio-protective effects, because it is a potential treatment for severe inflammation and acute respiratory distress syndrome. Furthermore, it is the main life-threatening condition in patients with COVID-19. This article provides a comprehensive review of the primary literature on the predictable effectiveness of quercetin and its derivatives docked to multi-target of SARS-CoV-2 and host cells via in silico and some of validation through in vitro, in vivo, and clinically to fight SARS-CoV-2 infections, contribute to the reduction of inflammation, which suggests the preventive and therapeutic latency of quercetin and its derived-products against COVID-19 pandemic, multisystem inflammatory syndromes (MIS), and long-COVID.
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Affiliation(s)
- Wan-Yi Ho
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Zi-Han Shen
- Department of Clinical Medicine, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yijing Chen
- Department of Dentisty, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Ting-Hsu Chen
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - XiaoLin Lu
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yaw-Syan Fu
- Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
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10
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Wang X, Zhu Y, Zhao Q, Lu W, Xu Y, Hu H, Lu X. Chemical Space Profiling of SARS-CoV-2 PL pro Using DNA-Encoded Focused Libraries. ACS Med Chem Lett 2024; 15:555-564. [PMID: 38628804 PMCID: PMC11017295 DOI: 10.1021/acsmedchemlett.4c00069] [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: 02/07/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-encoded library (DEL) technology is gaining attention for its rapid construction and deconvolution capabilities. Our study explored a novel strategy using rational DELs tailored for the SARS-CoV-2 papain-like protease, which revealed new fragments. Structural changes post-DEL screening mimic traditional medicinal chemistry lead optimization. We unveiled unique aromatic structures offering an alternative optimization path. Notably, we identified superior binding fragments targeting the BL2 groove. Derivative 16 emerged as the most promising by exhibiting IC50 values of 0.25 μM. Derivative 6, which features an aromatic fragment capped with a naphthalene moiety, showed IC50 values of 2.91 μM. Molecular modeling revealed hydrogen bond interactions with Lys157 residue and potential covalent interactions with nearby amino acid residues. This research underscored DEL's potential for fragment-based drug discovery against SARS-CoV-2 protease.
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Affiliation(s)
- Xudong Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ying Zhu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Qingyi Zhao
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Weiwei Lu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Yechun Xu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
| | - Hangchen Hu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced
Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| | - Xiaojie Lu
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
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11
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Tan B, Zhang X, Ansari A, Jadhav P, Tan H, Li K, Chopra A, Ford A, Chi X, Ruiz FX, Arnold E, Deng X, Wang J. Design of a SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. Science 2024; 383:1434-1440. [PMID: 38547259 DOI: 10.1126/science.adm9724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. We designed and synthesized 85 noncovalent PLpro inhibitors that bind to a recently discovered ubiquitin binding site and the known BL2 groove pocket near the S4 subsite. Leads inhibited PLpro with the inhibitory constant Ki values from 13.2 to 88.2 nanomolar. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 micromolar. Oral treatment with Jun12682 improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting that PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.
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Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ahmadullah Ansari
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexandra Ford
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Xiang Chi
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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12
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Valdés-Albuernes JL, Díaz-Pico E, Alfaro S, Caballero J. Modeling of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2024; 11:1374364. [PMID: 38601323 PMCID: PMC11004324 DOI: 10.3389/fmolb.2024.1374364] [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: 01/22/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
The papain-like protease (PLpro) found in coronaviruses that can be transmitted from animals to humans is a critical target in respiratory diseases linked to Severe Acute Respiratory Syndrome (SARS-CoV). Researchers have proposed designing PLpro inhibitors. In this study, a set of 89 compounds, including recently reported 2-phenylthiophenes with nanomolar inhibitory potency, were investigated as PLpro noncovalent inhibitors using advanced molecular modeling techniques. To develop the work with these inhibitors, multiple structures of the SARS-CoV-2 PLpro binding site were generated using a molecular sampling method. These structures were then clustered to select a group that represents the flexibility of the site. Subsequently, models of the protein-ligand complexes were created for the set of inhibitors within the chosen conformations. The quality of the complex models was assessed using LigRMSD software to verify similarities in the orientations of the congeneric series and interaction fingerprints to determine the recurrence of chemical interactions. With the multiple models constructed, a protocol was established to choose one per ligand, optimizing the correlation between the calculated docking energy values and the biological activities while incorporating the effect of the binding site's flexibility. A strong correlation (R2 = 0.922) was found when employing this flexible docking protocol.
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Affiliation(s)
| | | | | | - Julio Caballero
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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13
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Saquib Q, Bakheit AH, Ahmed S, Ansari SM, Al-Salem AM, Al-Khedhairy AA. Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CL Pro and PL Pro) by Molecular Docking and Dynamic Simulation Studies. Molecules 2024; 29:998. [PMID: 38474509 DOI: 10.3390/molecules29050998] [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: 10/13/2023] [Revised: 02/04/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
We provide promising computational (in silico) data on phytochemicals (compounds 1-10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1-10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1-10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests.
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Affiliation(s)
- Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sarfaraz Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sabiha M Ansari
- Botany & Microbiology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah M Al-Salem
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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14
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Chan HTH, Brewitz L, Lukacik P, Strain-Damerell C, Walsh MA, Schofield CJ, Duarte F. Studies on the selectivity of the SARS-CoV-2 papain-like protease reveal the importance of the P2' proline of the viral polyprotein. RSC Chem Biol 2024; 5:117-130. [PMID: 38333195 PMCID: PMC10849127 DOI: 10.1039/d3cb00128h] [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: 07/13/2023] [Accepted: 10/13/2023] [Indexed: 02/10/2024] Open
Abstract
The SARS-CoV-2 papain-like protease (PLpro) is an antiviral drug target that catalyzes the hydrolysis of the viral polyproteins pp1a/1ab, so releasing the non-structural proteins (nsps) 1-3 that are essential for the coronavirus lifecycle. The LXGG↓X motif in pp1a/1ab is crucial for recognition and cleavage by PLpro. We describe molecular dynamics, docking, and quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how oligopeptide substrates derived from the viral polyprotein bind to PLpro. The results reveal how the substrate sequence affects the efficiency of PLpro-catalyzed hydrolysis. In particular, a proline at the P2' position promotes catalysis, as validated by residue substitutions and mass spectrometry-based analyses. Analysis of PLpro catalyzed hydrolysis of LXGG motif-containing oligopeptides derived from human proteins suggests that factors beyond the LXGG motif and the presence of a proline residue at P2' contribute to catalytic efficiency, possibly reflecting the promiscuity of PLpro. The results will help in identifying PLpro substrates and guiding inhibitor design.
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Affiliation(s)
- H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0DE UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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15
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Quagliata M, Papini AM, Rovero P. Chemically modified antiviral peptides against SARS-CoV-2. J Pept Sci 2024; 30:e3541. [PMID: 37699615 DOI: 10.1002/psc.3541] [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: 07/03/2023] [Revised: 07/31/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023]
Abstract
To date, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) COVID-19 pandemic continues to be a potentially lethal disease. Although both vaccines and specific antiviral drugs have been approved, the search for more specific therapeutic approaches is still ongoing. The infection mechanism of SARS-CoV-2 consists of several stages, and each one can be selectively blocked to disrupt viral infection. Peptides are a promising class of antiviral compounds, which may be suitably modified to be more stable, more effective, and more selective towards a specific viral replication step. The latter two goals might be obtained by increasing the specificity and/or the affinity of the interaction with a specific target and often imply the stabilization of the secondary structure of the active peptide. This review is focused on modified antiviral peptides against SARS-CoV-2 acting at different stages of virus replication, including ACE2-RBD interaction, membrane fusion mechanism, and the proteolytic cleavage by different viral proteases. Therefore, the landscape presented herein provides a useful springboard for the design of new and powerful antiviral therapeutics.
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Affiliation(s)
- Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Italy
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16
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Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
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Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
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17
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Kralj S, Jukič M, Bahun M, Kranjc L, Kolarič A, Hodošček M, Ulrih NP, Bren U. Identification of Triazolopyrimidinyl Scaffold SARS-CoV-2 Papain-Like Protease (PL pro) Inhibitor. Pharmaceutics 2024; 16:169. [PMID: 38399230 PMCID: PMC10893172 DOI: 10.3390/pharmaceutics16020169] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
The global impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its companion disease, COVID-19, has reminded us of the importance of basic coronaviral research. In this study, a comprehensive approach using molecular docking, in vitro assays, and molecular dynamics simulations was applied to identify potential inhibitors for SARS-CoV-2 papain-like protease (PLpro), a key and underexplored viral enzyme target. A focused protease inhibitor library was initially created and molecular docking was performed using CmDock software (v0.2.0), resulting in the selection of hit compounds for in vitro testing on the isolated enzyme. Among them, compound 372 exhibited promising inhibitory properties against PLpro, with an IC50 value of 82 ± 34 μM. The compound also displayed a new triazolopyrimidinyl scaffold not yet represented within protease inhibitors. Molecular dynamics simulations demonstrated the favorable binding properties of compound 372. Structural analysis highlighted its key interactions with PLpro, and we stress its potential for further optimization. Moreover, besides compound 372 as a candidate for PLpro inhibitor development, this study elaborates on the PLpro binding site dynamics and provides a valuable contribution for further efforts in pan-coronaviral PLpro inhibitor development.
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Affiliation(s)
- Sebastjan Kralj
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Marko Jukič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
| | - Miha Bahun
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Luka Kranjc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
- National Institute of Biology, Večna Pot 111, SI-1000 Ljubljana, Slovenia
| | - Anja Kolarič
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
| | - Milan Hodošček
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška Ulica 8, SI-6000 Koper, Slovenia
- Institute of Enviormental Protection and Sensors, Beloruska Ulica 7, SI-2000 Maribor, Slovenia
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18
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Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [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: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
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Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
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19
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Jadhav P, Huang B, Osipiuk J, Zhang X, Tan H, Tesar C, Endres M, Jedrzejczak R, Tan B, Deng X, Joachimiak A, Cai J, Wang J. Structure-based design of SARS-CoV-2 papain-like protease inhibitors. Eur J Med Chem 2024; 264:116011. [PMID: 38065031 PMCID: PMC11194760 DOI: 10.1016/j.ejmech.2023.116011] [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: 11/01/2023] [Revised: 11/21/2023] [Accepted: 11/25/2023] [Indexed: 12/30/2023]
Abstract
The COVID-19 pandemic is caused by SARS-CoV-2, an RNA virus with high transmissibility and mutation rate. Given the paucity of orally bioavailable antiviral drugs to combat SARS-CoV-2 infection, there is a critical need for additional antivirals with alternative mechanisms of action. Papain-like protease (PLpro) is one of the two SARS-CoV-2 encoded viral cysteine proteases essential for viral replication. PLpro cleaves at three sites of the viral polyproteins. In addition, PLpro antagonizes the host immune response upon viral infection by cleaving ISG15 and ubiquitin from host proteins. Therefore, PLpro is a validated antiviral drug target. In this study, we report the X-ray crystal structures of papain-like protease (PLpro) with two potent inhibitors, Jun9722 and Jun9843. Subsequently, we designed and synthesized several series of analogs to explore the structure-activity relationship, which led to the discovery of PLpro inhibitors with potent enzymatic inhibitory activity and antiviral activity against SARS-CoV-2. Together, the lead compounds are promising drug candidates for further development.
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Affiliation(s)
- Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Bo Huang
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Jerzy Osipiuk
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Christine Tesar
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA; Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - Michael Endres
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA; Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - Robert Jedrzejczak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA; Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA
| | - Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA; Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA; Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, 60667, USA; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60367, USA.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA.
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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20
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Li X, Song Y. Targeting SARS-CoV-2 nonstructural protein 3: Function, structure, inhibition, and perspective in drug discovery. Drug Discov Today 2024; 29:103832. [PMID: 37977285 PMCID: PMC10872262 DOI: 10.1016/j.drudis.2023.103832] [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: 09/22/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
As a highly contagious human pathogen, severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) has infected billions of people worldwide with more than 6 million deaths. With several effective vaccines and antiviral drugs now available, the SARS-CoV-2 pandemic been brought under control. However, a new pathogenic coronavirus could emerge in the future, given the zoonotic nature of this virus. Natural evolution and drug-induced mutations of SARS-CoV-2 also require continued efforts for new anti-coronavirus drugs. Nonstructural protein (nsp) 3 of CoVs is a large, multifunctional protein, containing a papain-like protease (PLpro) and a macrodomain (Mac1), which are essential for viral replication. Here, we provide a comprehensive review of the function, structure, and inhibition of SARS-CoV/-CoV-2 PLpro and Mac1. We also discuss advances in, and challenges to, the discovery of drugs against these targets.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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21
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Tan B, Zhang X, Ansari A, Jadhav P, Tan H, Li K, Chopra A, Ford A, Chi X, Ruiz FX, Arnold E, Deng X, Wang J. Design of SARS-CoV-2 papain-like protease inhibitor with antiviral efficacy in a mouse model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569653. [PMID: 38076941 PMCID: PMC10705561 DOI: 10.1101/2023.12.01.569653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
The emergence of SARS-CoV-2 variants and drug-resistant mutants calls for additional oral antivirals. The SARS-CoV-2 papain-like protease (PLpro) is a promising but challenging drug target. In this study, we designed and synthesized 85 noncovalent PLpro inhibitors that bind to the newly discovered Val70Ub site and the known BL2 groove pocket. Potent compounds inhibited PLpro with inhibitory constant Ki values from 13.2 to 88.2 nM. The co-crystal structures of PLpro with eight leads revealed their interaction modes. The in vivo lead Jun12682 inhibited SARS-CoV-2 and its variants, including nirmatrelvir-resistant strains with EC50 from 0.44 to 2.02 μM. Oral treatment with Jun12682 significantly improved survival and reduced lung viral loads and lesions in a SARS-CoV-2 infection mouse model, suggesting PLpro inhibitors are promising oral SARS-CoV-2 antiviral candidates.
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Affiliation(s)
- Bin Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xiaoming Zhang
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Ahmadullah Ansari
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Prakash Jadhav
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Ashima Chopra
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Alexandra Ford
- Deprtment of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiang Chi
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Xufang Deng
- Department Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
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22
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Wallace I, Baek K, Prabu JR, Vollrath R, von Gronau S, Schulman BA, Swatek KN. Insights into the ISG15 transfer cascade by the UBE1L activating enzyme. Nat Commun 2023; 14:7970. [PMID: 38042859 PMCID: PMC10693564 DOI: 10.1038/s41467-023-43711-3] [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] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
The attachment of the ubiquitin-like protein ISG15 to substrates by specific E1-E2-E3 enzymes is a well-established signalling mechanism of the innate immune response. Here, we present a 3.45 Å cryo-EM structure of a chemically trapped UBE1L-UBE2L6 complex bound to activated ISG15. This structure reveals the details of the first steps of ISG15 recognition and UBE2L6 recruitment by UBE1L (also known as UBA7). Taking advantage of viral effector proteins from severe acute respiratory coronavirus 2 (SARS-CoV-2) and influenza B virus (IBV), we validate the structure and confirm the importance of the ISG15 C-terminal ubiquitin-like domain in the adenylation reaction. Moreover, biochemical characterization of the UBE1L-ISG15 and UBE1L-UBE2L6 interactions enables the design of ISG15 and UBE2L6 mutants with altered selectively for the ISG15 and ubiquitin conjugation pathways. Together, our study helps to define the molecular basis of these interactions and the specificity determinants that ensure the fidelity of ISG15 signalling during the antiviral response.
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Affiliation(s)
- Iona Wallace
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Ronnald Vollrath
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Kirby N Swatek
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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23
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Yang M, Mariano J, Su R, Smith CE, Das S, Gill C, Andresson T, Loncarek J, Tsai YC, Weissman AM. SARS-CoV-2 papain-like protease plays multiple roles in regulating cellular proteins in the endoplasmic reticulum. J Biol Chem 2023; 299:105346. [PMID: 37838170 PMCID: PMC10692909 DOI: 10.1016/j.jbc.2023.105346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023] Open
Abstract
Nsp3s are the largest nonstructural proteins of coronaviruses. These transmembrane proteins include papain-like proteases (PLpro) that play essential roles in cleaving viral polyproteins into their mature units. The PLpro of SARS-CoV viruses also have deubiquitinating and deISGylating activities. As Nsp3 is an endoplasmic reticulum (ER)-localized protein, we asked if the deubiquitinating activity of SARS-CoV-2 PLpro affects proteins that are substrates for ER-associated degradation (ERAD). Using full-length Nsp3 as well as a truncated transmembrane form we interrogated, by coexpression, three potential ERAD substrates, all of which play roles in regulating lipid biosynthesis. Transmembrane PLpro increases the level of INSIG-1 and decreases its ubiquitination. However, different effects were seen with SREBP-1 and SREBP-2. Transmembrane PLpro cleaves SREBP-1 at three sites, including two noncanonical sites in the N-terminal half of the protein, resulting in a decrease in precursors of the active transcription factor. Conversely, cleavage of SREBP-2 occurs at a single canonical site that disrupts a C-terminal degron, resulting in increased SREBP-2 levels. When this site is mutated and the degron can no longer be interrupted, SREBP-2 is still stabilized by transmembrane PLpro, which correlates with a decrease in SREBP-2 ubiquitination. All of these observations are dependent on PLpro catalytic activity. Our findings demonstrate that, when anchored to the ER membrane, SARS-CoV-2 Nsp3 PLpro can function as a deubiquitinating enzyme to stabilize ERAD substrates. Additionally, SARS-CoV-2 Nsp3 PLpro can cleave ER-resident proteins, including at sites that could escape analyses based on the established consensus sequence.
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Affiliation(s)
- Mei Yang
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Jennifer Mariano
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Rebecca Su
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Christopher E Smith
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Catherine Gill
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jadranka Loncarek
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Yien Che Tsai
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA
| | - Allan M Weissman
- Cancer Innovation Laboratory, Center for Cancer Research, National Institutes of Health, Frederick, Maryland, USA.
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24
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Meng H, Zhou J, Wang M, Zheng M, Xing Y, Wang Y. SARS-CoV-2 Papain-like Protease Negatively Regulates the NLRP3 Inflammasome Pathway and Pyroptosis by Reducing the Oligomerization and Ubiquitination of ASC. Microorganisms 2023; 11:2799. [PMID: 38004809 PMCID: PMC10673202 DOI: 10.3390/microorganisms11112799] [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: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The interaction of viruses with hosts is complex, especially so with the antiviral immune systems of hosts, and the underlying mechanisms remain perplexing. Infection with SARS-CoV-2 may result in cytokine syndrome in the later stages, reflecting the activation of the antiviral immune response. However, viruses also encode molecules to negatively regulate the antiviral immune systems of hosts to achieve immune evasion and benefit viral replication during the early stage of infection. It has been observed that the papain-like protease (PLP) encoded by coronavirus could negatively regulate the host's IFNβ innate immunity. In this study, we first found that eight inflammasome-related genes were downregulated in CD14+ monocytes from COVID-19 patients. Subsequently, we observed that SARS-CoV-2 PLP negatively regulated the NLRP3 inflammasome pathway, inhibited the secretion of IL-1β, and decreased the caspase-1-mediated pyroptosis of human monocytes. The mechanisms for this may arise because PLP coimmunoprecipitates with ASC, reduces ASC ubiquitination, and inhibits ASC oligomerization and the formation of ASC specks. These findings suggest that PLP may inhibit strong immune defenses and provide the maximum advantage for viral replication. This research may allow us to better understand the flex function of CoV-encoding proteases and provide a new perspective on the innate immune responses against SARS-CoV-2 and other viruses.
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Affiliation(s)
- Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Chaoyang District, Beijing 100015, China
- Bioinformatics Center of Academy of Military Medicine Science, Beijing 100850, China
| | - Jianglin Zhou
- Bioinformatics Center of Academy of Military Medicine Science, Beijing 100850, China
| | - Mingyu Wang
- Bioinformatics Center of Academy of Military Medicine Science, Beijing 100850, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Chaoyang District, Beijing 100015, China
| | - Yaling Xing
- Bioinformatics Center of Academy of Military Medicine Science, Beijing 100850, China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Chaoyang District, Beijing 100015, China
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25
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Brewitz L, Henry Chan HT, Lukacik P, Strain-Damerell C, Walsh MA, Duarte F, Schofield CJ. Mass spectrometric assays monitoring the deubiquitinase activity of the SARS-CoV-2 papain-like protease inform on the basis of substrate selectivity and have utility for substrate identification. Bioorg Med Chem 2023; 95:117498. [PMID: 37857256 PMCID: PMC10933793 DOI: 10.1016/j.bmc.2023.117498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/07/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
The SARS-CoV-2 papain-like protease (PLpro) and main protease (Mpro) are nucleophilic cysteine enzymes that catalyze hydrolysis of the viral polyproteins pp1a/1ab. By contrast with Mpro, PLpro is also a deubiquitinase (DUB) that accepts post-translationally modified human proteins as substrates. Here we report studies on the DUB activity of PLpro using synthetic Nε-lysine-branched oligopeptides as substrates that mimic post-translational protein modifications by ubiquitin (Ub) or Ub-like modifiers (UBLs), such as interferon stimulated gene 15 (ISG15). Mass spectrometry (MS)-based assays confirm the DUB activity of isolated recombinant PLpro. They reveal that the sequence of both the peptide fragment derived from the post-translationally modified protein and that derived from the UBL affects PLpro catalysis; the nature of substrate binding in the S sites appears to be more important for catalytic efficiency than binding in the S' sites. Importantly, the results reflect the reported cellular substrate selectivity of PLpro, i.e. human proteins conjugated to ISG15 are better substrates than those conjugated to Ub or other UBLs. The combined experimental and modelling results imply that PLpro catalysis is affected not only by the identity of the substrate residues binding in the S and S' sites, but also by the substrate fold and the conformational dynamics of the blocking loop 2 of the PLpro:substrate complex. Nε-Lysine-branched oligopeptides thus have potential to help the identification of PLpro substrates. More generally, the results imply that MS-based assays with Nε-lysine-branched oligopeptides have potential to monitor catalysis by human DUBs and hence to inform on their substrate preferences.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
| | - H T Henry Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, OX11 0DE Didcot, United Kingdom; Research Complex at Harwell, Harwell Science and Innovation Campus, OX11 0FA Didcot, United Kingdom
| | - Fernanda Duarte
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom; The Ineos Oxford Institute for Antimicrobial Research, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom.
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26
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Schneider T, Sawade K, Berner F, Peter C, Kovermann M. Specifying conformational heterogeneity of multi-domain proteins at atomic resolution. Structure 2023; 31:1259-1274.e10. [PMID: 37557171 DOI: 10.1016/j.str.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing a large interdomain mobility. However, molecular recognition and signal transduction are associated with particular conformational substates that are populated in solution. Here, we apply high-resolution NMR spectroscopy in combination with dual-scale MD simulations to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far. We propose a general application of the approach developed here to demystify multi-domain proteins occurring in nature.
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Affiliation(s)
- Tobias Schneider
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kevin Sawade
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Graduate School Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Frederic Berner
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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27
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Tamayo-Ordóñez MC, Rosas-García NM, Ayil-Gutiérrez BA, Bello-López JM, Tamayo-Ordóñez FA, Anguebes-Franseschi F, Damas-Damas S, Tamayo-Ordóñez YDJ. Non-Structural Proteins (Nsp): A Marker for Detection of Human Coronavirus Families. Pathogens 2023; 12:1185. [PMID: 37764993 PMCID: PMC10537875 DOI: 10.3390/pathogens12091185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
SARS-CoV-2 was the cause of the global pandemic that caused a total of 14.9 million deaths during the years 2020 and 2021, according to the WHO. The virus presents a mutation rate between 10-5 and 10-3 substitutions per nucleotide site per cell infection (s/n/c). Due to this, studies aimed at knowing the evolution of this virus could help us to foresee (through the future development of new detection strategies and vaccines that prevent the infection of this virus in human hosts) that a pandemic caused by this virus will be generated again. In this research, we performed a functional annotation and identification of changes in Nsp (non-structural proteins) domains in the coronavirus genome. The comparison of the 13 selected coronavirus pangenomes demonstrated a total of 69 protein families and 57 functions associated with the structural domain's differentials between genomes. A marked evolutionary conservation of non-structural proteins was observed. This allowed us to identify and classify highly pathogenic human coronaviruses into alpha, beta, gamma, and delta groups. The designed Nsp cluster provides insight into the trajectory of SARS-CoV-2, demonstrating that it continues to evolve rapidly. An evolutionary marker allows us to discriminate between phylogenetically divergent groups, viral genotypes, and variants between the alpha and betacoronavirus genera. These types of evolutionary studies provide a window of opportunity to use these Nsp as targets of viral therapies.
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Affiliation(s)
- María Concepción Tamayo-Ordóñez
- Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico;
| | - Ninfa María Rosas-García
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
| | - Benjamín Abraham Ayil-Gutiérrez
- CONAHCYT-Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnología Vegetal, Reynosa 88710, Tamaulipas, Mexico
| | - Juan Manuel Bello-López
- División de Investigación, Hospital Juárez de México, Ciudad de México 07760, Campeche, Mexico
| | - Francisco Alberto Tamayo-Ordóñez
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Francisco Anguebes-Franseschi
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Siprian Damas-Damas
- Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico (S.D.-D.)
| | - Yahaira de Jesús Tamayo-Ordóñez
- Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
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28
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Valipour M. Therapeutic prospects of naturally occurring p38 MAPK inhibitors tanshinone IIA and pinocembrin for the treatment of SARS-CoV-2-induced CNS complications. Phytother Res 2023; 37:3724-3743. [PMID: 37282807 DOI: 10.1002/ptr.7902] [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: 01/30/2023] [Revised: 04/20/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023]
Abstract
P38 mitogen-activated protein kinase (p38 MAPK) signaling pathway is closely related to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication and hyperinflammatory responses in coronavirus disease 2019 (COVID-19). Therefore, blood-brain barrier-penetrating p38 MAPK inhibitors have good potential for the treatment of central nervous system (CNS) complications of COVID-19. The aim of the present study is the characterization of the therapeutic potential of tanshinone IIA and pinocembrin for the treatment of CNS complications of COVID-19. Studies published in high-quality journals indexed in databases Scopus, Web of Science, PubMed, and so forth were used to review the therapeutic capabilities of selected compounds. In continuation of our previous efforts to identify agents with favorable activity/toxicity profiles for the treatment of COVID-19, tanshinone IIA and pinocembrin were identified with a high ability to penetrate the CNS. Considering the nature of the study, no specific time frame was determined for the selection of studies, but the focus was strongly on studies published after the emergence of COVID-19. By describing the association of COVID-19-induced CNS disorders with p38 MAPK pathway disruption, this study concludes that tanshinone IIA and pinocembrin have great potential for better treatment of these complications. The inclusion of these compounds in the drug regimen of COVID-19 patients requires confirmation of their effectiveness through the conduction of high-quality clinical trials.
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Affiliation(s)
- Mehdi Valipour
- Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
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29
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Tam D, Lorenzo-Leal AC, Hernández LR, Bach H. Targeting SARS-CoV-2 Non-Structural Proteins. Int J Mol Sci 2023; 24:13002. [PMID: 37629182 PMCID: PMC10455537 DOI: 10.3390/ijms241613002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped respiratory β coronavirus that causes coronavirus disease (COVID-19), leading to a deadly pandemic that has claimed millions of lives worldwide. Like other coronaviruses, the SARS-CoV-2 genome also codes for non-structural proteins (NSPs). These NSPs are found within open reading frame 1a (ORF1a) and open reading frame 1ab (ORF1ab) of the SARS-CoV-2 genome and encode NSP1 to NSP11 and NSP12 to NSP16, respectively. This study aimed to collect the available literature regarding NSP inhibitors. In addition, we searched the natural product database looking for similar structures. The results showed that similar structures could be tested as potential inhibitors of the NSPs.
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Affiliation(s)
- Donald Tam
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Ana C. Lorenzo-Leal
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Luis Ricardo Hernández
- Laboratorio de Investigación Fitoquímica, Departamento de Ciencias Químico Biológicas, Universidad de las Américas Puebla, Ex Hacienda Sta. Catarina Mártir S/N, San Andrés Cholula 72810, Mexico;
| | - Horacio Bach
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
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30
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Soleimani Asl S, Roozbahani MH. A novel robust inhibitor of papain-like protease (PLpro) as a COVID-19 drug. J Biomol Struct Dyn 2023:1-8. [PMID: 37578047 DOI: 10.1080/07391102.2023.2245474] [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: 04/09/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023]
Abstract
Regarding the significance of SARS-CoV-2, scientists have shown considerable interest in developing effective drugs. Inhibitors for PLpro are the primary strategies for locating suitable COVID-19 drugs. Natural compounds comprise the majority of COVID-19 drugs. Due to limitations on the safety of clinical trials in cases of COVID, computational methods are typically utilized for inhibition studies. Whereas papain is highly similar to PLpro and is entirely safe, the current study aimed to examine several plant secondary metabolites to identify the most effective papain inhibitor and validate the results using molecular dynamics and docking. This simulation was conducted identically for PLpro and the optimal inhibitor. The results indicated that the experimental results are comparable to those obtained In-Silico, and the inhibition effects of Chlorogenic acid (CGA) on papain attained in the experiment were validated (IC50=0.54 mM). CGA as an inhibitor was located in the active site of PLpro and papain (total energy -2009410 and -456069 kJ/mol, respectively) at the desired location and distance. The study revealed that CGA and its derivatives are effective PLpro inhibitors against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saeed Soleimani Asl
- Iran Digital Twin Laboratory (IDT-Lab)- Incubator Center, Iran University of Science and Technology, Tehran, Iran
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31
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Afsar M, Liu G, Jia L, Ruben EA, Nayak D, Sayyad Z, Bury PDS, Cano KE, Nayak A, Zhao XR, Shukla A, Sung P, Wasmuth EV, Gack MU, Olsen SK. Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer. Nat Commun 2023; 14:4786. [PMID: 37553340 PMCID: PMC10409785 DOI: 10.1038/s41467-023-39780-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] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin-like protein that is activated by an E1 enzyme (Uba7) and transferred to a cognate E2 enzyme (UBE2L6) to form a UBE2L6-ISG15 intermediate that functions with E3 ligases that catalyze conjugation of ISG15 to target proteins. Despite its biological importance, the molecular basis by which Uba7 catalyzes ISG15 activation and transfer to UBE2L6 is unknown as there is no available structure of Uba7. Here, we present cryo-EM structures of human Uba7 in complex with UBE2L6, ISG15 adenylate, and ISG15 thioester intermediate that are poised for catalysis of Uba7-UBE2L6-ISG15 thioester transfer. Our structures reveal a unique overall architecture of the complex compared to structures from the ubiquitin conjugation pathway, particularly with respect to the location of ISG15 thioester intermediate. Our structures also illuminate the molecular basis for Uba7 activities and for its exquisite specificity for ISG15 and UBE2L6. Altogether, our structural, biochemical, and human cell-based data provide significant insights into the functions of Uba7, UBE2L6, and ISG15 in cells.
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Affiliation(s)
- Mohammad Afsar
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Eliza A Ruben
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Zuberwasim Sayyad
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA
| | - Priscila Dos Santos Bury
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kristin E Cano
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Anindita Nayak
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Xiang Ru Zhao
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Ankita Shukla
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Patrick Sung
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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32
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Khalifa M, Fahim JR, Allam AE, Shoman ME, El Zawily A, Kamel MS, Shimizu K, Attia EZ. Studies on the Nonalkaloidal Secondary Metabolites of Hippeastrum vittatum (L'Her.) Herb. Bulbs. ACS OMEGA 2023; 8:26749-26761. [PMID: 37546665 PMCID: PMC10398848 DOI: 10.1021/acsomega.2c07886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/06/2023] [Indexed: 08/08/2023]
Abstract
Sixteen chemically varied metabolites were isolated from the bulbs of Hippeastrum vittatum (L'Her.) Herb., including eight flavonoids [3'-methyl isoliquiritigenin (2), 7-hydroxyflavan (8), 7-hydroxyflavanone (9), 7-hydroxyflavan-3-ol (10), 7-methoxy-3',4'-methylenedioxyflavan-3-ol (11), 7-hydroxy-3',4'-methylenedioxy flavan (12), 2',4'-dihydroxy-3'-methyl-3,4-methylenedioxychalcone (13), and isoliquiritigenin (14)], four acetophenones [2,6-dimethoxy-4-hydroxyacetophenone (3), 2,4-dihydroxyacetophenone (4), 2,4-dihydroxy-6-methoxy-3-methylacetophenone (6), and 2,4,6-trimethoxyacetophenone (7)], two alkaloids [lycorine (1) and narciprimine (15)], one phenol derivative [p-nitrophenol (5)], and one steroid [β-sitosterol 3-O-β-glucopyranoside (16)]. Their structures were elucidated by combining one- and two-dimensional NMR and ESI-MS techniques and by comparison with the reported literature data and some authentic samples. Except for lycorine (1), the isolated metabolites were obtained herein for the first time from Hippeastrum plants, among which compound 13 was identified as a new chalcone derivative. Additionally, the total phenolic and flavonoid contents of the total ethanol extract and different fractions of the bulbs were determined by the Folin-Ciocalteu and aluminum chloride colorimetric methods, respectively, whereas their antioxidant potential was compared using the phosphomolybdenum and 2,2'-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assays. Finally, the binding affinities of compounds 1-16 to some key target proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), namely, main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp), were screened and compared using molecular docking analysis. The possible chemotaxonomic significance of the identified metabolites was also discussed.
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Affiliation(s)
- Marwa
Fathy Khalifa
- Department
of Pharmacognosy, Faculty of Pharmacy, Minia
University, 61519 Minia, Egypt
| | - John Refaat Fahim
- Department
of Pharmacognosy, Faculty of Pharmacy, Minia
University, 61519 Minia, Egypt
| | - Ahmed E. Allam
- Department
of Pharmacognosy, Faculty of Pharmacy, Al-Azhar
University, 71524 Assiut, Egypt
| | - Mai E. Shoman
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
| | - Amr El Zawily
- Department
of Plant and Microbiology, Faculty of Science, Damanhour University, 22511 Damanhour, Egypt
- Department
of Biology, University of Iowa, Iowa City, Iowa 52242-1324, United
States
| | - Mohamed Salah Kamel
- Department
of Pharmacognosy, Faculty of Pharmacy, Minia
University, 61519 Minia, Egypt
| | - Kuniyoshi Shimizu
- Department
of Agro-Environmental Sciences, Graduate School of Bioresource and
Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, 819-0395 Fukuoka, Japan
| | - Eman Zekry Attia
- Department
of Pharmacognosy, Faculty of Pharmacy, Minia
University, 61519 Minia, Egypt
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33
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Castillo-Campos L, Velázquez-Libera JL, Caballero J. Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking. Front Mol Biosci 2023; 10:1215499. [PMID: 37426421 PMCID: PMC10326900 DOI: 10.3389/fmolb.2023.1215499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
The papain-like protease (PLpro) from zoonotic coronaviruses (CoVs) has been identified as a target with an essential role in viral respiratory diseases caused by Severe Acute Respiratory Syndrome-associated coronaviruses (SARS-CoVs). The design of PLpro inhibitors has been proposed as an alternative to developing potential drugs against this disease. In this work, 67 naphthalene-derived compounds as noncovalent PLpro inhibitors were studied using molecular modeling methods. Structural characteristics of the bioactive conformations of these inhibitors and their interactions at the SARS-CoV-1 PLpro binding site were reported here in detail, taking into account the flexibility of the protein residues. Firstly, a molecular docking protocol was used to obtain the orientations of the inhibitors. After this, the orientations were compared, and the recurrent interactions between the PLpro residues and ligand chemical groups were described (with LigRMSD and interaction fingerprints methods). In addition, efforts were made to find correlations between docking energy values and experimentally determined binding affinities. For this, the PLpro was sampled by using Gaussian Accelerated Molecular Dynamics (GaMD), generating multiple conformations of the binding site. Diverse protein conformations were selected and a cross-docking experiment was performed, yielding models of the 67 naphthalene-derived compounds adopting different binding modes. Representative complexes for each ligand were selected to obtain the highest correlation between docking energies and activities. A good correlation (R 2 = 0.948) was found when this flexible docking protocol was performed.
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Bajaj T, Wehri E, Suryawanshi RK, King E, Pardeshi KS, Behrouzi K, Khodabakhshi Z, Schulze-Gahmen U, Kumar GR, Mofrad MRK, Nomura DK, Ott M, Schaletzky J, Murthy N. Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication. RSC Adv 2023; 13:17667-17677. [PMID: 37312993 PMCID: PMC10259201 DOI: 10.1039/d3ra01915b] [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: 03/24/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
The papain-like protease (PLpro) plays a critical role in SARS-CoV-2 (SCoV-2) pathogenesis and is essential for viral replication and for allowing the virus to evade the host immune response. Inhibitors of PLpro have great therapeutic potential, however, developing them has been challenging due to PLpro's restricted substrate binding pocket. In this report, we screened a 115 000-compound library for PLpro inhibitors and identified a new pharmacophore, based on a mercapto-pyrimidine fragment that is a reversible covalent inhibitor (RCI) of PLpro and inhibits viral replication in cells. Compound 5 had an IC50 of 5.1 μM for PLpro inhibition and hit optimization yielded a derivative with increased potency (IC50 0.85 μM, 6-fold higher). Activity based profiling of compound 5 demonstrated that it reacts with PLpro cysteines. We show here that compound 5 represents a new class of RCIs, which undergo an addition elimination reaction with cysteines in their target proteins. We further show that their reversibility is catalyzed by exogenous thiols and is dependent on the size of the incoming thiol. In contrast, traditional RCIs are all based upon the Michael addition reaction mechanism and their reversibility is base-catalyzed. We identify a new class of RCIs that introduces a more reactive warhead with a pronounced selectivity profile based on thiol ligand size. This could allow the expansion of RCI modality use towards a larger group of proteins important for human disease.
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Affiliation(s)
- Teena Bajaj
- Graduate Program of Comparative Biochemistry, University of California Berkeley CA USA
| | - Eddie Wehri
- The Henry Wheeler Center of Emerging and Neglected Diseases 344 Li Ka Shing Berkeley CA USA
| | | | - Elizabeth King
- Chemical Biology Graduate Program, University of California Berkeley CA USA
| | | | - Kamyar Behrouzi
- Department of Mechanical Engineering, University of California Berkeley CA USA
| | | | | | - G Renuka Kumar
- Gladstone Institute of Virology Gladstone Institutes San Francisco CA USA
| | | | - Daniel K Nomura
- Department of Chemistry, University of California Berkeley CA USA
| | - Melanie Ott
- Gladstone Institute of Virology Gladstone Institutes San Francisco CA USA
- Department of Medicine, University of California San Francisco CA USA
- Chan Zuckerberg Biohub San Francisco CA USA
| | - Julia Schaletzky
- The Henry Wheeler Center of Emerging and Neglected Diseases 344 Li Ka Shing Berkeley CA USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley CA USA
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35
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Zmudzinski M, Rut W, Olech K, Granda J, Giurg M, Burda-Grabowska M, Kaleta R, Zgarbova M, Kasprzyk R, Zhang L, Sun X, Lv Z, Nayak D, Kesik-Brodacka M, Olsen SK, Weber J, Hilgenfeld R, Jemielity J, Drag M. Ebselen derivatives inhibit SARS-CoV-2 replication by inhibition of its essential proteins: PL pro and M pro proteases, and nsp14 guanine N7-methyltransferase. Sci Rep 2023; 13:9161. [PMID: 37280236 DOI: 10.1038/s41598-023-35907-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Proteases encoded by SARS-CoV-2 constitute a promising target for new therapies against COVID-19. SARS-CoV-2 main protease (Mpro, 3CLpro) and papain-like protease (PLpro) are responsible for viral polyprotein cleavage-a process crucial for viral survival and replication. Recently it was shown that 2-phenylbenzisoselenazol-3(2H)-one (ebselen), an organoselenium anti-inflammatory small-molecule drug, is a potent, covalent inhibitor of both the proteases and its potency was evaluated in enzymatic and antiviral assays. In this study, we screened a collection of 34 ebselen and ebselen diselenide derivatives for SARS-CoV-2 PLpro and Mpro inhibitors. Our studies revealed that ebselen derivatives are potent inhibitors of both the proteases. We identified three PLpro and four Mpro inhibitors superior to ebselen. Independently, ebselen was shown to inhibit the N7-methyltransferase activity of SARS-CoV-2 nsp14 protein involved in viral RNA cap modification. Hence, selected compounds were also evaluated as nsp14 inhibitors. In the second part of our work, we employed 11 ebselen analogues-bis(2-carbamoylaryl)phenyl diselenides-in biological assays to evaluate their anti-SARS-CoV-2 activity in Vero E6 cells. We present their antiviral and cytoprotective activity and also low cytotoxicity. Our work shows that ebselen, its derivatives, and diselenide analogues constitute a promising platform for development of new antivirals targeting the SARS-CoV-2 virus.
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Affiliation(s)
- Mikolaj Zmudzinski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Wioletta Rut
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Kamila Olech
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Jarosław Granda
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Mirosław Giurg
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Małgorzata Burda-Grabowska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Rafał Kaleta
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Michala Zgarbova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Renata Kasprzyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Linlin Zhang
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Xinyuanyuan Sun
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Zongyang Lv
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Digant Nayak
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | | | - Shaun K Olsen
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague, Czech Republic
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems Site, University of Lübeck, 23562, Lübeck, Germany
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland.
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36
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Li G, Hilgenfeld R, Whitley R, De Clercq E. Therapeutic strategies for COVID-19: progress and lessons learned. Nat Rev Drug Discov 2023; 22:449-475. [PMID: 37076602 PMCID: PMC10113999 DOI: 10.1038/s41573-023-00672-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2023] [Indexed: 04/21/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has stimulated tremendous efforts to develop therapeutic strategies that target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or human proteins to control viral infection, encompassing hundreds of potential drugs and thousands of patients in clinical trials. So far, a few small-molecule antiviral drugs (nirmatrelvir-ritonavir, remdesivir and molnupiravir) and 11 monoclonal antibodies have been marketed for the treatment of COVID-19, mostly requiring administration within 10 days of symptom onset. In addition, hospitalized patients with severe or critical COVID-19 may benefit from treatment with previously approved immunomodulatory drugs, including glucocorticoids such as dexamethasone, cytokine antagonists such as tocilizumab and Janus kinase inhibitors such as baricitinib. Here, we summarize progress with COVID-19 drug discovery, based on accumulated findings since the pandemic began and a comprehensive list of clinical and preclinical inhibitors with anti-coronavirus activities. We also discuss the lessons learned from COVID-19 and other infectious diseases with regard to drug repurposing strategies, pan-coronavirus drug targets, in vitro assays and animal models, and platform trial design for the development of therapeutics to tackle COVID-19, long COVID and pathogenic coronaviruses in future outbreaks.
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Affiliation(s)
- Guangdi Li
- Xiangya School of Public Health, Central South University; Hunan Children's Hospital, Changsha, China.
| | - Rolf Hilgenfeld
- Institute of Molecular Medicine & German Center for Infection Research (DZIF), University of Lübeck, Lübeck, Germany.
| | - Richard Whitley
- Department of Paediatrics, Microbiology, Medicine and Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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37
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Maltarollo VG, da Silva EB, Kronenberger T, Sena Andrade MM, de Lima Marques GV, Cândido Oliveira NJ, Santos LH, Oliveira Rezende Júnior CD, Cassiano Martinho AC, Skinner D, Fajtová P, M Fernandes TH, Silveira Dos Santos ED, Rodrigues Gazolla PA, Martins de Souza AP, da Silva ML, Dos Santos FS, Lavorato SN, Oliveira Bretas AC, Carvalho DT, Franco LL, Luedtke S, Giardini MA, Poso A, Dias LC, Podust LM, Alves RJ, McKerrow J, Andrade SF, Teixeira RR, Siqueira-Neto JL, O'Donoghue A, de Oliveira RB, Ferreira RS. Structure-based discovery of thiosemicarbazones as SARS-CoV-2 main protease inhibitors. Future Med Chem 2023; 15:959-985. [PMID: 37435731 DOI: 10.4155/fmc-2023-0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023] Open
Abstract
Aim: Discovery of novel SARS-CoV-2 main protease (Mpro) inhibitors using a structure-based drug discovery strategy. Materials & methods: Virtual screening employing covalent and noncovalent docking was performed to discover Mpro inhibitors, which were subsequently evaluated in biochemical and cellular assays. Results: 91 virtual hits were selected for biochemical assays, and four were confirmed as reversible inhibitors of SARS CoV-2 Mpro with IC50 values of 0.4-3 μM. They were also shown to inhibit SARS-CoV-1 Mpro and human cathepsin L. Molecular dynamics simulations indicated the stability of the Mpro inhibitor complexes and the interaction of ligands at the subsites. Conclusion: This approach led to the discovery of novel thiosemicarbazones as potent SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Thales Kronenberger
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Marina Mol Sena Andrade
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Gabriel V de Lima Marques
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Nereu J Cândido Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucianna H Santos
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Celso de Oliveira Rezende Júnior
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Ana C Cassiano Martinho
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
| | - Danielle Skinner
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Institute of Organic Chemistry & Biochemistry, Academy of Sciences of the Czech Republic, Prague, 16610, Czech Republic
| | - Thaís H M Fernandes
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Eduardo da Silveira Dos Santos
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Poliana A Rodrigues Gazolla
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Ana P Martins de Souza
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Milene Lopes da Silva
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Fabíola S Dos Santos
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Stefânia N Lavorato
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
- Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, 47810-047, Brazil
| | - Ana C Oliveira Bretas
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Diogo Teixeira Carvalho
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucas Lopardi Franco
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Stephanie Luedtke
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Miriam A Giardini
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Antti Poso
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Luiz C Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Larissa M Podust
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Ricardo J Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - James McKerrow
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Saulo F Andrade
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Róbson R Teixeira
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Anthony O'Donoghue
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Renata B de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Rafaela S Ferreira
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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Wang Q, Chen G, He J, Li J, Xiong M, Su H, Li M, Hu H, Xu Y. Structure-Based Design of Potent Peptidomimetic Inhibitors Covalently Targeting SARS-CoV-2 Papain-like Protease. Int J Mol Sci 2023; 24:ijms24108633. [PMID: 37239980 DOI: 10.3390/ijms24108633] [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: 02/27/2023] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
The papain-like protease (PLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a critical role in the proteolytic processing of viral polyproteins and the dysregulation of the host immune response, providing a promising therapeutic target. Here, we report the structure-guide design of novel peptidomimetic inhibitors covalently targeting SARS-CoV-2 PLpro. The resulting inhibitors demonstrate submicromolar potency in the enzymatic assay (IC50 = 0.23 μM) and significant inhibition of SARS-CoV-2 PLpro in the HEK293T cells using a cell-based protease assay (EC50 = 3.61 μM). Moreover, an X-ray crystal structure of SARS-CoV-2 PLpro in complex with compound 2 confirms the covalent binding of the inhibitor to the catalytic residue cysteine 111 (C111) and emphasizes the importance of interactions with tyrosine 268 (Y268). Together, our findings reveal a new scaffold of SARS-CoV-2 PLpro inhibitors and provide an attractive starting point for further optimization.
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Affiliation(s)
- Qian Wang
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Guofeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Minjun Li
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hangchen Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yechun Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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Shao Q, Xiong M, Li J, Hu H, Su H, Xu Y. Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches. Chem Sci 2023; 14:4681-4696. [PMID: 37181765 PMCID: PMC10171076 DOI: 10.1039/d3sc00166k] [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: 01/11/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Papain-like protease (PLpro) is a promising therapeutic target against SARS-CoV-2, but its restricted S1/S2 subsites pose an obstacle in developing active site-directed inhibitors. We have recently identified C270 as a novel covalent allosteric site for SARS-CoV-2 PLpro inhibitors. Here we present a theoretical investigation of the proteolysis reaction catalyzed by the wild-type SARS-CoV-2 PLpro as well as the C270R mutant. Enhanced sampling MD simulations were first performed to explore the influence of C270R mutation on the protease dynamics, and sampled thermodynamically favorable conformations were then submitted to MM/PBSA and QM/MM MD simulations for thorough characterization of the protease-substrate binding and covalent reactions. The disclosed proteolysis mechanism of PLpro, as characterized by the occurrence of proton transfer from the catalytic C111 to H272 prior to the substrate binding and with deacylation being the rate-determining step of the whole proteolysis process, is not completely identical to that of the 3C-like protease, another key cysteine protease of coronaviruses. The C270R mutation alters the structural dynamics of the BL2 loop that indirectly impairs the catalytic function of H272 and reduces the binding of the substrate with the protease, ultimately showing an inhibitory effect on PLpro. Together, these results provide a comprehensive understanding at the atomic level of the key aspects of SARS-CoV-2 PLpro proteolysis, including the catalytic activity allosterically regulated by C270 modification, which is crucial to the follow-up inhibitor design and development.
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Affiliation(s)
- Qiang Shao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jiameng Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
| | - Hangchen Hu
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
- University of Chinese Academy of Sciences Beijing 100049 China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine Nanjing 210023 China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences Hangzhou 310024 China
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40
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Kattula B, Reddi B, Jangam A, Naik L, Adimoolam BM, Vavilapalli S, Are S, Thota JR, Jadav SS, Arifuddin M, Addlagatta A. Development of 2-chloroquinoline based heterocyclic frameworks as dual inhibitors of SARS-CoV-2 M Pro and PL Pro. Int J Biol Macromol 2023; 242:124772. [PMID: 37172706 PMCID: PMC10171901 DOI: 10.1016/j.ijbiomac.2023.124772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/21/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
Evolution of new variants of SARS-CoV-2 warrant the need for the continued efforts in identifying target-oriented new drugs. Dual targeting agents against MPro and PLPro not only overcome the incomplete efficacy but also the drug resistance, which is common problem. Since both these are cysteine proteases, we designed 2-chloroquinoline based molecules with additional imine moiety in the middle as possible nucleophilic warheads. In the first round of design and synthesis, three molecules (C3, C4 and C5) inhibited (Ki < 2 μM) only MPro by binding covalently to C145 and one molecule (C10) inhibited both the proteases non-covalently (Ki < 2 μM) with negligible cytotoxicity. Further conversion of the imine in C10 to azetidinone (C11) improved the potency against both the enzymes in the nanomolar range (820 nM against MPro and 350 nM against PLPro) with no cytotoxicity. Conversion of imine to thiazolidinone (C12), reduced the inhibition by 3-5 folds against both the enzymes. Biochemical and computational studies suggest that C10-C12 bind in the substrate binding pocket of MPro and in the BL2 loop of the PLPro. Since these dual inhibitors have least cytotoxicity, they could be further explored as therapeutics against the SARS-CoV-2 and other analogous viruses.
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Affiliation(s)
- Bhavita Kattula
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Bharati Reddi
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Aruna Jangam
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Lekhika Naik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, Telangana, India
| | - Bala Manikanta Adimoolam
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Suresh Vavilapalli
- Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Sayanna Are
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Jagadeshwar Reddy Thota
- Analytical and Structural Chemistry Department, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Surender Singh Jadav
- Department of Natural Products and Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India.
| | - Mohammed Arifuddin
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, Telangana, India.
| | - Anthony Addlagatta
- Division of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India.
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Xiong Y, Huang B, Yang Y, Fu X, Fu Z, Xu H, Liu M, Cao D, Zhang M, Yang H, Niu X, Yu C, Huang H. The substrate selectivity of papain-like proteases from human-infecting coronaviruses correlates with innate immune suppression. Sci Signal 2023; 16:eade1985. [PMID: 37130166 DOI: 10.1126/scisignal.ade1985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Coronaviruses that can infect humans can cause either common colds (HCoV-NL63, HCoV-229E, HCoV-HKU1, and HCoV-OC43) or severe respiratory symptoms (SARS-CoV-2, SARS-CoV, and MERS-CoV). The papain-like proteases (PLPs) of SARS-CoV, SARS-CoV-2, MERS-CoV, and HCoV-NL63 function in viral innate immune evasion and have deubiquitinating (DUB) and deISGylating activities. We identified the PLPs of HCoV-229E, HCoV-HKU1, and HCoV-OC43 and found that their enzymatic properties correlated with their ability to suppress innate immune responses. A conserved noncatalytic aspartic acid residue was critical for both DUB and deISGylating activities, but the PLPs had differing ubiquitin (Ub) chain cleavage selectivities and binding affinities for Ub, K48-linked diUb, and interferon-stimulated gene 15 (ISG15) substrates. The crystal structure of HKU1-PLP2 in complex with Ub revealed binding interfaces that accounted for the unusually high binding affinity between this PLP and Ub. In cellular assays, the PLPs from the severe disease-causing coronaviruses strongly suppressed innate immune IFN-I and NF-κB signaling and stimulated autophagy, whereas the PLPs from the mild disease-causing coronaviruses generally showed weaker effects on immune suppression and autophagy induction. In addition, a PLP from a SARS-CoV-2 variant of concern showed increased suppression of innate immune signaling pathways. Overall, these results demonstrated that the DUB and deISGylating activities and substrate selectivities of these PLPs differentially contribute to viral innate immune evasion and may affect viral pathogenicity.
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Affiliation(s)
- Yuxian Xiong
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China
| | - Bin Huang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Ying Yang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Xinming Fu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Ziyang Fu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Huidong Xu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Ming Liu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Dan Cao
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Manman Zhang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
| | - Haibin Yang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Cong Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Hao Huang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China
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42
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In silico study of novel niclosamide derivatives, SARS-CoV-2 nonstructural proteins catalytic residue-targeting small molecules drug candidates. ARAB J CHEM 2023; 16:104654. [PMID: 36777994 PMCID: PMC9904858 DOI: 10.1016/j.arabjc.2023.104654] [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: 07/26/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-mediated coronavirus disease 2019 (COVID-19) infection remains a global pandemic and health emergency with overwhelming social and economic impacts throughout the world. Therapeutics for COVID-19 are limited to only remdesivir; therefore, there is a need for combined, multidisciplinary efforts to develop new therapeutic molecules and explore the effectiveness of existing drugs against SARS-CoV-2. In the present study, we reported eight (SCOV-L-02, SCOV-L-09, SCOV-L-10, SCOV-L-11, SCOV-L-15, SCOV-L-18, SCOV-L-22, and SCOV-L-23) novel structurally related small-molecule derivatives of niclosamide (SCOV-L series) for their targeting potential against angiotensin-converting enzyme-2 (ACE2), type II transmembrane serine protease (TMPRSS2), and SARS-COV-2 nonstructural proteins (NSPs) including NSP5 (3CLpro), NSP3 (PLpro), and RdRp. Our correlation analysis suggested that ACE2 and TMPRSS2 modulate host immune response via regulation of immune-infiltrating cells at the site of tissue/organs entries. In addition, we identified some TMPRSS2 and ACE2 microRNAs target regulatory networks in SARS-CoV-2 infection and thus open up a new window for microRNAs-based therapy for the treatment of SARS-CoV-2 infection. Our in vitro study revealed that with the exception of SCOV-L-11 and SCOV-L-23 which were non-active, the SCOV-L series exhibited strict antiproliferative activities and non-cytotoxic effects against ACE2- and TMPRSS2-expressing cells. Our molecular docking for the analysis of receptor-ligand interactions revealed that SCOV-L series demonstrated high ligand binding efficacies (at higher levels than clinical drugs) against the ACE2, TMPRSS2, and SARS-COV-2 NSPs. SCOV-L-18, SCOV-L-15, and SCOV-L-09 were particularly found to exhibit strong binding affinities with three key SARS-CoV-2's proteins: 3CLpro, PLpro, and RdRp. These compounds bind to the several catalytic residues of the proteins, and satisfied the criteria of drug-like candidates, having good adsorption, distribution, metabolism, excretion, and toxicity (ADMET) pharmacokinetic profile. Altogether, the present study suggests the therapeutic potential of SCOV-L series for preventing and managing SARs-COV-2 infection and are currently under detailed investigation in our lab.
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Hersi F, Sebastian A, Tarazi H, Srinivasulu V, Mostafa A, Allayeh AK, Zeng C, Hachim IY, Liu SL, Abu-Yousef IA, Majdalawieh AF, Zaher DM, Omar HA, Al-Tel TH. Discovery of novel papain-like protease inhibitors for potential treatment of COVID-19. Eur J Med Chem 2023; 254:115380. [PMID: 37075625 PMCID: PMC10106510 DOI: 10.1016/j.ejmech.2023.115380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/09/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
The recent emergence of different SARS-CoV-2 variants creates an urgent need to develop more effective therapeutic agents to prevent COVID-19 outbreaks. Among SARS-CoV-2 essential proteases is papain-like protease (SARS-CoV-2 PLpro), which plays multiple roles in regulating SARS-CoV-2 viral spread and innate immunity such as deubiquitinating and deISG15ylating (interferon-induced gene 15) activities. Many studies are currently focused on targeting this protease to tackle SARS-CoV-2 infection. In this context, we performed a phenotypic screening using an in-house pilot compounds collection possessing a diverse skeleta against SARS-CoV-2 PLpro. This screen identified SIMR3030 as a potent inhibitor of SARS-CoV-2. SIMR3030 has been shown to exhibit deubiquitinating activity and inhibition of SARS-CoV-2 specific gene expression (ORF1b and Spike) in infected host cells and possessing virucidal activity. Moreover, SIMR3030 was demonstrated to inhibit the expression of inflammatory markers, including IFN-α, IL-6, and OAS1, which are reported to mediate the development of cytokine storms and aggressive immune responses. In vitro absorption, distribution, metabolism, and excretion (ADME) assessment of the drug-likeness properties of SIMR3030 demonstrated good microsomal stability in liver microsomes. Furthermore, SIMR3030 demonstrated very low potency as an inhibitor of CYP450, CYP3A4, CYP2D6 and CYP2C9 which rules out any potential drug-drug interactions. In addition, SIMR3030 showed moderate permeability in Caco2-cells. Critically, SIMR3030 has maintained a high in vivo safety profile at different concentrations. Molecular modeling studies of SIMR3030 in the active sites of SARS-CoV-2 and MERS-CoV PLpro were performed to shed light on the binding modes of this inhibitor. This study demonstrates that SIMR3030 is a potent inhibitor of SARS-CoV-2 PLpro that forms the foundation for developing new drugs to tackle the COVID-19 pandemic and may pave the way for the development of novel therapeutics for a possible future outbreak of new SARS-CoV-2 variants or other Coronavirus species.
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Affiliation(s)
- Fatema Hersi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Anusha Sebastian
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hamadeh Tarazi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Vunnam Srinivasulu
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, Environment and Climate Change Institute, National Research Centre, Giza, 12622, Egypt
| | - Abdou Kamal Allayeh
- Virology Lab 176, Water Pollution Research Department, Environment and Climate Change Institute, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Cong Zeng
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Ibrahim Y Hachim
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shan-Lu Liu
- Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA; Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Imad A Abu-Yousef
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Amin F Majdalawieh
- Department of Biology, Chemistry and Environmental Sciences, College of Arts and Sciences, American University of Sharjah, P.O. Box 26666, Sharjah, United Arab Emirates
| | - Dana M Zaher
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hany A Omar
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt.
| | - Taleb H Al-Tel
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates.
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Luo SY, Moussa EW, Lopez-Orozco J, Felix-Lopez A, Ishida R, Fayad N, Gomez-Cardona E, Wang H, Wilson JA, Kumar A, Hobman TC, Julien O. Identification of Human Host Substrates of the SARS-CoV-2 M pro and PL pro Using Subtiligase N-Terminomics. ACS Infect Dis 2023; 9:749-761. [PMID: 37011043 PMCID: PMC10081575 DOI: 10.1021/acsinfecdis.2c00458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Indexed: 04/04/2023]
Abstract
The recent emergence of SARS-CoV-2 in the human population has caused a global pandemic. The virus encodes two proteases, Mpro and PLpro, that are thought to play key roles in the suppression of host protein synthesis and immune response evasion during infection. To identify the specific host cell substrates of these proteases, active recombinant SARS-CoV-2 Mpro and PLpro were added to A549 and Jurkat human cell lysates, and subtiligase-mediated N-terminomics was used to capture and enrich protease substrate fragments. The precise location of each cleavage site was identified using mass spectrometry. Here, we report the identification of over 200 human host proteins that are potential substrates for SARS-CoV-2 Mpro and PLpro and provide a global mapping of proteolysis for these two viral proteases in vitro. Modulating proteolysis of these substrates will increase our understanding of SARS-CoV-2 pathobiology and COVID-19.
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Affiliation(s)
- Shu Y. Luo
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joaquin Lopez-Orozco
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Alberto Felix-Lopez
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ray Ishida
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Nawell Fayad
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Erik Gomez-Cardona
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Henry Wang
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joyce A. Wilson
- Department
of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Anil Kumar
- Department
of Biochemistry, Microbiology & Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Tom C. Hobman
- Department
of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department
of Medical Microbiology & Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, Edmonton, Alberta T6G
2E1, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, Edmonton, Alberta T6G
2E1, Canada
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45
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Xia Y, Pan X, Shen HB. LigBind: identifying binding residues for over 1000 ligands with relation-aware graph neural networks. J Mol Biol 2023; 435:168091. [PMID: 37054909 DOI: 10.1016/j.jmb.2023.168091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/22/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Identifying the interactions between proteins and ligands is significant for drug discovery and design. Considering the diverse binding patterns of ligands, the ligand-specific methods are trained per ligand to predict binding residues. However, most of the existing ligand-specific methods ignore shared binding preferences among various ligands and generally only cover a limited number of ligands with a sufficient number of known binding proteins. In this study, we propose a relation-aware framework LigBind with graph-level pre-training to enhance the ligand-specific binding residue predictions for 1159 ligands, which can effectively cover the ligands with a few known binding proteins. LigBind first pre-trains a graph neural network-based feature extractor for ligand-residue pairs and relation-aware classifiers for similar ligands. Then, LigBind is fine-tuned with ligand-specific binding data, where a domain adaptive neural network is designed to automatically leverage the diversity and similarity of various ligand-binding patterns for accurate binding residue prediction. We construct ligand-specific benchmark datasets of 1159 ligands and 16 unseen ligands, which are used to evaluate the effectiveness of LigBind. The results demonstrate the LigBind's efficacy on the large-scale ligand-specific benchmark datasets, and generalizes well to unseen ligands. LigBind also enables accurate identification of the ligand-binding residues in the main protease, papain-like protease and the RNA-dependent RNA polymerase of SARS-CoV-2. The webserver and source codes of LigBind are available at http://www.csbio.sjtu.edu.cn/bioinf/LigBind/ and https://github.com/YYingXia/LigBind/ for academic use.
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Affiliation(s)
- Ying Xia
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China.
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46
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Preparation and characterization of nanobodies targeting SARS-CoV-2 papain-like protease. Protein Expr Purif 2023; 207:106267. [PMID: 37030644 PMCID: PMC10076250 DOI: 10.1016/j.pep.2023.106267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Coronavirus Papain-like protease (PLpro) mediates the cleavage of viral polyproteins and assists the virus escaping from innate immune response. Thus, PLpro is an attractive target for the development of broad-spectrum drugs as it has a conserved structure across different coronaviruses. In this study, we purified SARS-CoV-2 PLpro as an immune antigen, constructed a nanobody phage display library, and identified a set of nanobodies with high affinity for SARS-CoV-2. In addition, enzyme activity experiments demonstrated that two nanobodies had a significant inhibitory effect on the PLpro. These nanobodies should therefore be investigated as candidates for the treatment of coronaviruses.
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47
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Sadeghi K, Zadheidar S, Zebardast A, Nejati A, Faraji M, Ghavami N, Kalantari S, Salimi V, Yavarian J, Abedi A, Jandaghi NZS, Mokhtari‐Azad T. Genomic surveillance of SARS-CoV-2 strains circulating in Iran during six waves of the pandemic. Influenza Other Respir Viruses 2023; 17:e13135. [PMID: 37078070 PMCID: PMC10106497 DOI: 10.1111/irv.13135] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Background SARS-CoV-2 genomic surveillance is necessary for the detection, monitoring, and evaluation of virus variants, which can have increased transmissibility, disease severity, or other adverse effects. We sequenced 330 SARS-CoV-2 genomes during the sixth wave of the COVID pandemic in Iran and compared them with five previous waves, for identifying SARS-CoV-2 variants, the genomic behavior of the virus, and understanding its characteristics. Methods After viral RNA extraction from clinical samples collected during the COVID-19 pandemic, next generation sequencing was performed using the Nextseq and Nanopore platforms. The sequencing data were analyzed and compared with reference sequences. Results In Iran during the first wave, V and L clades were detected. The second wave was recognized by G, GH, and GR clades. Circulating clades during the third wave were GH and GR. In the fourth wave, GRY (alpha variant), GK (delta variant), and one GH clade (beta variant) were detected. All viruses in the fifth wave were in GK clade (delta variant). In the sixth wave, Omicron variant (GRA clade) was circulating. Conclusions Genome sequencing, a key strategy in genomic surveillance systems, helps to detect and monitor the prevalence of SARS-CoV-2 variants, monitor the viral evolution of SARS-CoV-2, identify new variants for disease prevention, control, and treatment, and also provide information for and conduct public health measures in this area. With this system, Iran could be ready for surveillance of other respiratory virus diseases besides influenza and SARS-CoV-2.
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Affiliation(s)
- Kaveh Sadeghi
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Sevrin Zadheidar
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Arghavan Zebardast
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Ahmad Nejati
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Marziyeh Faraji
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Nastaran Ghavami
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Shirin Kalantari
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Vahid Salimi
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
| | - Jila Yavarian
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
- Research Center for Antibiotic Stewardship & Antimicrobial ResistanceTehran University of Medical SciencesTehranIran
| | - Adel Abedi
- Mathematics DepartmentShahid Beheshti UniversityTehranIran
| | | | - Talat Mokhtari‐Azad
- Virology Department, School of Public HealthTehran University of Medical SciencesTehranIran
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48
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Abstract
Our understanding of the ubiquitin code has greatly evolved from conventional E1, E2 and E3 enzymes that modify Lys residues on specific substrates with a single type of ubiquitin chain to more complex processes that regulate and mediate ubiquitylation. In this Review, we discuss recently discovered endogenous mechanisms and unprecedented pathways by which pathogens rewrite the ubiquitin code to promote infection. These processes include unconventional ubiquitin modifications involving ester linkages with proteins, lipids and sugars, or ubiquitylation through a phosphoribosyl bridge involving Arg42 of ubiquitin. We also introduce the enzymatic pathways that write and reverse these modifications, such as the papain-like proteases of severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. Furthermore, structural studies have revealed that the ultimate functions of ubiquitin are mediated not simply by straightforward recognition by ubiquitin-binding domains. Instead, elaborate multivalent interactions between ubiquitylated targets or ubiquitin chains and their readers (for example, the proteasome, the MLL1 complex or DOT1L) can elicit conformational changes that regulate protein degradation or transcription. The newly discovered mechanisms provide opportunities for innovative therapeutic interventions for diseases such as cancer and infectious diseases.
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Affiliation(s)
- Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
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49
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Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nat Commun 2023; 14:1733. [PMID: 36977673 PMCID: PMC10044120 DOI: 10.1038/s41467-023-37254-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M-1 s-1, achieves sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.
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Affiliation(s)
- Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Suman Pokhrel
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Audrey D Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Manat Kaur
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jurgen G Schmidt
- B-11 Bioenergy and Biome Sciences, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Walter Reichard
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lexi Phillips
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Babak Andi
- Center for BioMolecular Structure, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Soichi Wakatsuki
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computational and Data Sciences, Center for Research Acceleration by Digital Innovation, Amgen, Inc., Thosand Oaks, CA, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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50
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Luo J, Zhang Z, Zhao S, Gao R. A Comparison of Etiology, Pathogenesis, Vaccinal and Antiviral Drug Development between Influenza and COVID-19. Int J Mol Sci 2023; 24:ijms24076369. [PMID: 37047339 PMCID: PMC10094131 DOI: 10.3390/ijms24076369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Influenza virus and coronavirus, two kinds of pathogens that exist widely in nature, are common emerging pathogens that cause respiratory tract infections in humans. In December 2019, a novel coronavirus SARS-CoV-2 emerged, causing a severe respiratory infection named COVID-19 in humans, and raising a global pandemic which has persisted in the world for almost three years. Influenza virus, a seasonally circulating respiratory pathogen, has caused four global pandemics in humans since 1918 by the emergence of novel variants. Studies have shown that there are certain similarities in transmission mode and pathogenesis between influenza and COVID-19, and vaccination and antiviral drugs are considered to have positive roles as well as several limitations in the prevention and control of both diseases. Comparative understandings would be helpful to the prevention and control of these diseases. Here, we review the study progress in the etiology, pathogenesis, vaccine and antiviral drug development for the two diseases.
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