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Mahmutović-Dizdarević I, Mesic A, Jerković-Mujkić A, Žujo B, Avdić M, Hukić M, Omeragić E, Osmanović A, Špirtović-Halilović S, Ahmetovski S, Mujkanović S, Pramenković E, Salihović M. Biological potential, chemical profiling, and molecular docking study of Morus alba L. extracts. Fitoterapia 2024; 177:106114. [PMID: 38971331 DOI: 10.1016/j.fitote.2024.106114] [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: 05/16/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Morus alba L. is a plant with a long history of dietary and medicinal uses. We hypothesized that M. alba possesses a significant biological potential. In that sense, we aimed to generate the chemical, antimicrobial, toxicological, and molecular profile of M. alba leaf and fruit extracts. Our results showed that extracts were rich in vitamin C, phenols, and flavonoids, with quercetin and pterostilbene concentrated in the leaf, while fisetin, hesperidin, resveratrol, and luteolin were detected in fruit. Extracts exhibited antimicrobial activity against all tested bacteria, including multidrug-resistant strains. The widest inhibition zones were in Staphylococcus aureus ATCC 33591. The values of the minimum inhibitory concentration ranged from 15.62 μg/ml in Enterococcus faecalis to 500 μg/ml in several bacteria. Minimum bactericidal concentration ranged from 31.25 μg/ml to 1000 μg/ml. Extracts impacted the biofilm formation in a concentration-dependent and species-specific manner. A significant difference in the frequency of nucleoplasmic bridges between the methanolic extract of fruit (0.5 μg/ml, 1 μg/ml, 2 μg/ml), as well as for the frequency of micronuclei between ethanolic extract of leaf (2 μg/ml) and the control group was observed. Molecular docking suggested that hesperidin possesses the highest binding affinity for multidrug efflux transporter AcrB and acyl-PBP2a from MRSA, as well as for the SARS-CoV-2 Mpro. This study, by complementing previous research in this field, gives new insights that could be of great value in obtaining a more comprehensive picture of the Morus alba L. bioactive potential, chemical composition, antimicrobial and toxicological features, as well as molecular profile.
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Affiliation(s)
- Irma Mahmutović-Dizdarević
- University of Sarajevo-Faculty of Science, Department of Biology, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Aner Mesic
- University of Sarajevo-Faculty of Science, Department of Biology, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina
| | - Anesa Jerković-Mujkić
- University of Sarajevo-Faculty of Science, Department of Biology, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina
| | - Belma Žujo
- University of Sarajevo-Faculty of Science, Department of Biology, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina
| | - Monia Avdić
- International Burch University, Faculty of Engineering, Natural and Medical Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71210 Ilidža, Bosnia and Herzegovina; Academy of Sciences and Arts of Bosnia and Herzegovina, Center for Disease Control and Geohealth Studies, Bistrik 7, 71000 Sarajevo, Bosnia and Herzegovina
| | - Mirsada Hukić
- Academy of Sciences and Arts of Bosnia and Herzegovina, Center for Disease Control and Geohealth Studies, Bistrik 7, 71000 Sarajevo, Bosnia and Herzegovina; Institute for Biomedical Diagnostics and Research Nalaz, Čekaluša 69, 71000 Sarajevo, Bosnia and Herzegovina
| | - Elma Omeragić
- University of Sarajevo-Faculty of Pharmacy, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Amar Osmanović
- University of Sarajevo-Faculty of Pharmacy, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Selma Špirtović-Halilović
- University of Sarajevo-Faculty of Pharmacy, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Sarah Ahmetovski
- University of Sarajevo-Faculty of Science, Department of Biology, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina
| | - Samra Mujkanović
- University of Sarajevo-Faculty of Science, Department of Biology, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina
| | - Emina Pramenković
- International Burch University, Faculty of Engineering, Natural and Medical Sciences, Department of Genetics and Bioengineering, Francuske revolucije bb, 71210 Ilidža, Bosnia and Herzegovina
| | - Mirsada Salihović
- University of Sarajevo-Faculty of Pharmacy, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
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2
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ElSawy KM. Competitive Interaction of the SGFRKMAF Peptide with 3CLpro Dimerization Intermediates: A Brownian Dynamics Investigation. J Phys Chem B 2024; 128:7313-7321. [PMID: 39028939 DOI: 10.1021/acs.jpcb.4c01938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
The SGFRKMAF peptide is known to inhibit the dimerization of 3CLpro monomers, which is essential for SARS-CoV-2 replication. The mechanism behind this, however, is largely unknown. In this work, we used Brownian dynamics simulations to compare and contrast 3CLpro monomer-monomer interactions and 3CLpro monomer-SGFRKMAF peptide interactions. We found that formation of the 3CLpro wild-type dimer could potentially involve formation of three intermediates that are primarily stabilized by G11-G124, S1-S301, and T118-G278 interactions. Analysis of 3CLpro monomer interaction with the SGFRKMAF peptide, however, revealed the presence of eight basins of interactions where the peptide assumes the highest local densities at the 3CLPro monomer surface. The second highest-density basin was found to coincide with the interface region of the wild-type 3CLpro dimer, thereby directly blocking the 3CLpro dimer-dimer interactions. The other basins, however, were found to lie far from the interface region. Notably, we found that only 6% of the BD trajectories end up directly into the basin at the interface region and ∼39% of the trajectories end up into those basins lying away from the interface region, indicating a greater role for peptide binding at sites away from the dimer interface region. Importantly, the locations of the basins lying away from the interface were found to coincide with the 3CLpro residues involved in stabilization of the 3CLpro monomer-monomer intermediates. Given that the rate constant of the peptide reaching the monomer surface was found to be almost an order of magnitude higher than the rate constant of monomer-monomer association, the SGFRKMAF peptide has the potential to inhibit dimerization of 3CLpro monomers not only through blocking the interface region but also through blocking the formation of the intermediates involved in the dimerization process. This could potentially open new avenues for 3CLpro dimerization inhibitors that transcend traditional X-ray-based discovery approaches.
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Affiliation(s)
- Karim M ElSawy
- Department of Chemistry, College of Science, Qassim University, Buraydah 52571, Saudi Arabia
- York Cross-disciplinary Centre for Systems Analysis (YCCSA), University of York, York YO10 5GE, United Kingdom
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3
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Papaneophytou C. Breaking the Chain: Protease Inhibitors as Game Changers in Respiratory Viruses Management. Int J Mol Sci 2024; 25:8105. [PMID: 39125676 PMCID: PMC11311956 DOI: 10.3390/ijms25158105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Respiratory viral infections (VRTIs) rank among the leading causes of global morbidity and mortality, affecting millions of individuals each year across all age groups. These infections are caused by various pathogens, including rhinoviruses (RVs), adenoviruses (AdVs), and coronaviruses (CoVs), which are particularly prevalent during colder seasons. Although many VRTIs are self-limiting, their frequent recurrence and potential for severe health complications highlight the critical need for effective therapeutic strategies. Viral proteases are crucial for the maturation and replication of viruses, making them promising therapeutic targets. This review explores the pivotal role of viral proteases in the lifecycle of respiratory viruses and the development of protease inhibitors as a strategic response to these infections. Recent advances in antiviral therapy have highlighted the effectiveness of protease inhibitors in curtailing the spread and severity of viral diseases, especially during the ongoing COVID-19 pandemic. It also assesses the current efforts aimed at identifying and developing inhibitors targeting key proteases from major respiratory viruses, including human RVs, AdVs, and (severe acute respiratory syndrome coronavirus-2) SARS-CoV-2. Despite the recent identification of SARS-CoV-2, within the last five years, the scientific community has devoted considerable time and resources to investigate existing drugs and develop new inhibitors targeting the virus's main protease. However, research efforts in identifying inhibitors of the proteases of RVs and AdVs are limited. Therefore, herein, it is proposed to utilize this knowledge to develop new inhibitors for the proteases of other viruses affecting the respiratory tract or to develop dual inhibitors. Finally, by detailing the mechanisms of action and therapeutic potentials of these inhibitors, this review aims to demonstrate their significant role in transforming the management of respiratory viral diseases and to offer insights into future research directions.
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Affiliation(s)
- Christos Papaneophytou
- Department of Life Sciences, School of Life and Health Sciences, University of Nicosia, Nicosia 2417, Cyprus
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4
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Nguyen HH, Tufts J, Minh DDL. On Inactivation of the Coronavirus Main Protease. J Chem Inf Model 2024; 64:1644-1656. [PMID: 38423522 PMCID: PMC10936523 DOI: 10.1021/acs.jcim.3c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
A deeper understanding of the inactive conformations of the coronavirus main protease (MPro) could inform the design of allosteric drugs. Based on extensive molecular dynamics simulations, we built a Markov State Model to investigate structural changes that can inactivate the SARS-CoV-2 MPro. In a subset of structures, one subunit of the homodimer assumes an inactive conformation that resembles an inactive crystal structure. However, contradicting the widely held half-of-sites activity hypothesis, the most populated enzyme structures have two active subunits. We then used transition path theory (TPT) and the Jensen-Shannon Divergence (JSD) to pinpoint residues involved in the inactivation process. A π stack between Phe140 and His163 is a key feature that can distinguish active and inactive conformations of MPro. Each subunit has unique inactive conformations stabilized by π stacking interactions involving residues Phe140, Tyr118, His163, and His172, a hydrogen bonding network centered around His163 and His172, and a modified network of interactions in the dimer interface. The importance of these residues in maintaining an active structure explains the sensitivity of enzymatic activity to site-directed mutagenesis.
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Affiliation(s)
- Hong Ha Nguyen
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Jim Tufts
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - David D. L. Minh
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
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5
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Wang G, Venegas FA, Rueda AM, Weerasinghe NW, Uggowitzer KA, Thibodeaux CJ, Moitessier N, Mittermaier AK. A naturally occurring G11S mutation in the 3C-like protease from the SARS-CoV-2 virus dramatically weakens the dimer interface. Protein Sci 2024; 33:e4857. [PMID: 38058248 PMCID: PMC10731504 DOI: 10.1002/pro.4857] [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: 08/16/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
The 3C-like protease (3CLpro ) is crucial to the replication of SARS-CoV-2, the causative agent of COVID-19, and is the target of several successful drugs including Paxlovid and Xocova. Nevertheless, the emergence of viral resistance underlines the need for alternative drug strategies. 3CLpro only functions as a homodimer, making the protein-protein interface an attractive drug target. Dimerization is partly mediated by a conserved glycine at position 11. However, some naturally occurring SARS-CoV-2 sequences contain a serine at this position, potentially disrupting the dimer. We have used concentration-dependent activity assays and mass spectrometry to show that indeed the G11S mutation reduces the stability of the dimer by 600-fold. This helps to set a quantitative benchmark for the minimum potency required of any future protein-protein interaction inhibitors targeting 3CLpro and raises interesting questions regarding how coronaviruses bearing such weakly dimerizing 3CLpro enzymes are capable of replication.
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Affiliation(s)
- Guanyu Wang
- Department of ChemistryMcGill UniversityMontrealQuebecCanada
| | | | - Andres M. Rueda
- Department of ChemistryMcGill UniversityMontrealQuebecCanada
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6
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Chen S, Arutyunova E, Lu J, Khan MB, Rut W, Zmudzinski M, Shahbaz S, Iyyathurai J, Moussa EW, Turner Z, Bai B, Lamer T, Nieman JA, Vederas JC, Julien O, Drag M, Elahi S, Young HS, Lemieux MJ. SARS-CoV-2 M pro Protease Variants of Concern Display Altered Viral Substrate and Cell Host Target Galectin-8 Processing but Retain Sensitivity toward Antivirals. ACS CENTRAL SCIENCE 2023; 9:696-708. [PMID: 37122453 PMCID: PMC10042146 DOI: 10.1021/acscentsci.3c00054] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Indexed: 05/03/2023]
Abstract
The main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter the structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOCs) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and the rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and a subsequent significant decrease in cytokine secretion, providing evidence for alterations in the escape of host-antiviral mechanisms. Accordingly, mutations associated with the Gamma VOC and highly virulent Delta VOC resulted in a significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.
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Affiliation(s)
- Sizhu
Amelia Chen
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Elena Arutyunova
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jimmy Lu
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Muhammad Bashir Khan
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wioletta Rut
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Mikolaj Zmudzinski
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shima Shahbaz
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Jegan Iyyathurai
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Eman W. Moussa
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Zoe Turner
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Bing Bai
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Tess Lamer
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - James A. Nieman
- Li
Ka Shing Applied Virology Institute, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Department
of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - John C. Vederas
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Marcin Drag
- Department
of Chemical Biology and Bioimaging, Wroclaw
University of Science and Technology, Wroclaw, 50-370, Poland
| | - Shokrollah Elahi
- Department
of Dentistry & Dental Hygiene, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Howard S. Young
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - M. Joanne Lemieux
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Li
Ka Shing Institute of Virology, University
of Alberta, Edmonton, Alberta T6G 2E1, Canada
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7
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Paciaroni A, Libera V, Ripanti F, Orecchini A, Petrillo C, Francisci D, Schiaroli E, Sabbatini S, Gidari A, Bianconi E, Macchiarulo A, Hussain R, Silvestrini L, Moretti P, Belhaj N, Vercelli M, Roque Y, Mariani P, Comez L, Spinozzi F. Stabilization of the Dimeric State of SARS-CoV-2 Main Protease by GC376 and Nirmatrelvir. Int J Mol Sci 2023; 24:ijms24076062. [PMID: 37047038 PMCID: PMC10093836 DOI: 10.3390/ijms24076062] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
The main protease (Mpro or 3CLpro) is an enzyme that is evolutionarily conserved among different genera of coronaviruses. As it is essential for processing and maturing viral polyproteins, Mpro has been identified as a promising target for the development of broad-spectrum drugs against coronaviruses. Like SARS-CoV and MERS-CoV, the mature and active form of SARS-CoV-2 Mpro is a dimer composed of identical subunits, each with a single active site. Individual monomers, however, have very low or no catalytic activity. As such, inhibition of Mpro can be achieved by molecules that target the substrate binding pocket to block catalytic activity or target the dimerization process. In this study, we investigated GC376, a transition-state analog inhibitor of the main protease of feline infectious peritonitis coronavirus, and Nirmatrelvir (NMV), an oral, bioavailable SARS-CoV-2 Mpro inhibitor with pan-human coronavirus antiviral activity. Our results show that both GC376 and NMV are capable of strongly binding to SARS-CoV-2 Mpro and altering the monomer-dimer equilibrium by stabilizing the dimeric state. This behavior is proposed to be related to a structured hydrogen-bond network established at the Mpro active site, where hydrogen bonds between Ser1' and Glu166/Phe140 are formed in addition to those achieved by the latter residues with GC376 or NMV.
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Affiliation(s)
- Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Elisabetta Schiaroli
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Samuele Sabbatini
- Department of Medicine and Surgery, Medical Microbiology Section, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Anna Gidari
- Department of Medicine and Surgery, Clinic of Infectious Diseases, University of Perugia, Piazzale Gambuli, 06129 Perugia, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo, 06123 Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo, 06123 Perugia, Italy
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Lucia Silvestrini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Paolo Moretti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Norhan Belhaj
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Matteo Vercelli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Yessica Roque
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 12, 60131 Ancona, Italy
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8
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Charles S, Edgar MP, Mahapatra RK. Artificial intelligence based virtual screening study for competitive and allosteric inhibitors of the SARS-CoV-2 main protease. J Biomol Struct Dyn 2023; 41:15286-15304. [PMID: 36943715 DOI: 10.1080/07391102.2023.2188419] [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: 12/07/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023]
Abstract
SARS-CoV-2 is a highly contagious and dangerous coronavirus that first appeared in late 2019 causing COVID-19, a pandemic of acute respiratory illnesses that is still a threat to health and the general public safety. We performed deep docking studies of 800 M unique compounds in both the active and allosteric sites of the SARS-COV-2 Main Protease (Mpro) and the 15 M and 13 M virtual hits obtained were further taken for conventional docking and molecular dynamic (MD) studies. The best XP Glide docking scores obtained were -14.242 and -12.059 kcal/mol by CHEMBL591669 and the highest binding affinities were -10.5 kcal/mol (from 444215) and -11.2 kcal/mol (from NPC95421) for active and allosteric sites, respectively. Some hits can bind both sites making them a great area of concern. Re-docking of 8 random allosteric complexes in the active site shows a significant reduction in docking scores with a t-test P value of 2.532 × 10-11 at 95% confidence. Some specific interactions have higher elevations in docking scores. MD studies on 15 complexes show that single-ligand systems are stable as compared to double-ligand systems, and the allosteric binders identified are shown to modulate the active site binding as evidenced by the changes in the interaction patterns and stability of ligands and active site residues. When an allosteric complex was docked to the second monomer to check for homodimer formation, the validated homodimer could not be re-established, further supporting the potential of the identified allosteric binders. These findings could be important in developing novel therapeutics against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ssemuyiga Charles
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, India
- Department of Microbiology, Biotechnology and Plant Sciences, School of Biological Sciences, Makerere University, Kampala, Uganda
| | - Mulumba Pius Edgar
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, India
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9
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Brier L, Hassan H, Hanoulle X, Landry V, Moschidi D, Desmarets L, Rouillé Y, Dumont J, Herledan A, Warenghem S, Piveteau C, Carré P, Ikherbane S, Cantrelle FX, Dupré E, Dubuisson J, Belouzard S, Leroux F, Deprez B, Charton J. Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses. Eur J Med Chem 2023; 250:115186. [PMID: 36796300 PMCID: PMC9901219 DOI: 10.1016/j.ejmech.2023.115186] [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: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Since end of 2019, the global and unprecedented outbreak caused by the coronavirus SARS-CoV-2 led to dramatic numbers of infections and deaths worldwide. SARS-CoV-2 produces two large viral polyproteins which are cleaved by two cysteine proteases encoded by the virus, the 3CL protease (3CLpro) and the papain-like protease, to generate non-structural proteins essential for the virus life cycle. Both proteases are recognized as promising drug targets for the development of anti-coronavirus chemotherapy. Aiming at identifying broad spectrum agents for the treatment of COVID-19 but also to fight emergent coronaviruses, we focused on 3CLpro that is well conserved within this viral family. Here we present a high-throughput screening of more than 89,000 small molecules that led to the identification of a new chemotype, potent inhibitor of the SARS-CoV-2 3CLpro. The mechanism of inhibition, the interaction with the protease using NMR and X-Ray, the specificity against host cysteine proteases and promising antiviral properties in cells are reported.
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Affiliation(s)
- Lucile Brier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Haitham Hassan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Xavier Hanoulle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Valerie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Danai Moschidi
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Lowiese Desmarets
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Yves Rouillé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Paul Carré
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sarah Ikherbane
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - François-Xavier Cantrelle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Elian Dupré
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Jean Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Sandrine Belouzard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France.
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France
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10
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Higashi-Kuwata N, Tsuji K, Hayashi H, Bulut H, Kiso M, Imai M, Ogata-Aoki H, Ishii T, Kobayakawa T, Nakano K, Takamune N, Kishimoto N, Hattori SI, Das D, Uemura Y, Shimizu Y, Aoki M, Hasegawa K, Suzuki S, Nishiyama A, Saruwatari J, Shimizu Y, Sukenaga Y, Takamatsu Y, Tsuchiya K, Maeda K, Yoshimura K, Iida S, Ozono S, Suzuki T, Okamura T, Misumi S, Kawaoka Y, Tamamura H, Mitsuya H. Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2. Nat Commun 2023; 14:1076. [PMID: 36841831 PMCID: PMC9958325 DOI: 10.1038/s41467-023-36729-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/14/2023] [Indexed: 02/27/2023] Open
Abstract
COVID-19 caused by SARS-CoV-2 has continually been serious threat to public health worldwide. While a few anti-SARS-CoV-2 therapeutics are currently available, their antiviral potency is not sufficient. Here, we identify two orally available 4-fluoro-benzothiazole-containing small molecules, TKB245 and TKB248, which specifically inhibit the enzymatic activity of main protease (Mpro) of SARS-CoV-2 and significantly more potently block the infectivity and replication of various SARS-CoV-2 strains than nirmatrelvir, molnupiravir, and ensitrelvir in cell-based assays employing various target cells. Both compounds also block the replication of Delta and Omicron variants in human-ACE2-knocked-in mice. Native mass spectrometric analysis reveals that both compounds bind to dimer Mpro, apparently promoting Mpro dimerization. X-ray crystallographic analysis shows that both compounds bind to Mpro's active-site cavity, forming a covalent bond with the catalytic amino acid Cys-145 with the 4-fluorine of the benzothiazole moiety pointed to solvent. The data suggest that TKB245 and TKB248 might serve as potential therapeutics for COVID-19 and shed light upon further optimization to develop more potent and safer anti-SARS-CoV-2 therapeutics.
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Affiliation(s)
- Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Kohei Tsuji
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hironori Hayashi
- Department of Infectious Diseases, International Research Institute of Disaster Science, Tohoku University, Miyagi, Japan
| | - Haydar Bulut
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Maki Kiso
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Masaki Imai
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Hiromi Ogata-Aoki
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Takahiro Ishii
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Kobayakawa
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenta Nakano
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nobutoki Takamune
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naoki Kishimoto
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yukari Uemura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yosuke Shimizu
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Manabu Aoki
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kazuya Hasegawa
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Satoshi Suzuki
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Akie Nishiyama
- Department of Infectious Diseases, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Junji Saruwatari
- Division of Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yukiko Shimizu
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshikazu Sukenaga
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Yuki Takamatsu
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Kiyoto Tsuchiya
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kenji Maeda
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | | | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shogo Misumi
- Department of Environmental and Molecular Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
- The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Hirokazu Tamamura
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, NIH, Bethesda, MD, USA.
- Kumamoto University Hospital, Kumamoto, Japan.
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11
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Banerjee A, Gosavi S. Potential Self-Peptide Inhibitors of the SARS-CoV-2 Main Protease. J Phys Chem B 2023; 127:855-865. [PMID: 36689738 PMCID: PMC9883841 DOI: 10.1021/acs.jpcb.2c05917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/23/2022] [Indexed: 01/24/2023]
Abstract
The SARS-CoV-2 main protease (Mpro) plays an essential role in viral replication, cleaving viral polyproteins into functional proteins. This makes Mpro an important drug target. Mpro consists of an N-terminal catalytic domain and a C-terminal α-helical domain (MproC). Previous studies have shown that peptides derived from a given protein sequence (self-peptides) can affect the folding and, in turn, the function of that protein. Since the SARS-CoV-1 MproC is known to stabilize its Mpro and regulate its function, we hypothesized that SARS-CoV-2 MproC-derived self-peptides may modulate the folding and the function of SARS-CoV-2 Mpro. To test this, we studied the folding of MproC in the presence of various self-peptides using coarse-grained structure-based models and molecular dynamics simulations. In these simulations of MproC and one self-peptide, we found that two self-peptides, the α1-helix and the loop between α4 and α5 (loop4), could replace the equivalent native sequences in the MproC structure. Replacement of either sequence in full-length Mpro should, in principle, be able to perturb Mpro function albeit through different mechanisms. Some general principles for the rational design of self-peptide inhibitors emerge: The simulations show that prefolded self-peptides are more likely to replace native sequences than those which do not possess structure. Additionally, the α1-helix self-peptide is kinetically stable and once inserted rarely exchanges with the native α1-helix, while the loop4 self-peptide is easily replaced by the native loop4, making it less useful for modulating function. In summary, a prefolded α1-derived peptide should be able to inhibit SARS-CoV-2 Mpro function.
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Affiliation(s)
- Arkadeep Banerjee
- Simons Centre for the Study
of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study
of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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12
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ElSawy KM, Alminderej FM, Caves LSD. Disruption of 3CLpro protease self-association by short peptides as a potential route to broad spectrum coronavirus inhibitors. J Biomol Struct Dyn 2022; 40:13901-13911. [PMID: 34720051 DOI: 10.1080/07391102.2021.1996462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Coronaviruses have posed a persistent threat to human health over the last two decades. Despite the accumulated knowledge about coronavirus-related pathogens, development of an effective treatment for its new variant COVID-19 is highly challenging. For the highly-conserved and main coronavirus protease 3CLpro, dimerization is known to be essential for its catalytic activity and thereby for virus proliferation. Here, we assess the potential of short peptide segments to disrupt dimerization of the 3CLpro protease as a route to block COVID-19 proliferation. Based on the X-ray structure of the 3CLpro dimer, we identified the SPSGVY126QCAMRP dodecapeptide segment as overlapping the hotspot regions on the 3CLpro dimer interface. Using computational blind docking of the peptide to the 3CLpro monomer, we found that the SPSGVY126QCAMRP peptide has favourable thermodynamic binding (ΔG= -5.93 kcal/mol) to the hotspot regions at the 3CLpro dimer interface. Importantly, the peptide was also found to preferentially bind to the hotspot regions compared to other potential binding sites lying away from the dimer interface (ΔΔG=-1.31 kcal/mol). Docking of peptides corresponding to systematic mutation of the V125 and Y126 residues led to the identification of seven peptides, SPSGHAQCAMRP, SPSGVTQCAMRP, SPSGKPQCAMRP, SPSGATQCAMRP, SPSGWLQCAMRP, SPSGAPQCAMRP and SPSGHPQCAMRP, that outperform the wild-type SPSGVY126QCAMRP peptide in terms of preferential binding to the 3CLpro dimer interface. These peptides have the potential to disrupt 3CLpro dimerization and therefore could provide lead structures for the development of broad spectrum COVID-19 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karim M ElSawy
- Department of Chemistry, College of Science, Qassim University, Buraydah, Saudi Arabia.,York Cross-Disciplinary Centre for Systems Analysis (YCCSA), University of York, York, UK
| | - Fahad M Alminderej
- Department of Chemistry, College of Science, Qassim University, Buraydah, Saudi Arabia
| | - Leo S D Caves
- York Cross-Disciplinary Centre for Systems Analysis (YCCSA), University of York, York, UK.,Independent Researcher, São Felix da Marinha, Portugal
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13
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Zhou Y, Gammeltoft KA, Ryberg LA, Pham LV, Tjørnelund HD, Binderup A, Duarte Hernandez CR, Fernandez-Antunez C, Offersgaard A, Fahnøe U, Peters GHJ, Ramirez S, Bukh J, Gottwein JM. Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system. SCIENCE ADVANCES 2022; 8:eadd7197. [PMID: 36542720 PMCID: PMC9770952 DOI: 10.1126/sciadv.add7197] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from nirmatrelvir in cell culture. Resistant variants harbored combinations of substitutions in the SARS-CoV-2 main protease (Mpro). Reverse genetics revealed that E166V and L50F + E166V conferred high resistance in infectious culture, replicon, and Mpro systems. While L50F, E166V, and L50F + E166V decreased replication and Mpro activity, L50F and L50F + E166V variants had high fitness in the infectious system. Naturally occurring L50F compensated for fitness cost of E166V and promoted viral escape. Molecular dynamics simulations revealed that E166V and L50F + E166V weakened nirmatrelvir-Mpro binding. Polymerase inhibitor remdesivir and monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, and combination with nirmatrelvir enhanced treatment efficacy compared to individual compounds. These findings have implications for monitoring and ensuring treatments with efficacy against SARS-CoV-2 and emerging sarbecoviruses.
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Affiliation(s)
- Yuyong Zhou
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Karen Anbro Gammeltoft
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Line Abildgaard Ryberg
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Long V. Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Alekxander Binderup
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Carlos Rene Duarte Hernandez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anna Offersgaard
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Judith Margarete Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital–Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Corresponding author.
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14
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Zhou Y, Gammeltoft KA, Ryberg LA, Pham LV, Tjørnelund HD, Binderup A, Duarte Hernandez CR, Fernandez-Antunez C, Offersgaard A, Fahnøe U, Peters GHJ, Ramirez S, Bukh J, Gottwein JM. Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system. SCIENCE ADVANCES 2022; 8:eadd7197. [PMID: 36542720 DOI: 10.1101/2022.06.06.494921] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) escape from nirmatrelvir in cell culture. Resistant variants harbored combinations of substitutions in the SARS-CoV-2 main protease (Mpro). Reverse genetics revealed that E166V and L50F + E166V conferred high resistance in infectious culture, replicon, and Mpro systems. While L50F, E166V, and L50F + E166V decreased replication and Mpro activity, L50F and L50F + E166V variants had high fitness in the infectious system. Naturally occurring L50F compensated for fitness cost of E166V and promoted viral escape. Molecular dynamics simulations revealed that E166V and L50F + E166V weakened nirmatrelvir-Mpro binding. Polymerase inhibitor remdesivir and monoclonal antibody bebtelovimab retained activity against nirmatrelvir-resistant variants, and combination with nirmatrelvir enhanced treatment efficacy compared to individual compounds. These findings have implications for monitoring and ensuring treatments with efficacy against SARS-CoV-2 and emerging sarbecoviruses.
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Affiliation(s)
- Yuyong Zhou
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Karen Anbro Gammeltoft
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Line Abildgaard Ryberg
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Long V Pham
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Alekxander Binderup
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Carlos Rene Duarte Hernandez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anna Offersgaard
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ulrik Fahnøe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Judith Margarete Gottwein
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital-Hvidovre, 2650 Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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15
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Iketani S, Hong SJ, Sheng J, Bahari F, Culbertson B, Atanaki FF, Aditham AK, Kratz AF, Luck MI, Tian R, Goff SP, Montazeri H, Sabo Y, Ho DD, Chavez A. Functional map of SARS-CoV-2 3CL protease reveals tolerant and immutable sites. Cell Host Microbe 2022; 30:1354-1362.e6. [PMID: 36029764 PMCID: PMC9365866 DOI: 10.1016/j.chom.2022.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/20/2022] [Accepted: 08/05/2022] [Indexed: 01/03/2023]
Abstract
The SARS-CoV-2 3CL protease (3CLpro) is an attractive therapeutic target, as it is essential to the virus and highly conserved among coronaviruses. However, our current understanding of its tolerance to mutations is limited. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the 3CLpro and validate a subset of our results within authentic viruses. We reveal that the 3CLpro is highly malleable and is capable of tolerating mutations throughout the protein. Yet, we also identify specific residues that appear immutable, suggesting that these may be targets for future 3CLpro inhibitors. Finally, we utilize our screening as a basis to identify E166V as a resistance-conferring mutation against the clinically used 3CLpro inhibitor, nirmatrelvir. Collectively, the functional map presented herein may serve as a guide to better understand the biological properties of the 3CLpro and for drug development against coronaviruses.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Seo Jung Hong
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jenny Sheng
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Farideh Bahari
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Bruce Culbertson
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA; Medical Scientist Training Program, Columbia University Irving Medical Center, New York, NY, USA
| | - Fereshteh Fallah Atanaki
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Arjun K Aditham
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alexander F Kratz
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, USA
| | - Maria I Luck
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ruxiao Tian
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Stephen P Goff
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Hesam Montazeri
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Yosef Sabo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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16
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Wang YT, Liao JM, Lin WW, Li CC, Huang BC, Cheng TL, Chen TC. Structural insights into Nirmatrelvir (PF-07321332)-3C-like SARS-CoV-2 protease complexation: a ligand Gaussian accelerated molecular dynamics study. Phys Chem Chem Phys 2022; 24:22898-22904. [PMID: 36124909 DOI: 10.1039/d2cp02882d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coronavirus 3C-like protease (3CLpro) is found in SARS-CoV-2 virus, which causes COVID-19. 3CLpro controls virus replication and is a major target for target-based antiviral discovery. As reported by Pfizer, Nirmatrelvir (PF-07321332) is a competitive protein inhibitor and a clinical candidate for orally delivered medication. However, the binding mechanisms between Nirmatrelvir and 3CLpro complex structures remain unknown. This study incorporated ligand Gaussian accelerated molecular dynamics, the one-dimensional and two-dimensional potential of mean force, normal molecular dynamics, and Kramers' rate theory to determine the binding and dissociation rate constants (koff and kon) associated with the binding of the 3CLpro protein to the Nirmatrelvir inhibitor. The proposed approach addresses the challenges in designing small-molecule antiviral drugs.
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Affiliation(s)
- Yeng-Tseng Wang
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Taiwan. .,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Jun-Min Liao
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Wei Lin
- School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Taiwan. .,Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Ching Li
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Bo-Cheng Huang
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tian-Lu Cheng
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tun-Chieh Chen
- Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Taiwan
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17
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Hu Q, Xiong Y, Zhu G, Zhang Y, Zhang Y, Huang P, Ge G. The SARS-CoV-2 main protease (M pro): Structure, function, and emerging therapies for COVID-19. MedComm (Beijing) 2022; 3:e151. [PMID: 35845352 PMCID: PMC9283855 DOI: 10.1002/mco2.151] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/06/2022] [Accepted: 06/06/2022] [Indexed: 12/21/2022] Open
Abstract
The main proteases (Mpro), also termed 3-chymotrypsin-like proteases (3CLpro), are a class of highly conserved cysteine hydrolases in β-coronaviruses. Increasing evidence has demonstrated that 3CLpros play an indispensable role in viral replication and have been recognized as key targets for preventing and treating coronavirus-caused infectious diseases, including COVID-19. This review is focused on the structural features and biological function of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease Mpro (also known as 3CLpro), as well as recent advances in discovering and developing SARS-CoV-2 3CLpro inhibitors. To better understand the characteristics of SARS-CoV-2 3CLpro inhibitors, the inhibition activities, inhibitory mechanisms, and key structural features of various 3CLpro inhibitors (including marketed drugs, peptidomimetic, and non-peptidomimetic synthetic compounds, as well as natural compounds and their derivatives) are summarized comprehensively. Meanwhile, the challenges in this field are highlighted, while future directions for designing and developing efficacious 3CLpro inhibitors as novel anti-coronavirus therapies are also proposed. Collectively, all information and knowledge presented here are very helpful for understanding the structural features and inhibitory mechanisms of SARS-CoV-2 3CLpro inhibitors, which offers new insights or inspiration to medicinal chemists for designing and developing more efficacious 3CLpro inhibitors as novel anti-coronavirus agents.
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Affiliation(s)
- Qing Hu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Yuan Xiong
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Guang‐Hao Zhu
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Ya‐Ni Zhang
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
| | - Yi‐Wen Zhang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Ping Huang
- Clinical Pharmacy CenterCancer CenterDepartment of PharmacyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical College, HangzhouZhejiangChina
| | - Guang‐Bo Ge
- Shanghai Frontiers Science Center of TCM Chemical BiologyInstitute of Interdisciplinary Integrative Medicine ResearchShanghai University of Traditional Chinese MedicineShanghaiChina
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18
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Muhammad S, Amin S, Iqbal J, Al-Sehemi AG, Alarfaji SS, Ilyas M, Atif M, Ullah S. Insighting the Therapeutic Potential of Fifty (50) Shogaol Derivatives Against M pro of SARS-CoV-2. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022. [DOI: 10.1142/s273741652250020x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2, which causes COVID-19 disease, has proven to be a disastrous pandemic due to its contagious nature. This study has been planned to theoretically explore some antidotes against this virus from natural compounds. A total of 150 compounds from the shogaol class and shogaol derivatives (SDs) have been screened whereas 50 among those, which obeyed Lipinski’s Rule of Five (Ro5), have further been investigated using molecular docking techniques. Furthermore, reference antiviral drug chloroquine (ChQ) and Co-Crystallized inhibitor have also been studied against Mpro of SARS-CoV-2 for comparing the potential of our docked ligands. Surprisingly, 78% of our docked ligands have shown binding energies and inhibition constants lower than ChQ and all ligands showed these values lower than an inhibitor. We further visualized the nature of intermolecular interactions for the best docked six ligands, which have shown higher binding affinities. We have also assessed ADMET properties for three ligands that displayed visually the best intermolecular interactions. Quantum analysis of three selected ligands L4, L5, and L9 has proved their reactivity and kinetic stability. Moreover, molecular dynamic simulations over 60[Formula: see text]ns have been run for free Mpro and its selected three ligand-protein complexes for evaluating conformational stability and residual flexibility of docked complexes. Furthermore, 100[Formula: see text]ns the MD simulations have been performed for two ligand complexes L4, L5 (with negative binding free energy), and inhibitor. Available parameters suggest stable complexes for our ligands and could be active drugs against SARS-CoV-2 in near future.
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Affiliation(s)
- Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Saniyah Amin
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Abdullah G. Al-Sehemi
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Saleh S. Alarfaji
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
| | - Mubashar Ilyas
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Atif
- Department of Chemistry, University of Education, Lahore (Vehari Campus), Punjab, Pakistan
| | - Sami Ullah
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, P.O. Box 9004, Saudi Arabia
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19
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Boonamnaj P, Pandey R, Sompornpisut P. Effect of pH on stability of dimer structure of the main protease of coronavirus-2. Biophys Chem 2022; 287:106829. [PMID: 35635893 PMCID: PMC9119281 DOI: 10.1016/j.bpc.2022.106829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/04/2022] [Accepted: 05/14/2022] [Indexed: 02/09/2023]
Abstract
The viral main protease (Mpro) from a novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a key enzyme essential for viral replication and has become an attractive target for antiviral drug development. The Mpro forms a functional dimer and exhibits a pH-dependent enzyme activity and dimerization. Here, we report a molecular dynamics (MD) investigation to gain insights into the structural stability of the enzyme dimer at neutral and acidic pH. Our data shows larger changes in structure of the protein with the acidic pH than that with the neutral pH. Structural analysis of MD trajectories reveals a substantial increase in intersubunit separation, the loss of domain contacts, binding free energy and interaction energy of the dimer which implies the protein instability and tendency of dimer dissociation at acidic pH. The loss in the interaction energy is mainly driven by electrostatic interactions. We have identified the intersubunit hydrogen-bonding residues involved in the decreased dimer stability. These findings may be helpful for rational drug design and target evaluation against COVID-19.
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Affiliation(s)
- Panisak Boonamnaj
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - R.B. Pandey
- School of Mathematics and Natural Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pornthep Sompornpisut
- The Center of Excellence in Computational Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand,Corresponding author
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20
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Iketani S, Hong SJ, Sheng J, Bahari F, Culbertson B, Atanaki FF, Aditham AK, Kratz AF, Luck MI, Tian R, Goff SP, Montazeri H, Sabo Y, Ho DD, Chavez A. The Functional Landscape of SARS-CoV-2 3CL Protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.23.497404. [PMID: 35860222 PMCID: PMC9298129 DOI: 10.1101/2022.06.23.497404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) as the etiologic agent of COVID-19 (coronavirus disease 2019) has drastically altered life globally. Numerous efforts have been placed on the development of therapeutics to treat SARS-CoV-2 infection. One particular target is the 3CL protease (3CL pro ), which holds promise as it is essential to the virus and highly conserved among coronaviruses, suggesting that it may be possible to find broad inhibitors that treat not just SARS-CoV-2 but other coronavirus infections as well. While the 3CL protease has been studied by many groups for SARS-CoV-2 and other coronaviruses, our understanding of its tolerance to mutations is limited, knowledge which is particularly important as 3CL protease inhibitors become utilized clinically. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the SARS-CoV-2 3CL pro , and validate our results both in yeast and in authentic viruses. We reveal that the 3CL pro is highly malleable and is capable of tolerating mutations throughout the protein, including within the substrate binding pocket. Yet, we also identify specific residues that appear immutable for function of the protease, suggesting that these interactions may be novel targets for the design of future 3CL pro inhibitors. Finally, we utilize our screening results as a basis to identify E166V as a resistance-conferring mutation against the therapeutic 3CL pro inhibitor, nirmatrelvir, in clinical use. Collectively, the functional map presented herein may serve as a guide for further understanding of the biological properties of the 3CL protease and for drug development for current and future coronavirus pandemics.
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21
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Flynn JM, Samant N, Schneider-Nachum G, Barkan DT, Yilmaz NK, Schiffer CA, Moquin SA, Dovala D, Bolon DNA. Comprehensive fitness landscape of SARS-CoV-2 M pro reveals insights into viral resistance mechanisms. eLife 2022; 11:e77433. [PMID: 35723575 PMCID: PMC9323007 DOI: 10.7554/elife.77433] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
With the continual evolution of new strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that are more virulent, transmissible, and able to evade current vaccines, there is an urgent need for effective anti-viral drugs. The SARS-CoV-2 main protease (Mpro) is a leading target for drug design due to its conserved and indispensable role in the viral life cycle. Drugs targeting Mpro appear promising but will elicit selection pressure for resistance. To understand resistance potential in Mpro, we performed a comprehensive mutational scan of the protease that analyzed the function of all possible single amino acid changes. We developed three separate high throughput assays of Mpro function in yeast, based on either the ability of Mpro variants to cleave at a defined cut-site or on the toxicity of their expression to yeast. We used deep sequencing to quantify the functional effects of each variant in each screen. The protein fitness landscapes from all three screens were strongly correlated, indicating that they captured the biophysical properties critical to Mpro function. The fitness landscapes revealed a non-active site location on the surface that is extremely sensitive to mutation, making it a favorable location to target with inhibitors. In addition, we found a network of critical amino acids that physically bridge the two active sites of the Mpro dimer. The clinical variants of Mpro were predominantly functional in our screens, indicating that Mpro is under strong selection pressure in the human population. Our results provide predictions of mutations that will be readily accessible to Mpro evolution and that are likely to contribute to drug resistance. This complete mutational guide of Mpro can be used in the design of inhibitors with reduced potential of evolving viral resistance.
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Affiliation(s)
- Julia M Flynn
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Neha Samant
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Gily Schneider-Nachum
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - David T Barkan
- Novartis Institutes for Biomedical ResearchEmeryvilleUnited States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | | | - Dustin Dovala
- Novartis Institutes for Biomedical ResearchEmeryvilleUnited States
| | - Daniel NA Bolon
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical SchoolWorcesterUnited States
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22
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Production of a functionally active recombinant SARS-CoV-2 (COVID-19) 3C-Like protease and a soluble inactive 3C-like protease-RBD chimeric in a prokaryotic expression system. Epidemiol Infect 2022; 150:e128. [PMID: 35723031 PMCID: PMC9300977 DOI: 10.1017/s0950268822001078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) intracellular life-cycle, two large polyproteins, pp1a and pp1ab, are produced. Processing of these by viral cysteine proteases, the papain-like protease (PLpro) and the chymotrypsin-like 3C-like protease (3CL-pro) release non-structural proteins necessary for the establishment of the viral replication and transcription complex (RTC), crucial for viral replication. Hence, these proteases are considered prime targets against which anti-coronavirus disease 2019 (COVID-19) drugs could be developed. Here, we describe the expression of a highly soluble and functionally active recombinant 3CL-pro using Escherichia coli BL21 cells. We show that the enzyme functions in a dimeric form and exhibits an unexpected inhibitory profile because its activity is potently blocked by serine rather than cysteine protease inhibitors. In addition, we assessed the ability of our 3CL-pro to function as a carrier for the receptor binding domain (RBD) of the Spike protein. The co-expressed chimeric protein, 3CLpro-RBD, did not exhibit 3CL-pro activity, but its enhanced solubility made purification easier and improved RBD antigenicity when tested against serum from vaccinated individuals in ELISAs. Chimeric proteins containing the 3CL-pro could represent an innovative approach to developing new COVID-19 vaccines.
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23
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Glab-ampai K, Kaewchim K, Saenlom T, Thepsawat W, Mahasongkram K, Sookrung N, Chaicumpa W, Chulanetra M. Human Superantibodies to 3CL pro Inhibit Replication of SARS-CoV-2 across Variants. Int J Mol Sci 2022; 23:ijms23126587. [PMID: 35743031 PMCID: PMC9223907 DOI: 10.3390/ijms23126587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Broadly effective and safe anti-coronavirus agent is existentially needed. Major protease (3CLpro) is a highly conserved enzyme of betacoronaviruses. The enzyme plays pivotal role in the virus replication cycle. Thus, it is a good target of a broadly effective anti-Betacoronavirus agent. In this study, human single-chain antibodies (HuscFvs) of the SARS-CoV-2 3CLpro were generated using phage display technology. The 3CLpro-bound phages were used to infect Escherichia coli host for the production the 3CLpro-bound HuscFvs. Computerized simulation was used to guide the selection of the phage infected-E. coli clones that produced HuscFvs with the 3CLpro inhibitory potential. HuscFvs of three phage infected-E. coli clones were predicted to form contact interface with residues for 3CLpro catalytic activity, substrate binding, and homodimerization. These HuscFvs were linked to a cell-penetrating peptide to make them cell-penetrable, i.e., became superantibodies. The superantibodies blocked the 3CLpro activity in vitro, were not toxic to human cells, traversed across membrane of 3CLpro-expressing cells to co-localize with the intracellular 3CLpro and most of all, they inhibited replication of authentic SARS-CoV-2 Wuhan wild type and α, β, δ, and Omicron variants that were tested. The superantibodies should be investigated further towards clinical application as a safe and broadly effective anti-Betacoronavirus agent.
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Affiliation(s)
- Kittirat Glab-ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Kanasap Kaewchim
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Thanatsaran Saenlom
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Watayagorn Thepsawat
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Kodchakorn Mahasongkram
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Nitat Sookrung
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
| | - Monrat Chulanetra
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.G.-a.); (K.K.); (T.S.); (W.T.); (K.M.); (N.S.); (W.C.)
- Correspondence: ; Tel.: +662-419-2934
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24
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Ferreira JC, Fadl S, Rabeh WM. Key dimer interface residues impact the catalytic activity of 3CLpro, the main protease of SARS-CoV-2. J Biol Chem 2022; 298:102023. [PMID: 35568197 PMCID: PMC9091064 DOI: 10.1016/j.jbc.2022.102023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
3C-like protease (3CLpro) is one of two proteases that process and liberate functional viral proteins essential for the maturation and infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. It has been suggested that 3CLpro is catalytically active as a dimer, making the dimerization interface a target for antiviral development. Guided by structural analysis, here we introduced single amino acid substitutions at nine residues at three key sites of the dimer interface to assess their impact on dimerization and activity. We show that at site 1, alanine substitution of S1 or E166 increased by 2-fold or reduced relative activity, respectively. At site 2, alanine substitution of S10 or E14 eliminated activity, whereas K12A exhibited ∼60% relative activity. At site 3, alanine substitution of R4, E290, or Q299 eliminated activity, whereas S139A exhibited 46% relative activity. We further found the oligomerization states of the dimer interface mutants varied; the inactive mutants R4A, R4Q, S10A/C, E14A/D/Q/S, E290A, and Q299A/E were present as dimers, demonstrating that dimerization is not an indication of catalytically active 3CLpro. In addition, present mostly as monomers, K12A displayed residual activity, which could be attributed to the conspicuous amount of dimer present. Finally, differential scanning calorimetry did not reveal a direct relationship between the thermodynamic stability of mutants with oligomerization or catalytic activity. These results provide insights on two allosteric sites, R4/E290 and S10/E14, that may promote the design of antiviral compounds that target the dimer interface rather than the active site of SARS-CoV-2 3CLpro.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
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25
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Padhi AK, Tripathi T. High-throughput design of symmetrical dimeric SARS-CoV-2 main protease: structural and physical insights into hotspots for adaptation and therapeutics. Phys Chem Chem Phys 2022; 24:9141-9145. [PMID: 35411366 DOI: 10.1039/d2cp00171c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Dimerization of SARS-CoV-2 main protease (Mpro) is a prerequisite for its processing activity. With >2000 mutations already reported in Mpro, SARS-CoV-2 may accumulate mutations in the Mpro dimeric interface to stabilize it further. We employed high-throughput protein design strategies to design the symmetrical dimeric interface of Mpro (300 000 designs) to identify mutational hotspots that render the Mpro more stable. We found that ∼22% of designed mutations that yield stable Mpro dimers already exist in SARS-CoV-2 genomes and are currently circulating. Our multi-parametric analyses highlight potential Mpro mutations that SARS-CoV-2 may develop, providing a foundation for assessing viral adaptation and mutational surveillance.
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Affiliation(s)
- Aditya K Padhi
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa 230-0045, Japan.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong - 793022, India.
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Abstract
SignificanceThe coronavirus main protease (Mpro) is required for viral replication. Here, we obtained the extended conformation of the native monomer of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Mpro by trapping it with nanobodies and found that the catalytic domain and the helix domain dissociate, revealing allosteric targets. Another monomeric state is termed compact conformation and is similar to one protomer of the dimeric form. We designed a Nanoluc Binary Techonology (NanoBiT)-based high-throughput allosteric inhibitor assay based on structural conformational change. Our results provide insight into the maturation, dimerization, and catalysis of the coronavirus Mpro and pave a way to develop an anticoronaviral drug through targeting the maturation process to inhibit the autocleavage of Mpro.
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Zhang Y, Zheng L, Yang Y, Qu Y, Li YQ, Zhao M, Mu Y, Li W. Structural and energetic features of the dimerization of the main proteinase of SARS-CoV-2 using molecular dynamic simulations. Phys Chem Chem Phys 2022; 24:4324-4333. [PMID: 35107451 DOI: 10.1039/d1cp04630f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has been declared a global health crisis. The development of anti-SARS-CoV-2 drugs heavily depends on the systematic study of the critical biological processes of key proteins of coronavirus among which the main proteinase (Mpro) dimerization is a key step for virus maturation. Because inhibiting the Mpro dimerization can efficiently suppress virus maturation, the key residues that mediate dimerization can be treated as targets of drug and antibody developments. In this work, the structure and energy features of the Mpro dimer of SARS-CoV-2 and SARS-CoV were studied using molecular dynamics (MD) simulations. The free energy calculations using the Generalized Born (GB) model showed that the dimerization free energy of the SARS-CoV-2 Mpro dimer (-107.5 ± 10.89 kcal mol-1) is larger than that of the SARS-CoV Mpro dimer (-92.83 ± 9.81 kcal mol-1), indicating a more stable and possibly a quicker formation of the Mpro dimer of SARS-CoV-2. In addition, the energy decomposition of each residue revealed 11 key attractive residues. Furthermore, Thr285Ala weakens the steric hindrance between the two protomers of SARS-CoV-2 that can form more intimate interactions. It is interesting to find 11 repulsive residues which effectively inhibit the dimerization process. At the interface of the Mpro dimer, we detected three regions that are rich in interfacial water which stabilize the SARS-CoV-2 Mpro dimer by forming hydrogen bonds with two protomers. The key residues and rich water regions provide important targets for the future design of anti-SARS-CoV-2 drugs through inhibiting Mpro dimerization.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | | | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | - Yong-Qiang Li
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | - Mingwen Zhao
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637650, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, Shandong, 250100, China.,National Demonstration Center for Experimental Physics Education, Shandong University, China.
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Pro108Ser mutation of SARS-CoV-2 3CL pro reduces the enzyme activity and ameliorates the clinical severity of COVID-19. Sci Rep 2022; 12:1299. [PMID: 35079088 PMCID: PMC8789791 DOI: 10.1038/s41598-022-05424-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, an international randomized controlled clinical trial showed that patients with SARS-CoV-2 infection treated orally with the 3-chymotrypsin-like protease (3CLpro) inhibitor PF-07321332 within three days of symptom onset showed an 89% lower risk of COVID-19-related hospital admission/ death from any cause as compared with the patients who received placebo. Lending support to this critically important result of the aforementioned trial, we demonstrated in our study that patients infected with a SARS-Cov-2 sub-lineage (B.1.1.284) carrying the Pro108Ser mutation in 3CLpro tended to have a comparatively milder clinical course (i.e., a smaller proportion of patients required oxygen supplementation during the clinical course) than patients infected with the same sub-lineage of virus not carrying the mutation. Characterization of the mutant 3CLpro revealed that the Kcat/Km of the 3CLpro enzyme containing Ser108 was 58% lower than that of Pro108 3CLpro. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) revealed that the reduced activity was associated with structural perturbation surrounding the substrate-binding region of the enzyme, which is positioned behind and distant from the 108th amino acid residue. Our findings of the attenuated clinical course of COVID-19 in patients infected with SARS-CoV-2 strains with reduced 3CLpro enzymatic activity greatly endorses the promising result of the aforementioned clinical trial of the 3CLpro inhibitor.
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In silico evidence of beauvericin antiviral activity against SARS-CoV-2. Comput Biol Med 2021; 141:105171. [PMID: 34968860 PMCID: PMC8709726 DOI: 10.1016/j.compbiomed.2021.105171] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022]
Abstract
Background Scientists are still battling severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus 2019 (COVID-19) pandemic so human lives can be saved worldwide. Secondary fungal metabolites are of intense interest due to their broad range of pharmaceutical properties. Beauvericin (BEA) is a secondary metabolite produced by the fungus Beauveria bassiana. Although promising anti-viral activity has previously been reported for BEA, studies investigating its therapeutic potential are limited. Methods The objective of this study was to assess the potential usage of BEA as an anti-viral molecule via protein–protein docking approaches using MolSoft. Results In-silico results revealed relatively favorable binding energies for BEA to different viral proteins implicated in the vital life stages of this virus. Of particular interest is the capability of BEA to dock to both the main coronavirus protease (Pockets A and B) and spike proteins. These results were validated by molecular dynamic simulation (Gromacs). Several parameters, such as root-mean-square deviation/fluctuation, the radius of gyration, H-bonding, and free binding energy were analyzed. Computational analyses revealed that interaction of BEA with the main protease pockets in addition to the spike glycoprotein remained stable. Conclusion Altogether, our results suggest that BEA might be considered as a potential competitive and allosteric agonist inhibitor with therapeutic options for treating COVID-19 pending in vitro and in vivo validation.
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Razali R, Asis H, Budiman C. Structure-Function Characteristics of SARS-CoV-2 Proteases and Their Potential Inhibitors from Microbial Sources. Microorganisms 2021; 9:2481. [PMID: 34946083 PMCID: PMC8706127 DOI: 10.3390/microorganisms9122481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is considered the greatest challenge to the global health community of the century as it continues to expand. This has prompted immediate urgency to discover promising drug targets for the treatment of COVID-19. The SARS-CoV-2 viral proteases, 3-chymotrypsin-like protease (3CLpro) and papain-like cysteine protease (PLpro), have become the promising target to study due to their essential functions in spreading the virus by RNA transcription, translation, protein synthesis, processing and modification, virus replication, and infection of the host. As such, understanding of the structure and function of these two proteases is unavoidable as platforms for the development of inhibitors targeting this protein which further arrest the infection and spread of the virus. While the abundance of reports on the screening of natural compounds such as SARS-CoV-2 proteases inhibitors are available, the microorganisms-based compounds (peptides and non-peptides) remain less studied. Indeed, microorganisms-based compounds are also one of the potent antiviral candidates against COVID-19. Microbes, especially bacteria and fungi, are other resources to produce new drugs as well as nucleosides, nucleotides, and nucleic acids. Thus, we have compiled various reported literature in detail on the structures, functions of the SARS-CoV-2 proteases, and potential inhibitors from microbial sources as assistance to other researchers working with COVID-19. The compounds are also compared to HIV protease inhibitors which suggested the microorganisms-based compounds are advantageous as SARS-CoV2 proteases inhibitors. The information should serve as a platform for further development of COVID-19 drug design strategies.
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Affiliation(s)
| | | | - Cahyo Budiman
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia; (R.R.); (H.A.)
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Arutyunova E, Khan MB, Fischer C, Lu J, Lamer T, Vuong W, van Belkum MJ, McKay RT, Tyrrell DL, Vederas JC, Young HS, Lemieux MJ. N-Terminal Finger Stabilizes the S1 Pocket for the Reversible Feline Drug GC376 in the SARS-CoV-2 M pro Dimer. J Mol Biol 2021; 433:167003. [PMID: 33895266 PMCID: PMC8061786 DOI: 10.1016/j.jmb.2021.167003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 12/24/2022]
Abstract
The main protease (Mpro, also known as 3CL protease) of SARS-CoV-2 is a high priority drug target in the development of antivirals to combat COVID-19 infections. A feline coronavirus antiviral drug, GC376, has been shown to be effective in inhibiting the SARS-CoV-2 main protease and live virus growth. As this drug moves into clinical trials, further characterization of GC376 with the main protease of coronaviruses is required to gain insight into the drug's properties, such as reversibility and broad specificity. Reversibility is an important factor for therapeutic proteolytic inhibitors to prevent toxicity due to off-target effects. Here we demonstrate that GC376 has nanomolar Ki values with the Mpro from both SARS-CoV-2 and SARS-CoV strains. Restoring enzymatic activity after inhibition by GC376 demonstrates reversible binding with both proteases. In addition, the stability and thermodynamic parameters of both proteases were studied to shed light on physical chemical properties of these viral enzymes, revealing higher stability for SARS-CoV-2 Mpro. The comparison of a new X-ray crystal structure of Mpro from SARS-CoV complexed with GC376 reveals similar molecular mechanism of inhibition compared to SARS-CoV-2 Mpro, and gives insight into the broad specificity properties of this drug. In both structures, we observe domain swapping of the N-termini in the dimer of the Mpro, which facilitates coordination of the drug's P1 position. These results validate that GC376 is a drug with an off-rate suitable for clinical trials.
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Affiliation(s)
- Elena Arutyunova
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - Muhammad Bashir Khan
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Conrad Fischer
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Jimmy Lu
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - Tess Lamer
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Wayne Vuong
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Marco J van Belkum
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Ryan T McKay
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
| | - John C Vederas
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton T6G 2G2, Alberta, Canada
| | - Howard S Young
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada.
| | - M Joanne Lemieux
- Department of Biochemistry, Faculty of Medicine and Dentistry, Membrane Protein Disease Research Group, University of Alberta, Edmonton T6G 2R3, Alberta, Canada; Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton T6G 2E1, Alberta, Canada.
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32
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Ferreira JC, Fadl S, Villanueva AJ, Rabeh WM. Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease. Front Chem 2021; 9:692168. [PMID: 34249864 PMCID: PMC8264439 DOI: 10.3389/fchem.2021.692168] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/14/2021] [Indexed: 01/18/2023] Open
Abstract
Coronaviruses are responsible for multiple pandemics and millions of deaths globally, including the current pandemic of coronavirus disease 2019 (COVID-19). Development of antivirals against coronaviruses, including the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) responsible for COVID-19, is essential for containing the current and future coronavirus outbreaks. SARS-CoV-2 proteases represent important targets for the development of antivirals because of their role in the processing of viral polyproteins. 3-Chymotrypsin-like protease (3CLpro) is one such protease. The cleavage of SARS-CoV-2 polyproteins by 3CLpro is facilitated by a Cys145–His41 catalytic dyad. We here characterized the catalytic roles of the cysteine–histidine pair for improved understanding of the 3CLpro reaction mechanism, to inform the development of more effective antivirals against Sars-CoV-2. The catalytic dyad residues were substituted by site-directed mutagenesis. All substitutions tested (H41A, H41D, H41E, C145A, and C145S) resulted in a complete inactivation of 3CLpro, even when amino acids with a similar catalytic function to that of the original residues were used. The integrity of the structural fold of enzyme variants was investigated by circular dichroism spectroscopy to test if the catalytic inactivation of 3CLpro was caused by gross changes in the enzyme secondary structure. C145A, but not the other substitutions, shifted the oligomeric state of the enzyme from dimeric to a higher oligomeric state. Finally, the thermodynamic stability of 3CLpro H41A, H41D, and C145S variants was reduced relative the wild-type enzyme, with a similar stability of the H41E and C145A variants. Collectively, the above observations confirm the roles of His41 and Cys145 in the catalytic activity and the overall conformational fold of 3CLpro SARS-CoV-2. We conclude that the cysteine–histidine pair should be targeted for inhibition of 3CLpro and development of antiviral against COVID-19 and coronaviruses.
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Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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33
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Kumari A, Mittal L, Srivastava M, Asthana S. Binding mode characterization of 13b in the monomeric and dimeric states of SARS-CoV-2 main protease using molecular dynamics simulations. J Biomol Struct Dyn 2021; 40:9287-9305. [PMID: 34029506 DOI: 10.1080/07391102.2021.1927844] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The main protease, Mpro/3CLpro, plays an essential role in processing polyproteins translated from viral RNA to produce functional viral proteins and therefore serve as an attractive target for discovering COVID-19 therapeutics. The availability of both monomer and dimer crystal bound with a common ligand, '13b' (α-ketoamide inhibitor), opened up opportunities to understand the Mpro mechanism of action. A comparative analysis of both forms of Mpro was carried out to elucidate the binding site architectural differences in the presence and absence of '13b'. Molecular dynamics simulations suggest that the presence of '13b' enhances the stability of Mpro than the unbound APO form. The N- and C- terminals of both the protomers stabilize each other, and making it's interface essential for the active form of Mpro. In comparison to monomer, the relatively high affinity of '13b' is gained in dimer pocket due to the high stability of the pocket by the interaction of S1 residue of chain B with residues F140, E166 and H172 of chain A, which is absent in monomer. The comprehensive essential dynamics, protein structure network analysis and thermodynamic profiling highlight the hot-spots, pivotal in molecular recognition process at protein-ligand and protein-protein interaction levels, cross-validated through computational alanine scanning study. A comparative description of '13b' binding mechanism in both forms illustrates valuable insights into the inhibition mechanism and the selection of critical residues suitable for the structure-based approaches for the identification of more potent Mpro inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anita Kumari
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India
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34
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Yan S, Wu G. Potential 3-chymotrypsin-like cysteine protease cleavage sites in the coronavirus polyproteins pp1a and pp1ab and their possible relevance to COVID-19 vaccine and drug development. FASEB J 2021; 35:e21573. [PMID: 33913206 PMCID: PMC8206714 DOI: 10.1096/fj.202100280rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus (CoV) 3-chymotrypsin (C)-like cysteine protease (3CLpro ) is a target for anti-CoV drug development and drug repurposing because along with papain-like protease, it cleaves CoV-encoded polyproteins (pp1a and pp1ab) into nonstructural proteins (nsps) for viral replication. However, the cleavage sites of 3CLpro and their relevant nsps remain unclear, which is the subject of this perspective. Here, we address the subject from three standpoints. First, we explore the inconsistency in the cleavage sites and relevant nsps across CoVs, and investigate the function of nsp11. Second, we consider the nsp16 mRNA overlapping of the spike protein mRNA, and analyze the effect of this overlapping on mRNA vaccines. Finally, we study nsp12, whose existence depends on ribosomal frameshifting, and investigate whether 3CLpro requires a large number of inhibitors to achieve full inhibition. This perspective helps us to clarify viral replication and is useful for developing anti-CoV drugs with 3CLpro as a target in the current coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
| | - Guang Wu
- National Engineering Research Center for Non‐Food Biorefinery, State Key Laboratory of Non‐Food Biomass and Enzyme Technology, Guangxi Biomass Engineering Technology Research Center, Guangxi Key Laboratory of BiorefineryGuangxi Academy of SciencesNanningChina
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35
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Xiong M, Su H, Zhao W, Xie H, Shao Q, Xu Y. What coronavirus 3C-like protease tells us: From structure, substrate selectivity, to inhibitor design. Med Res Rev 2021; 41:1965-1998. [PMID: 33460213 PMCID: PMC8014231 DOI: 10.1002/med.21783] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 12/17/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
The emergence of a variety of coronaviruses (CoVs) in the last decades has posed huge threats to human health. Especially, the ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to more than 70 million infections and over 1.6 million of deaths worldwide in the past few months. None of the efficacious antiviral agents against human CoVs have been approved yet. 3C-like protease (3CLpro ) is an attractive target for antiviral intervention due to its essential role in processing polyproteins translated from viral RNA, and its conserved structural feature and substrate specificity among CoVs in spite of the sequence variation. This review focuses on all available crystal structures of 12 CoV 3CLpro s and their inhibitors, and intends to provide a comprehensive understanding of this protease from multiple aspects including its structural features, substrate specificity, inhibitor binding modes, and more importantly, to recapitulate the similarity and diversity among different CoV 3CLpro s and the structure-activity relationship of various types of inhibitors. Such an attempt could gain a deep insight into the inhibition mechanisms and drive future structure-based drug discovery targeting 3CLpro s.
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Affiliation(s)
- Muya Xiong
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haixia Su
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenfeng Zhao
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hang Xie
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Shao
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
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36
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El‐Baba TJ, Lutomski CA, Kantsadi AL, Malla TR, John T, Mikhailov V, Bolla JR, Schofield CJ, Zitzmann N, Vakonakis I, Robinson CV. Allosteric Inhibition of the SARS-CoV-2 Main Protease: Insights from Mass Spectrometry Based Assays*. Angew Chem Int Ed Engl 2020; 59:23544-23548. [PMID: 32841477 PMCID: PMC7461284 DOI: 10.1002/anie.202010316] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/20/2020] [Indexed: 12/14/2022]
Abstract
The SARS-CoV-2 main protease (Mpro ) cleaves along the two viral polypeptides to release non-structural proteins required for viral replication. MPro is an attractive target for antiviral therapies to combat the coronavirus-2019 disease. Here, we used native mass spectrometry to characterize the functional unit of Mpro . Analysis of the monomer/dimer equilibria reveals a dissociation constant of Kd =0.14±0.03 μM, indicating MPro has a strong preference to dimerize in solution. We characterized substrate turnover rates by following temporal changes in the enzyme-substrate complexes, and screened small molecules, that bind distant from the active site, for their ability to modulate activity. These compounds, including one proposed to disrupt the dimer, slow the rate of substrate processing by ≈35 %. This information, together with analysis of the x-ray crystal structures, provides a starting point for the development of more potent molecules that allosterically regulate MPro activity.
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Affiliation(s)
- Tarick J. El‐Baba
- Physical and Theoretical Chemistry LaboratoryUniversity of OxfordSouth Parks Rd.OX1 3QZOxfordUK
| | - Corinne A. Lutomski
- Physical and Theoretical Chemistry LaboratoryUniversity of OxfordSouth Parks Rd.OX1 3QZOxfordUK
| | | | - Tika R. Malla
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RdOX1 3TAOxfordUK
| | - Tobias John
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RdOX1 3TAOxfordUK
| | - Victor Mikhailov
- Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RdOX1 3TAOxfordUK
| | - Jani R. Bolla
- Physical and Theoretical Chemistry LaboratoryUniversity of OxfordSouth Parks Rd.OX1 3QZOxfordUK
| | | | - Nicole Zitzmann
- Department of BiochemistryUniversity of OxfordSouth Parks Rd.OX1 3QUOxfordUK
| | - Ioannis Vakonakis
- Department of BiochemistryUniversity of OxfordSouth Parks Rd.OX1 3QUOxfordUK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry LaboratoryUniversity of OxfordSouth Parks Rd.OX1 3QZOxfordUK
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37
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Liu XH, Zhang X, Lu ZH, Zhu YS, Wang T. Potential molecular targets of nonstructural proteins for the development of antiviral drugs against SARS-CoV-2 infection. Biomed Pharmacother 2020; 133:111035. [PMID: 33254013 PMCID: PMC7671653 DOI: 10.1016/j.biopha.2020.111035] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 02/08/2023] Open
Abstract
The pandemic of SARS-CoV-2 has posed significant threats to public health worldwide. Target-based drug development is a promising approach against SARS-CoV-2 infection. Nonstructural proteins may play critical roles from drug design perspectives. Insights into NSPs of different viruses could streamline novel drug development.
Outbreaks of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2 have produced high pathogenicity and mortality rates in human populations. However, to meet the increasing demand for treatment of these pathogenic coronaviruses, accelerating novel antiviral drug development as much as possible has become a public concern. Target-based drug development may be a promising approach to achieve this goal. In this review, the relevant features of potential molecular targets in human coronaviruses (HCoVs) are highlighted, including the viral protease, RNA-dependent RNA polymerase, and methyltransferases. Additionally, recent advances in the development of antivirals based on these targets are summarized. This review is expected to provide new insights and potential strategies for the development of novel antiviral drugs to treat SARS-CoV-2 infection.
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Affiliation(s)
- Xiao-Huan Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Xiao Zhang
- School of Biological Science, Jining Medical University, Jining, China
| | - Zhen-Hua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - You-Shuang Zhu
- School of Biological Science, Jining Medical University, Jining, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Jining, China.
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38
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El‐Baba TJ, Lutomski CA, Kantsadi AL, Malla TR, John T, Mikhailov V, Bolla JR, Schofield CJ, Zitzmann N, Vakonakis I, Robinson CV. Allosteric Inhibition of the SARS‐CoV‐2 Main Protease: Insights from Mass Spectrometry Based Assays**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tarick J. El‐Baba
- Physical and Theoretical Chemistry Laboratory University of Oxford South Parks Rd. OX1 3QZ Oxford UK
| | - Corinne A. Lutomski
- Physical and Theoretical Chemistry Laboratory University of Oxford South Parks Rd. OX1 3QZ Oxford UK
| | | | - Tika R. Malla
- Chemistry Research Laboratory University of Oxford 12 Mansfield Rd OX1 3TA Oxford UK
| | - Tobias John
- Chemistry Research Laboratory University of Oxford 12 Mansfield Rd OX1 3TA Oxford UK
| | - Victor Mikhailov
- Chemistry Research Laboratory University of Oxford 12 Mansfield Rd OX1 3TA Oxford UK
| | - Jani R. Bolla
- Physical and Theoretical Chemistry Laboratory University of Oxford South Parks Rd. OX1 3QZ Oxford UK
| | | | - Nicole Zitzmann
- Department of Biochemistry University of Oxford South Parks Rd. OX1 3QU Oxford UK
| | - Ioannis Vakonakis
- Department of Biochemistry University of Oxford South Parks Rd. OX1 3QU Oxford UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory University of Oxford South Parks Rd. OX1 3QZ Oxford UK
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Douangamath A, Fearon D, Gehrtz P, Krojer T, Lukacik P, Owen CD, Resnick E, Strain-Damerell C, Aimon A, Ábrányi-Balogh P, Brandão-Neto J, Carbery A, Davison G, Dias A, Downes TD, Dunnett L, Fairhead M, Firth JD, Jones SP, Keeley A, Keserü GM, Klein HF, Martin MP, Noble MEM, O'Brien P, Powell A, Reddi RN, Skyner R, Snee M, Waring MJ, Wild C, London N, von Delft F, Walsh MA. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun 2020; 11:5047. [PMID: 33028810 PMCID: PMC7542442 DOI: 10.1038/s41467-020-18709-w] [Citation(s) in RCA: 306] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.
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Affiliation(s)
- Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Paul Gehrtz
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Efrat Resnick
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anna Carbery
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Gemma Davison
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Thomas D Downes
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael Fairhead
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - James D Firth
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - S Paul Jones
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - György M Keserü
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Hanna F Klein
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Mathew P Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Martin E M Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Ailsa Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Rambabu N Reddi
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Matthew Snee
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Conor Wild
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Nir London
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa.
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
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40
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Goyal B, Goyal D. Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy. ACS COMBINATORIAL SCIENCE 2020; 22:297-305. [PMID: 32402186 PMCID: PMC7252589 DOI: 10.1021/acscombsci.0c00058] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/13/2020] [Indexed: 12/12/2022]
Abstract
A new coronavirus (CoV) caused a pandemic named COVID-19, which has become a global health care emergency in the present time. The virus is referred to as SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) and has a genome similar (∼82%) to that of the previously known SARS-CoV (SARS coronavirus). An attractive therapeutic target for CoVs is the main protease (Mpro) or 3-chymotrypsin-like cysteine protease (3CLpro), as this enzyme plays a key role in polyprotein processing and is active in a dimeric form. Further, Mpro is highly conserved among various CoVs, and a mutation in Mpro is often lethal to the virus. Thus, drugs targeting the Mpro enzyme significantly reduce the risk of mutation-mediated drug resistance and display broad-spectrum antiviral activity. The combinatorial design of peptide-based inhibitors targeting the dimerization of SARS-CoV Mpro represents a potential therapeutic strategy. In this regard, we have compiled the literature reports highlighting the effect of mutations and N-terminal deletion of residues of SARS-CoV Mpro on its dimerization and, thus, catalytic activity. We believe that the present review will stimulate research in this less explored yet quite significant area. The effect of the COVID-19 epidemic and the possibility of future CoV outbreaks strongly emphasize the urgent need for the design and development of potent antiviral agents against CoV infections.
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Affiliation(s)
- Bhupesh Goyal
- School of Chemistry & Biochemistry,
Thapar Institute of Engineering & Technology,
Patiala-147004, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied
Sciences, Sri Guru Granth Sahib World University, Fatehgarh
Sahib-140406, Punjab, India
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41
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Chen YW, Yiu CPB, Wong KY. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Res 2020; 9:129. [PMID: 32194944 PMCID: PMC7062204 DOI: 10.12688/f1000research.22457.1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL pro) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CL pro molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.
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Affiliation(s)
- Yu Wai Chen
- Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong
- State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong
| | | | - Kwok-Yin Wong
- Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong
- State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong
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42
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Chen YW, Yiu CPB, Wong KY. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates. F1000Res 2020; 9:129. [PMID: 32194944 PMCID: PMC7062204 DOI: 10.12688/f1000research.22457.2] [Citation(s) in RCA: 295] [Impact Index Per Article: 73.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/02/2020] [Indexed: 01/26/2023] Open
Abstract
We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL pro) using the crystal structure of the highly similar (96% identity) ortholog from the SARS-CoV. All residues involved in the catalysis, substrate binding and dimerisation are 100% conserved. Comparison of the polyprotein PP1AB sequences showed 86% identity. The 3C-like cleavage sites on the coronaviral polyproteins are highly conserved. Based on the near-identical substrate specificities and high sequence identities, we are of the opinion that some of the previous progress of specific inhibitors development for the SARS-CoV enzyme can be conferred on its SARS-CoV-2 counterpart. With the 3CL pro molecular model, we performed virtual screening for purchasable drugs and proposed 16 candidates for consideration. Among these, the antivirals ledipasvir or velpatasvir are particularly attractive as therapeutics to combat the new coronavirus with minimal side effects, commonly fatigue and headache. The drugs Epclusa (velpatasvir/sofosbuvir) and Harvoni (ledipasvir/sofosbuvir) could be very effective owing to their dual inhibitory actions on two viral enzymes.
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Affiliation(s)
- Yu Wai Chen
- Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong
- State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong
| | | | - Kwok-Yin Wong
- Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hunghom, Hong Kong
- State Key Laboratory of Chemical Biology and Drug Discovery, Hunghom, Hong Kong
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43
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SARS-CoV 3CL protease cleaves its C-terminal autoprocessing site by novel subsite cooperativity. Proc Natl Acad Sci U S A 2016; 113:12997-13002. [PMID: 27799534 DOI: 10.1073/pnas.1601327113] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 3C-like protease (3CLpro) of severe acute respiratory syndrome coronavirus (SARS-CoV) cleaves 11 sites in the polyproteins, including its own N- and C-terminal autoprocessing sites, by recognizing P4-P1 and P1'. In this study, we determined the crystal structure of 3CLpro with the C-terminal prosequence and the catalytic-site C145A mutation, in which the enzyme binds the C-terminal prosequence of another molecule. Surprisingly, Phe at the P3' position [Phe(P3')] is snugly accommodated in the S3' pocket. Mutations of Phe(P3') impaired the C-terminal autoprocessing, but did not affect N-terminal autoprocessing. This difference was ascribed to the P2 residue, Phe(P2) and Leu(P2), in the C- and N-terminal sites, as follows. The S3' subsite is formed by Phe(P2)-induced conformational changes of 3CLpro and the direct involvement of Phe(P2) itself. In contrast, the N-terminal prosequence with Leu(P2) does not cause such conformational changes for the S3' subsite formation. In fact, the mutation of Phe(P2) to Leu in the C-terminal autoprocessing site abolishes the dependence on Phe(P3'). These mechanisms explain why Phe is required at the P3' position when the P2 position is occupied by Phe rather than Leu, which reveals a type of subsite cooperativity. Moreover, the peptide consisting of P4-P1 with Leu(P2) inhibits protease activity, whereas that with Phe(P2) exhibits a much smaller inhibitory effect, because Phe(P3') is missing. Thus, this subsite cooperativity likely exists to avoid the autoinhibition of the enzyme by its mature C-terminal sequence, and to retain the efficient C-terminal autoprocessing by the use of Phe(P2).
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44
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Laitinen OH, Svedin E, Kapell S, Nurminen A, Hytönen VP, Flodström-Tullberg M. Enteroviral proteases: structure, host interactions and pathogenicity. Rev Med Virol 2016; 26:251-67. [PMID: 27145174 PMCID: PMC7169145 DOI: 10.1002/rmv.1883] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/22/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022]
Abstract
Enteroviruses are common human pathogens, and infections are particularly frequent in children. Severe infections can lead to a variety of diseases, including poliomyelitis, aseptic meningitis, myocarditis and neonatal sepsis. Enterovirus infections have also been implicated in asthmatic exacerbations and type 1 diabetes. The large disease spectrum of the closely related enteroviruses may be partially, but not fully, explained by differences in tissue tropism. The molecular mechanisms by which enteroviruses cause disease are poorly understood, but there is increasing evidence that the two enteroviral proteases, 2Apro and 3Cpro, are important mediators of pathology. These proteases perform the post‐translational proteolytic processing of the viral polyprotein, but they also cleave several host‐cell proteins in order to promote the production of new virus particles, as well as to evade the cellular antiviral immune responses. Enterovirus‐associated processing of cellular proteins may also contribute to pathology, as elegantly demonstrated by the 2Apro‐mediated cleavage of dystrophin in cardiomyocytes contributing to Coxsackievirus‐induced cardiomyopathy. It is likely that improved tools to identify targets for these proteases will reveal additional host protein substrates that can be linked to specific enterovirus‐associated diseases. Here, we discuss the function of the enteroviral proteases in the virus replication cycle and review the current knowledge regarding how these proteases modulate the infected cell in order to favour virus replication, including ways to avoid detection by the immune system. We also highlight new possibilities for the identification of protease‐specific cellular targets and thereby a way to discover novel mechanisms contributing to disease. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Olli H Laitinen
- BioMediTech, Finland and Fimlab Laboratories, University of Tampere, Tampere, Finland
| | - Emma Svedin
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Stockholm, Sweden
| | - Sebastian Kapell
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Stockholm, Sweden
| | - Anssi Nurminen
- BioMediTech, Finland and Fimlab Laboratories, University of Tampere, Tampere, Finland
| | - Vesa P Hytönen
- BioMediTech, Finland and Fimlab Laboratories, University of Tampere, Tampere, Finland
| | - Malin Flodström-Tullberg
- BioMediTech, Finland and Fimlab Laboratories, University of Tampere, Tampere, Finland.,The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Stockholm, Sweden
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45
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Ye G, Deng F, Shen Z, Luo R, Zhao L, Xiao S, Fu ZF, Peng G. Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease. Virology 2016; 494:225-35. [PMID: 27128350 PMCID: PMC7111274 DOI: 10.1016/j.virol.2016.04.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/16/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CLpro), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CLpro and a molecular complex between an inactive PEDV 3CLpro variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CLpro. The dimerization of PEDV 3CLpro is similar to that of other Alphacoronavirus 3CLpros but has several differences from that of SARS-CoV 3CLpro from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CLpros, which may provide new insights into the recognition of substrates by 3CLpros in various coronavirus genera. The substrate binding mechanism of PEDV 3CLpro has been characterized. The large buried surface area is responsible for dimerization of PEDV 3CLpro. Non-conserved motifs cause different cleavage between PEDV and SARS-CoV 3CLpros.
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Affiliation(s)
- Gang Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Feng Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhou Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China.
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46
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Tomar S, Johnston ML, St John SE, Osswald HL, Nyalapatla PR, Paul LN, Ghosh AK, Denison MR, Mesecar AD. Ligand-induced Dimerization of Middle East Respiratory Syndrome (MERS) Coronavirus nsp5 Protease (3CLpro): IMPLICATIONS FOR nsp5 REGULATION AND THE DEVELOPMENT OF ANTIVIRALS. J Biol Chem 2015; 290:19403-22. [PMID: 26055715 PMCID: PMC4528106 DOI: 10.1074/jbc.m115.651463] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 12/20/2022] Open
Abstract
All coronaviruses, including the recently emerged Middle East respiratory
syndrome coronavirus (MERS-CoV) from the β-CoV subgroup, require the
proteolytic activity of the nsp5 protease (also known as 3C-like protease,
3CLpro) during virus replication, making it a high value target
for the development of anti-coronavirus therapeutics. Kinetic studies indicate
that in contrast to 3CLpro from other β-CoV 2c members,
including HKU4 and HKU5, MERS-CoV 3CLpro is less efficient at
processing a peptide substrate due to MERS-CoV 3CLpro being a weakly
associated dimer. Conversely, HKU4, HKU5, and SARS-CoV 3CLpro enzymes
are tightly associated dimers. Analytical ultracentrifugation studies support
that MERS-CoV 3CLpro is a weakly associated dimer
(Kd ∼52 μm) with a
slow off-rate. Peptidomimetic inhibitors of MERS-CoV 3CLpro were
synthesized and utilized in analytical ultracentrifugation experiments and
demonstrate that MERS-CoV 3CLpro undergoes significant ligand-induced
dimerization. Kinetic studies also revealed that designed reversible inhibitors
act as activators at a low compound concentration as a result of induced
dimerization. Primary sequence comparisons and x-ray structural analyses of two
MERS-CoV 3CLpro and inhibitor complexes, determined to 1.6 Å, reveal
remarkable structural similarity of the dimer interface with 3CLpro
from HKU4-CoV and HKU5-CoV. Despite this structural similarity, substantial
differences in the dimerization ability suggest that long range interactions by
the nonconserved amino acids distant from the dimer interface may control
MERS-CoV 3CLpro dimerization. Activation of MERS-CoV
3CLpro through ligand-induced dimerization appears to be unique
within the genogroup 2c and may potentially increase the complexity in the
development of MERS-CoV 3CLpro inhibitors as antiviral agents.
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Affiliation(s)
| | | | | | | | | | - Lake N Paul
- the Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907, and
| | - Arun K Ghosh
- Chemistry, Purdue University, West Lafayette, Indiana 47907
| | - Mark R Denison
- the Departments of Pediatrics and Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Andrew D Mesecar
- From the Departments of Biological Sciences and Chemistry, Purdue University, West Lafayette, Indiana 47907,
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47
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Schomburg D, Schomburg I. SARS coronavirus main proteinase 3.4.22.69. CLASS 3.4–6 HYDROLASES, LYASES, ISOMERASES, LIGASES 2013. [PMCID: PMC7123336 DOI: 10.1007/978-3-642-36260-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
EC number 3.4.22.69 Recommended name SARS coronavirus main proteinase Synonyms 3C-like protease <2,3> [9,16,38,49,51] 3CL protease <2> [14,48] 3cLpro <1,2,3> [7,11,13,16,19,28,38,49,51] C30.004 (Merops-ID) Mpro SARS 3C-like protease <2> [17] SARS 3C-like proteinase <2> [15,18,27] SARS 3CL protease <2> [31] SARS 3CLpro <2> [49] SARS CoV main proteinase <2> [1,2,4,5] SARS CoVMpro <2> [33] SARS Mpro <2> [25] SARS coronavirus 3C-like protease <2> [48] SARS coronavirus 3C-like proteinase <2> [50] SARS coronavirus 3CL protease <2> [20] SARS coronavirus main peptidase <2> [23] SARS coronavirus main protease <2> [25] SARS coronavirus main proteinase <2> [5,33] SARS main protease <2> [12,25] SARS-3CL protease <2> [48] SARS-3CLpro <2> [29,50] SARS-CoV 3C-like peptidaseSARS-CoV 3C-like peptidase<2> [24] SARS-CoV 3C-like protease<1> [19] SARS-CoV 3CL protease <2> [22,30,44,46] SARS-CoV 3CLpro <2> [32,36,38,44,45] SARS-CoV 3CLpro enzyme <2> [11] SARS-CoV Mpro <2> [21,40] SARS-CoV main protease <2> [21,26,43] SARS-coronavirus 3CL protease <2> [8] SARS-coronavirus main protease <2> [47] TGEV Mpro coronavirus 3C-like protease <1> [19] porcine transmissible gastroenteritis virus Mpro severe acute respiratory syndrome coronavirus 3C-like protease <2> [41,42] severe acute respiratory syndrome coronavirus main protease <2> [21] severe acute respiratory syndrome coronavirus main proteinase <2> [33] CAS registry number 218925-73-6 37353-41-6
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Affiliation(s)
- Dietmar Schomburg
- Bioinformatics & Systems Biology, Technical University Braunschweig, Langer Kamp 19b, 38106 Braunschweig, Germany
| | - Ida Schomburg
- Bioinformatics & Systems Biology, Technical University Braunschweig, Langer Kamp 19b, 38106 Braunschweig, Germany
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48
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Activation and maturation of SARS-CoV main protease. Protein Cell 2011; 2:282-90. [PMID: 21533772 PMCID: PMC4875205 DOI: 10.1007/s13238-011-1034-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 04/07/2011] [Indexed: 12/30/2022] Open
Abstract
The worldwide outbreak of the severe acute respiratory syndrome (SARS) in 2003 was due to the transmission of SARS coronavirus (SARS-CoV). The main protease (Mpro) of SARS-CoV is essential for the viral life cycle, and is considered to be an attractive target of anti-SARS drug development. As a key enzyme for proteolytic processing of viral polyproteins to produce functional non-structure proteins, Mpro is first auto-cleaved out of polyproteins. The monomeric form of Mpro is enzymatically inactive, and it is activated through homo-dimerization which is strongly affected by extra residues to both ends of the mature enzyme. This review provides a summary of the related literatures on the study of the quaternary structure, activation, and self-maturation of Mpro over the past years.
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49
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Barrila J, Gabelli SB, Bacha U, Amzel LM, Freire E. Mutation of Asn28 disrupts the dimerization and enzymatic activity of SARS 3CL(pro) . Biochemistry 2010; 49:4308-17. [PMID: 20420403 DOI: 10.1021/bi1002585] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Coronaviruses are responsible for a significant proportion of annual respiratory and enteric infections in humans and other mammals. The most prominent of these viruses is the severe acute respiratory syndrome coronavirus (SARS-CoV) which causes acute respiratory and gastrointestinal infection in humans. The coronavirus main protease, 3CL(pro), is a key target for broad-spectrum antiviral development because of its critical role in viral maturation and high degree of structural conservation among coronaviruses. Dimerization is an indispensable requirement for the function of SARS 3CL(pro) and is regulated through mechanisms involving both direct and long-range interactions in the enzyme. While many of the binding interactions at the dimerization interface have been extensively studied, those that are important for long-range control are not well-understood. Characterization of these dimerization mechanisms is important for the structure-based design of new treatments targeting coronavirus-based infections. Here we report that Asn28, a residue 11 A from the closest residue in the opposing monomer, is essential for the enzymatic activity and dimerization of SARS 3CL(pro). Mutation of this residue to alanine almost completely inactivates the enzyme and results in a 19.2-fold decrease in the dimerization K(d). The crystallographic structure of the N28A mutant determined at 2.35 A resolution reveals the critical role of Asn28 in maintaining the structural integrity of the active site and in orienting key residues involved in binding at the dimer interface and substrate catalysis. These findings provide deeper insight into complex mechanisms regulating the activity and dimerization of SARS 3CL(pro).
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Affiliation(s)
- Jennifer Barrila
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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50
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Chen S, Jonas F, Shen C, Hilgenfeld R, Higenfeld R. Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode. Protein Cell 2010; 1:59-74. [PMID: 21203998 PMCID: PMC4875104 DOI: 10.1007/s13238-010-0011-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 11/17/2009] [Indexed: 11/29/2022] Open
Abstract
The main protease (Mpro) plays a vital role in proteolytic processing of the polyproteins in the replicative cycle of SARS coronavirus (SARS-CoV). Dimerization of this enzyme has been shown to be indispensable for transcleavage activity. However, the auto-processing mechanism of Mpro, i.e. its own release from the polyproteins through autocleavage, remains unclear. This study elucidates the relationship between the N-terminal autocleavage activity and the dimerization of “immature” Mpro. Three residues (Arg4, Glu290, and Arg298), which contribute to the active dimer conformation of mature Mpro, are selected for mutational analyses. Surprisingly, all three mutants still perform N-terminal autocleavage, while the dimerization of mature protease and transcleavage activity following auto-processing are completely inhibited by the E290R and R298E mutations and partially so by the R4E mutation. Furthermore, the mature E290R mutant can resume N-terminal autocleavage activity when mixed with the “immature” C145A/E290R double mutant whereas its trans-cleavage activity remains absent. Therefore, the N-terminal auto-processing of Mpro appears to require only two “immature” monomers approaching one another to form an “intermediate” dimer structure and does not strictly depend on the active dimer conformation existing in mature protease. In conclusion, an auto-release model of Mpro from the polyproteins is proposed, which will help understand the auto-processing mechanism and the difference between the autocleavage and trans-cleavage proteolytic activities of SARS-CoV Mpro.
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Affiliation(s)
- Shuai Chen
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
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