1
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Bosch A, Guzman HV, Pérez R. Adsorption-Driven Deformation and Footprints of the RBD Proteins in SARS-CoV-2 Variants on Biological and Inanimate Surfaces. J Chem Inf Model 2024; 64:5977-5990. [PMID: 39083670 PMCID: PMC11323246 DOI: 10.1021/acs.jcim.4c00460] [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: 03/15/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 08/02/2024]
Abstract
Respiratory viruses, carried through airborne microdroplets, frequently adhere to surfaces, including plastics and metals. However, our understanding of the interactions between viruses and materials remains limited, particularly in scenarios involving polarizable surfaces. Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein's receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore, the distribution of adsorbed amino acids (landing footprints) on the inanimate surface reveals a distinct regional asymmetry relative to the biological interface, with roughly half of the adsorbed amino acids arranged in opposite sites. In spite of the H-bonds formed at the hydrophilic substrate, the simulations consistently show a higher number of contacts and interfacial area with the hydrophobic surface, where the wild-type RBD adsorbs more strongly than the Delta or Omicron RBDs. In contrast, the adsorption of Delta and Omicron to hydrophilic surfaces was characterized by a distinctive hopping-pattern. The novel shock-absorbing mechanisms identified in the virus adsorption on inanimate surfaces show the embedded high-deformation capacity of the RBD without losing its secondary structure, which could lead to current experimental strategies in the design of virucidal surfaces.
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Affiliation(s)
- Antonio
M. Bosch
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Horacio V. Guzman
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Department
of Theoretical Physics, Jožef Stefan
Institute, SI-1000 Ljubljana, Slovenia
| | - Rubén Pérez
- Departamento
de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, E-28049 Madrid, Spain
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2
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Nazir F, John Kombe Kombe A, Khalid Z, Bibi S, Zhang H, Wu S, Jin T. SARS-CoV-2 replication and drug discovery. Mol Cell Probes 2024; 77:101973. [PMID: 39025272 DOI: 10.1016/j.mcp.2024.101973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
The coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed millions of people and continues to wreak havoc across the globe. This sudden and deadly pandemic emphasizes the necessity for anti-viral drug development that can be rapidly administered to reduce morbidity, mortality, and virus propagation. Thus, lacking efficient anti-COVID-19 treatment, and especially given the lengthy drug development process as well as the critical death tool that has been associated with SARS-CoV-2 since its outbreak, drug repurposing (or repositioning) constitutes so far, the ideal and ready-to-go best approach in mitigating viral spread, containing the infection, and reducing the COVID-19-associated death rate. Indeed, based on the molecular similarity approach of SARS-CoV-2 with previous coronaviruses (CoVs), repurposed drugs have been reported to hamper SARS-CoV-2 replication. Therefore, understanding the inhibition mechanisms of viral replication by repurposed anti-viral drugs and chemicals known to block CoV and SARS-CoV-2 multiplication is crucial, and it opens the way for particular treatment options and COVID-19 therapeutics. In this review, we highlighted molecular basics underlying drug-repurposing strategies against SARS-CoV-2. Notably, we discussed inhibition mechanisms of viral replication, involving and including inhibition of SARS-CoV-2 proteases (3C-like protease, 3CLpro or Papain-like protease, PLpro) by protease inhibitors such as Carmofur, Ebselen, and GRL017, polymerases (RNA-dependent RNA-polymerase, RdRp) by drugs like Suramin, Remdesivir, or Favipiravir, and proteins/peptides inhibiting virus-cell fusion and host cell replication pathways, such as Disulfiram, GC376, and Molnupiravir. When applicable, comparisons with SARS-CoV inhibitors approved for clinical use were made to provide further insights to understand molecular basics in inhibiting SARS-CoV-2 replication and draw conclusions for future drug discovery research.
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Affiliation(s)
- Farah Nazir
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Arnaud John Kombe Kombe
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zunera Khalid
- Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shaheen Bibi
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China
| | - Hongliang Zhang
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China
| | - Songquan Wu
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China.
| | - Tengchuan Jin
- Center of Disease Immunity and Investigation, College of Medicine, Lishui University, Lishui, 323000, China; Laboratory of Structural Immunology, Key Laboratory of Immune Response and Immunotherapy, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, University of Science and Technology of China, Anhui, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China; Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China; Clinical Research Hospital of Chinese Academy of Sciences (Hefei), University of Science and Technology of China, Hefei, 230001, China.
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3
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Chmielewski D, Wilson EA, Pintilie G, Zhao P, Chen M, Schmid MF, Simmons G, Wells L, Jin J, Singharoy A, Chiu W. Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans. Nat Commun 2023; 14:7175. [PMID: 37935678 PMCID: PMC10630519 DOI: 10.1038/s41467-023-42836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectrometry. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a role of hinge glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays implicated involvement of N1242-glyan in virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.
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Affiliation(s)
- David Chmielewski
- Biophysics Graduate Program, Stanford University, Stanford, CA, 94305, USA
| | - Eric A Wilson
- School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Grigore Pintilie
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Graham Simmons
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Jing Jin
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.
- Vitalant Research Institute, San Francisco, CA, 94118, USA.
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA.
| | - Abhishek Singharoy
- School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Wah Chiu
- Biophysics Graduate Program, Stanford University, Stanford, CA, 94305, USA.
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
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4
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Gonzalez-Rodriguez E, Zol-Hanlon M, Bineva-Todd G, Marchesi A, Skehel M, Mahoney KE, Roustan C, Borg A, Di Vagno L, Kjær S, Wrobel AG, Benton DJ, Nawrath P, Flitsch SL, Joshi D, González-Ramírez A, Wilkinson KA, Wilkinson RJ, Wall EC, Hurtado-Guerrero R, Malaker SA, Schumann B. O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern. ACS CENTRAL SCIENCE 2023; 9:393-404. [PMID: 36968546 PMCID: PMC10037455 DOI: 10.1021/acscentsci.2c01349] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 06/18/2023]
Abstract
The emergence of a polybasic cleavage motif for the protease furin in SARS-CoV-2 spike has been established as a major factor for human viral transmission. The region N-terminal to that motif is extensively mutated in variants of concern (VOCs). Besides furin, spikes from these variants appear to rely on other proteases for maturation, including TMPRSS2. Glycans near the cleavage site have raised questions about proteolytic processing and the consequences of variant-borne mutations. Here, we identify that sialic acid-containing O-linked glycans on Thr678 of SARS-CoV-2 spike influence furin and TMPRSS2 cleavage and posit O-linked glycosylation as a likely driving force for the emergence of VOC mutations. We provide direct evidence that the glycosyltransferase GalNAc-T1 primes glycosylation at Thr678 in the living cell, an event that is suppressed by mutations in the VOCs Alpha, Delta, and Omicron. We found that the sole incorporation of N-acetylgalactosamine did not impact furin activity in synthetic O-glycopeptides, but the presence of sialic acid reduced the furin rate by up to 65%. Similarly, O-glycosylation with a sialylated trisaccharide had a negative impact on TMPRSS2 cleavage. With a chemistry-centered approach, we substantiate O-glycosylation as a major determinant of spike maturation and propose disruption of O-glycosylation as a substantial driving force for VOC evolution.
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Affiliation(s)
- Edgar Gonzalez-Rodriguez
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mia Zol-Hanlon
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Signalling
and Structural Biology Lab, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
| | - Andrea Marchesi
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mark Skehel
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Keira E. Mahoney
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Chloë Roustan
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Annabel Borg
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lucia Di Vagno
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjær
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Antoni G. Wrobel
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Donald J. Benton
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Philipp Nawrath
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Sabine L. Flitsch
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Dhira Joshi
- Chemical
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Katalin A. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Robert J. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
- Department
of Infectious Diseases, Imperial College
London, W12 0NN London, United Kingdom
- Institute
of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Emma C. Wall
- The Francis
Crick Institute, NW1 1AT London, United Kingdom
- University
College London Hospitals (UCLH) Biomedical Research Centre, W1T 7DN London, United Kingdom
| | - Ramón Hurtado-Guerrero
- Institute
of Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Stacy A. Malaker
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Benjamin Schumann
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
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5
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Chmielewski D, Wilson EA, Pintilie G, Zhao P, Chen M, Schmid MF, Simmons G, Wells L, Jin J, Singharoy A, Chiu W. Integrated analyses reveal a hinge glycan regulates coronavirus spike tilting and virus infectivity. RESEARCH SQUARE 2023:rs.3.rs-2553619. [PMID: 36824920 PMCID: PMC9949256 DOI: 10.21203/rs.3.rs-2553619/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectroscopy. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a novel role of stalk glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays support the hypothesis that this glycan-dependent motion impacts virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.
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Affiliation(s)
- David Chmielewski
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Eric A. Wilson
- School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Grigore Pintilie
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Peng Zhao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Muyuan Chen
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Graham Simmons
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Jing Jin
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Abhishek Singharoy
- School of Molecular Sciences, Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Wah Chiu
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, and of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
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6
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Li Q, Shah T, Wang B, Qu L, Wang R, Hou Y, Baloch Z, Xia X. Cross-species transmission, evolution and zoonotic potential of coronaviruses. Front Cell Infect Microbiol 2023; 12:1081370. [PMID: 36683695 PMCID: PMC9853062 DOI: 10.3389/fcimb.2022.1081370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
Coronaviruses (CoVs) continuously evolve, crossing species barriers and spreading across host ranges. Over the last two decades, several CoVs (HCoV-229E, HCoV-NL63, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) have emerged in animals and mammals, causing significant economic and human life losses. Due to CoV cross-species transmission and the evolution of novel viruses, it is critical to identify their natural reservoiurs and the circumstances under which their transmission occurs. In this review, we use genetic and ecological data to disentangle the evolution of various CoVs in wildlife, humans, and domestic mammals. We thoroughly investigate several host species and outline the epidemiology of CoVs toward specific hosts. We also discuss the cross-species transmission of CoVs at the interface of wildlife, animals, and humans. Clarifying the epidemiology and diversity of species reservoirs will significantly impact our ability to respond to the future emergence of CoVs in humans and domestic animals.
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Affiliation(s)
- Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,The First Affiliated Hospital & Clinical Medical College, Dali University, Dali, Yunnan, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Linyu Qu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Rui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, China,Affiliated Anning First People’s Hospital, Kunming University of Science and Technology, Kunming, China,*Correspondence: Xueshan Xia,
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7
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Kumawat A, Namsani S, Pramanik D, Roy S, Singh JK. Integrated docking and enhanced sampling-based selection of repurposing drugs for SARS-CoV-2 by targeting host dependent factors. J Biomol Struct Dyn 2022; 40:9897-9908. [PMID: 34155961 PMCID: PMC8220434 DOI: 10.1080/07391102.2021.1937319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Since the onset of global pandemic, the most focused research currently in progress is the development of potential drug candidates and clinical trials of existing FDA approved drugs for other relevant diseases, in order to repurpose them for the COVID-19. At the same time, several high throughput screenings of drugs have been reported to inhibit the viral components during the early course of infection but with little proven efficacies. Here, we investigate the drug repurposing strategies to counteract the coronavirus infection which involves several potential targetable host proteins involved in viral replication and disease progression. We report the high throughput analysis of literature-derived repurposing drug candidates that can be used to target the genetic regulators known to interact with viral proteins based on experimental and interactome studies. In this work we have performed integrated molecular docking followed by molecular dynamics (MD) simulations and free energy calculations through an expedite in silico process where the number of screened candidates reduces sequentially at every step based on physicochemical interactions. We elucidate that in addition to the pre-clinical and FDA approved drugs that targets specific regulatory proteins, a range of chemical compounds (Nafamostat, Chloramphenicol, Ponatinib) binds to the other gene transcription and translation regulatory proteins with higher affinity and may harbour potential for therapeutic uses. There is a rapid growing interest in the development of combination therapy for COVID-19 to target multiple enzymes/pathways. Our in silico approach would be useful in generating leads for experimental screening for rapid drug repurposing against SARS-CoV-2 interacting host proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amit Kumawat
- Prescience Insilico Private Limited, Bangalore, India,Department of Chemical Engineering, Indian Institute of Technology, Kanpur, India
| | | | - Debabrata Pramanik
- Department of Chemical Engineering, Indian Institute of Technology, Kanpur, India
| | - Sudip Roy
- Prescience Insilico Private Limited, Bangalore, India,CONTACT Sudip Roy ;
| | - Jayant K. Singh
- Prescience Insilico Private Limited, Bangalore, India,Department of Chemical Engineering, Indian Institute of Technology, Kanpur, India,Jayant K. Singh
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8
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Thakur V, Bhola S, Thakur P, Patel SKS, Kulshrestha S, Ratho RK, Kumar P. Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe. Infection 2022; 50:309-325. [PMID: 34914036 PMCID: PMC8675301 DOI: 10.1007/s15010-021-01734-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/16/2021] [Indexed: 02/06/2023]
Abstract
The coronavirus disease-19 has left a permanent mark on the history of the human race. Severe acute respiratory syndrome coronavirus-2 is a positive-sense single-stranded RNA virus, first reported in Wuhan, China, in December 2019 and from there took over the world. Being highly susceptible to mutations, the virus's numerous variants started to appear, and some were more lethal and infectious than the parent. The effectiveness of the vaccine is also affected severely against the new variant. In this study, the infectious mechanism of the coronavirus is explained with a focus on different variants and their respective mutations, which play a critical role in the increased transmissibility, infectivity, and immune escape of the virus. As India has already faced the second wave of the pandemic, the future outlook on the likeliness of a third wave with respect to the Indian variants such as kappa, delta, and Delta Plus is also discussed. This review article aims to reflect the catastrophe of the variants of SARS-CoV-2 and the possibility of developing even more severe variants in the near future.
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Affiliation(s)
- Vikram Thakur
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
- Viral Regional Diagnostic Laboratory (VRDL), Government Medical College, Patiala, 147001, India
| | - Shivam Bhola
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Pryanka Thakur
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | | | - Saurabh Kulshrestha
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India
| | - Radha Kanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India.
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, India.
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9
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Mashayekhi G, Vant J, Polavarapu A, Ourmazd A, Singharoy A. Energy landscape of the SARS-CoV-2 reveals extensive conformational heterogeneity. Curr Res Struct Biol 2022; 4:68-77. [PMID: 35284830 PMCID: PMC8902891 DOI: 10.1016/j.crstbi.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 12/24/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has produced a number of structural models of the SARS-CoV-2 spike, already prompting biomedical outcomes. However, these reported models and their associated electrostatic potential maps represent an unknown admixture of conformations stemming from the underlying energy landscape of the spike protein. As with any protein, some of the spike's conformational motions are expected to be biophysically relevant, but cannot be interpreted only by static models. Using experimental cryo-EM images, we present the energy landscape of the glycosylated spike protein, and identify the diversity of low-energy conformations in the vicinity of its open (so called 1RBD-up) state. The resulting atomic refinement reveal global and local molecular rearrangements that cannot be inferred from an average 1RBD-up cryo-EM model. Here we report varied degrees of "openness" in global conformations of the 1RBD-up state, not revealed in the single-model interpretations of the density maps, together with conformations that overlap with the reported models. We discover how the glycan shield contributes to the stability of these low-energy conformations. Five out of six binding sites we analyzed, including those for engaging ACE2, therapeutic mini-proteins, linoleic acid, two different kinds of antibodies, switch conformations between their known apo- and holo-conformations, even when the global spike conformation is 1RBD-up. This apo-to-holo switching is reminiscent of a conformational preequilibrium. We found only one binding site, namely that of AB-C135 remains in apo state within all the sampled free energy-minimizing models, suggesting an induced fit mechanism for the docking of this antibody to the spike.
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Affiliation(s)
- Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - John Vant
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Abbas Ourmazd
- Department of Physics, University of Wisconsin Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI, 53211, USA
| | - Abhishek Singharoy
- School of Molecular Sciences, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
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10
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Wu CR, Yin WC, Jiang Y, Xu HE. Structure genomics of SARS-CoV-2 and its Omicron variant: drug design templates for COVID-19. Acta Pharmacol Sin 2022; 43:3021-3033. [PMID: 35058587 PMCID: PMC8771608 DOI: 10.1038/s41401-021-00851-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/21/2021] [Indexed: 02/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has brought an unprecedented public health crisis and persistently threatens to humanity. With tireless efforts from scientists around the world, understanding of the biology of coronavirus has been greatly enhanced over the past 2 years. Structural biology has demonstrated its powerful impact on uncovering structures and functions for the vast majority of SARS-CoV-2 proteins and guided the development of drugs and vaccines against COVID-19. In this review, we summarize current progress in the structural biology of SARS-CoV-2 and discuss important biological issues that remain to be addressed. We present the examples of structure-based design of Pfizer’s novel anti-SARS-CoV-2 drug PF-07321332 (Paxlovid), Merck’s nucleotide inhibitor molnupiravir (Lagevrio), and VV116, an oral drug candidate for COVID-19. These examples highlight the importance of structure in drug discovery to combat COVID-19. We also discussed the recent variants of Omicron and its implication in immunity escape from existing vaccines and antibody therapies.
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11
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Koehler M, Ray A, Moreira RA, Juniku B, Poma AB, Alsteens D. Molecular insights into receptor binding energetics and neutralization of SARS-CoV-2 variants. Nat Commun 2021; 12:6977. [PMID: 34848718 PMCID: PMC8633007 DOI: 10.1038/s41467-021-27325-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
Despite an unprecedented global gain in knowledge since the emergence of SARS-CoV-2, almost all mechanistic knowledge related to the molecular and cellular details of viral replication, pathology and virulence has been generated using early prototypic isolates of SARS-CoV-2. Here, using atomic force microscopy and molecular dynamics, we investigated how these mutations quantitatively affected the kinetic, thermodynamic and structural properties of RBD-ACE2 complex formation. We observed for several variants of concern a significant increase in the RBD-ACE2 complex stability. While the N501Y and E484Q mutations are particularly important for the greater stability, the N501Y mutation is unlikely to significantly affect antibody neutralization. This work provides unprecedented atomistic detail on the binding of SARS-CoV-2 variants and provides insight into the impact of viral mutations on infection-induced immunity.
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Affiliation(s)
- Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rodrigo A Moreira
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106, Warsaw, Poland
| | - Blinera Juniku
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Adolfo B Poma
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)-International Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924, Lodz, Poland.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300, Wavre, Belgium.
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12
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Hikisz P, Bernasinska-Slomczewska J. Beneficial Properties of Bromelain. Nutrients 2021; 13:4313. [PMID: 34959865 PMCID: PMC8709142 DOI: 10.3390/nu13124313] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 12/21/2022] Open
Abstract
Bromelain is a major sulfhydryl proteolytic enzyme found in pineapple plants, having multiple activities in many areas of medicine. Due to its low toxicity, high efficiency, high availability, and relative simplicity of acquisition, it is the object of inexhaustible interest of scientists. This review summarizes scientific reports concerning the possible application of bromelain in treating cardiovascular diseases, blood coagulation and fibrinolysis disorders, infectious diseases, inflammation-associated diseases, and many types of cancer. However, for the proper application of such multi-action activities of bromelain, further exploration of the mechanism of its action is needed. It is supposed that the anti-viral, anti-inflammatory, cardioprotective and anti-coagulatory activity of bromelain may become a complementary therapy for COVID-19 and post-COVID-19 patients. During the irrepressible spread of novel variants of the SARS-CoV-2 virus, such beneficial properties of this biomolecule might help prevent escalation and the progression of the COVID-19 disease.
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Affiliation(s)
- Pawel Hikisz
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, ul. Pomorska 141/143, 90-236 Lodz, Poland;
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13
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Yang L, Li J, Guo S, Hou C, Liao C, Shi L, Ma X, Jiang S, Zheng B, Fang Y, Ye L, He X. SARS-CoV-2 Variants, RBD Mutations, Binding Affinity, and Antibody Escape. Int J Mol Sci 2021; 22:12114. [PMID: 34829998 PMCID: PMC8619214 DOI: 10.3390/ijms222212114] [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: 10/07/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of "variants of concern", probably in response to the vaccine-driven alteration of immune profiles of the human population. The Delta variant, in particular, has become the most prevalent variant of the epidemic, and it is spreading in countries with the highest vaccination rates, causing the world to face the risk of a new wave of the contagion. Understanding the physical mechanism responsible for the mutation-induced changes in the RBD's binding affinity, its transmissibility, and its capacity to escape vaccine-induced immunity is the "urgent challenge" in the development of preventive measures, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID-19) pandemic. In this study, entropy-enthalpy compensation and the Gibbs free energy change were used to analyze the impact of the RBD mutations on the binding affinity of SARS-CoV-2 variants with the receptor angiotensin converting enzyme 2 (ACE2) and existing antibodies. Through the analysis, we found that the existing mutations have already covered almost all possible detrimental mutations that could result in an increase of transmissibility, and that a possible mutation in amino-acid position 498 of the RBD can potentially enhance its binding affinity. A new calculation method for the binding energies of protein-protein complexes is proposed based on the entropy-enthalpy compensation rule. All known structures of RBD-antibody complexes and the RBD-ACE2 complex comply with the entropy-enthalpy compensation rule in providing the driving force behind the spontaneous protein-protein docking. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation's reduction of the binding affinity of many antibodies. Mutations reversing the hydrophobic or hydrophilic performance of residues in the spike RBD potentially cause breakthrough infections of coronaviruses due to the changes in geometric complementarity in the entropy-enthalpy compensations between antibodies and the virus at the binding sites.
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Affiliation(s)
- Lin Yang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Jiacheng Li
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Shuai Guo
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Chengyu Hou
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Chenchen Liao
- School of Electronics and Information Engineering, Harbin Institute of Technology, Harbin 150080, China; (C.H.); (C.L.)
| | - Liping Shi
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Xiaoliang Ma
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Shenda Jiang
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
| | - Bing Zheng
- Key Laboratory of Functional Inorganic Material Chemistry (Ministry of Education) and School of Chemistry and Materials Science, Heilongjiang University, Harbin 150001, China;
| | - Yi Fang
- Mathematical Science Institute, The Australian National University, Canberra, ACT 0200, Australia;
| | - Lin Ye
- School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Xiaodong He
- National Key Laboratory of Science and Technology on Advanced Composites in Special Environments, Center for Composite Materials and Structures, Harbin Institute of Technology, Harbin 150080, China; (J.L.); (S.G.); (L.S.); (X.M.); (S.J.)
- Shenzhen STRONG Advanced Materials Research Institute Co., Ltd., Shenzhen 518035, China
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14
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Insights into COVID-19 Vaccine Development Based on Immunogenic Structural Proteins of SARS-CoV-2, Host Immune Responses, and Herd Immunity. Cells 2021; 10:cells10112949. [PMID: 34831172 PMCID: PMC8616290 DOI: 10.3390/cells10112949] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 01/18/2023] Open
Abstract
The first quarter of the 21st century has remarkably been characterized by a multitude of challenges confronting human society as a whole in terms of several outbreaks of infectious viral diseases, such as the 2003 severe acute respiratory syndrome (SARS), China; the 2009 influenza H1N1, Mexico; the 2012 Middle East respiratory syndrome (MERS), Saudi Arabia; and the ongoing coronavirus disease 19 (COVID-19), China. COVID-19, caused by SARS-CoV-2, reportedly broke out in December 2019, Wuhan, the capital of China’s Hubei province, and continues unabated, leading to considerable devastation and death worldwide. The most common target organ of SARS-CoV-2 is the lungs, especially the bronchial and alveolar epithelial cells, culminating in acute respiratory distress syndrome (ARDS) in severe patients. Nevertheless, other tissues and organs are also known to be critically affected following infection, thereby complicating the overall aetiology and prognosis. Excluding H1N1, the SARS-CoV (also referred as SARS-CoV-1), MERS, and SARS-CoV-2 are collectively referred to as coronaviruses, and taxonomically placed under the realm Riboviria, order Nidovirales, suborder Cornidovirineae, family Coronaviridae, subfamily Orthocoronavirinae, genus Betacoronavirus, and subgenus Sarbecovirus. As of 23 September 2021, the ongoing SARS-CoV-2 pandemic has globally resulted in around 229 million and 4.7 million reported infections and deaths, respectively, apart from causing huge psychosomatic debilitation, academic loss, and deep economic recession. Such an unprecedented pandemic has compelled researchers, especially epidemiologists and immunologists, to search for SARS-CoV-2-associated potential immunogenic molecules to develop a vaccine as an immediate prophylactic measure. Amongst multiple structural and non-structural proteins, the homotrimeric spike (S) glycoprotein has been empirically found as the most suitable candidate for vaccine development owing to its immense immunogenic potential, which makes it capable of eliciting both humoral and cell-mediated immune responses. As a consequence, it has become possible to design appropriate, safe, and effective vaccines, apart from related therapeutic agents, to reduce both morbidity and mortality. As of 23 September 2021, four vaccines, namely, Comirnaty, COVID-19 vaccine Janssen, Spikevax, and Vaxzevria, have received the European Medicines Agency’s (EMA) approval, and around thirty are under the phase three clinical trial with emergency authorization by the vaccine-developing country-specific National Regulatory Authority (NRA). In addition, 100–150 vaccines are under various phases of pre-clinical and clinical trials. The mainstay of global vaccination is to introduce herd immunity, which would protect the majority of the population, including immunocompromised individuals, from infection and disease. Here, we primarily discuss category-wise vaccine development, their respective advantages and disadvantages, associated efficiency and potential safety aspects, antigenicity of SARS-CoV-2 structural proteins and immune responses to them along with the emergence of SARS-CoV-2 VOC, and the urgent need of achieving herd immunity to contain the pandemic.
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15
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Barh D, Tiwari S, Gabriel Rodrigues Gomes L, Weener ME, Alzahrani KJ, Alsharif KF, Aljabali AAA, Tambuwala MM, Lundstrom K, Hassan SS, Serrano-Aroca Á, Takayama K, Ghosh P, Redwan EM, Silva Andrade B, Soares SDC, Azevedo V, Uversky VN. Potential Molecular Mechanisms of Rare Anti-Tumor Immune Response by SARS-CoV-2 in Isolated Cases of Lymphomas. Viruses 2021; 13:1927. [PMID: 34696358 PMCID: PMC8539762 DOI: 10.3390/v13101927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Recently, two cases of complete remission of classical Hodgkin lymphoma (cHL) and follicular lymphoma (FL) after SARS-CoV-2 infection were reported. However, the precise molecular mechanism of this rare event is yet to be understood. Here, we hypothesize a potential anti-tumor immune response of SARS-CoV-2 and based on a computational approach show that: (i) SARS-CoV-2 Spike-RBD may bind to the extracellular domains of CD15, CD27, CD45, and CD152 receptors of cHL or FL and may directly inhibit cell proliferation. (ii) Alternately, upon internalization after binding to these CD molecules, the SARS-CoV-2 membrane (M) protein and ORF3a may bind to gamma-tubulin complex component 3 (GCP3) at its tubulin gamma-1 chain (TUBG1) binding site. (iii) The M protein may also interact with TUBG1, blocking its binding to GCP3. (iv) Both the M and ORF3a proteins may render the GCP2-GCP3 lateral binding where the M protein possibly interacts with GCP2 at its GCP3 binding site and the ORF3a protein to GCP3 at its GCP2 interacting residues. (v) Interactions of the M and ORF3a proteins with these gamma-tubulin ring complex components potentially block the initial process of microtubule nucleation, leading to cell-cycle arrest and apoptosis. (vi) The Spike-RBD may also interact with and block PD-1 signaling similar to pembrolizumab and nivolumab- like monoclonal antibodies and may induce B-cell apoptosis and remission. (vii) Finally, the TRADD interacting "PVQLSY" motif of Epstein-Barr virus LMP-1, that is responsible for NF-kB mediated oncogenesis, potentially interacts with SARS-CoV-2 Mpro, NSP7, NSP10, and spike (S) proteins, and may inhibit the LMP-1 mediated cell proliferation. Taken together, our results suggest a possible therapeutic potential of SARS-CoV-2 in lymphoproliferative disorders.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Sandeep Tiwari
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Lucas Gabriel Rodrigues Gomes
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Marianna E. Weener
- Clinical Research Center, Oftalmic, CRO, 119334 Bardina Str. 22/4, 119991 Moscow, Russia;
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (K.J.A.); (K.F.A.)
| | - Khalaf F. Alsharif
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (K.J.A.); (K.F.A.)
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, UK;
| | | | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India;
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan;
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Elrashdy M. Redwan
- Department of Biological Science, Faculty of Science, King Abdulazizi University, Jeddah 21589, Saudi Arabia;
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié 45206-190, Brazil;
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba 38025-180, Brazil;
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, 141700 Dolgoprudny, Russia
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Shukla SP, Cho KB, Rustagi V, Gao X, Fu X, Zhang SX, Guo B, Udugamasooriya DG. "Molecular Masks" for ACE2 to Effectively and Safely Block SARS-CoV-2 Virus Entry. Int J Mol Sci 2021; 22:ijms22168963. [PMID: 34445669 PMCID: PMC8396575 DOI: 10.3390/ijms22168963] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 01/14/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) remains a global health crisis, despite the development and success of vaccines in certain countries. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, uses its spike protein to bind to the human cell surface receptor angiotensin-converting enzyme 2 (ACE2), which allows the virus to enter the human body. Using our unique cell screening technology, we identified two ACE2-binding peptoid compounds and developed dimeric derivatives (ACE2P1D1 and ACE2P2D1) that effectively blocked spike protein-ACE2 interaction, resulting in the inhibition of SARS-CoV-2 pseudovirus entry into human cells. ACE2P1D1 and ACE2P2D1 also blocked infection by a D614G mutant pseudovirus. More importantly, these compounds do not decrease ACE2 expression nor its enzyme activity (which is important in normal blood pressure regulation), suggesting safe applicability in humans
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Affiliation(s)
- Satya Prakash Shukla
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Kwang Bog Cho
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Vineeta Rustagi
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xiang Gao
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
| | - Xinping Fu
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Shaun Xiaoliu Zhang
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5037, USA; (X.F.); (S.X.Z.)
| | - Bin Guo
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- Correspondence: (B.G.); (D.G.U.)
| | - D. Gomika Udugamasooriya
- Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Houston, TX 77204-5037, USA; (S.P.S.); (K.B.C.); (V.R.); (X.G.)
- MD Anderson Cancer Center, Department of Cancer Systems Imaging, 1881 East Road, Houston, TX 77030-4009, USA
- Correspondence: (B.G.); (D.G.U.)
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17
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Cong Y, Feng Y, Ni H, Zhi F, Miao Y, Fang B, Zhang L, Zhang JZH. Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis. J Chem Inf Model 2021; 61:3529-3542. [PMID: 34156227 PMCID: PMC8265722 DOI: 10.1021/acs.jcim.1c00241] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/11/2022]
Abstract
COVID-19 has emerged as the most serious international pandemic in early 2020 and the lack of comprehensive knowledge in the recognition and transmission mechanisms of this virus hinders the development of suitable therapeutic strategies. The specific recognition during the binding of the spike glycoprotein (S protein) of coronavirus to the angiotensin-converting enzyme 2 (ACE2) in the host cell is widely considered the first step of infection. However, detailed insights on the underlying mechanism of dynamic recognition and binding of these two proteins remain unknown. In this work, molecular dynamics simulation and binding free energy calculation were carried out to systematically compare and analyze the receptor-binding domain (RBD) of six coronavirus' S proteins. We found that affinity and stability of the RBD from SARS-CoV-2 under the binding state with ACE2 are stronger than those of other coronaviruses. The solvent-accessible surface area (SASA) and binding free energy of different RBD subunits indicate an "anchor-locker" recognition mechanism involved in the binding of the S protein to ACE2. Loop 2 (Y473-F490) acts as an anchor for ACE2 recognition, and Loop 3 (G496-V503) locks ACE2 at the other nonanchoring end. Then, the charged or long-chain residues in the β-sheet 1 (N450-F456) region reinforce this binding. The proposed binding mechanism was supported by umbrella sampling simulation of the dissociation process. The current computational study provides important theoretical insights for the development of new vaccines against SARS-CoV-2.
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Affiliation(s)
- Yalong Cong
- Shanghai Engineering Research Center of Molecular
Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry &
Chemical Process, School of Chemistry and Molecular Engineering, East China
Normal University, Shanghai 200062, China
| | - Yinghui Feng
- Shanghai Engineering Research Center of Molecular
Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry &
Chemical Process, School of Chemistry and Molecular Engineering, East China
Normal University, Shanghai 200062, China
| | - Hui Ni
- College of Food and Biology Engineering,
Jimei University, Xiamen, Fujian 361021,
China
| | - Fengdong Zhi
- Shanghai Engineering Research Center of Molecular
Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry &
Chemical Process, School of Chemistry and Molecular Engineering, East China
Normal University, Shanghai 200062, China
| | - Yulu Miao
- Shanghai Engineering Research Center of Molecular
Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry &
Chemical Process, School of Chemistry and Molecular Engineering, East China
Normal University, Shanghai 200062, China
| | - Bohuan Fang
- Shanghai Engineering Research Center of Molecular
Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry &
Chemical Process, School of Chemistry and Molecular Engineering, East China
Normal University, Shanghai 200062, China
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular
Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry &
Chemical Process, School of Chemistry and Molecular Engineering, East China
Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry
at NYU Shanghai, Shanghai 200062, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular
Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry &
Chemical Process, School of Chemistry and Molecular Engineering, East China
Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry
at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York
University, New York, New York 10003, United
States
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18
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Spaeth A, Masetto T, Brehm J, Wey L, Kochem C, Brehm M, Peter C, Grimmler M. Characterization of the Diagnostic Performance of a Novel COVID-19 PETIA in Comparison to Four Routine N-, S- and RBD-Antigen Based Immunoassays. Diagnostics (Basel) 2021; 11:1332. [PMID: 34441268 PMCID: PMC8394885 DOI: 10.3390/diagnostics11081332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 12/26/2022] Open
Abstract
In 2019, a novel coronavirus emerged in Wuhan in the province of Hubei, China. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) quickly spread across the globe, causing the neoteric COVID-19 pandemic. SARS-CoV-2 is commonly transmitted by droplet infection and aerosols when coughing or sneezing, as well as high-risk exposures to infected individuals by face-to-face contact without protective gear. To date, a broad variety of techniques have emerged to assess and quantify the specific antibody response of a patient towards a SARS-CoV-2 infection. Here, we report the first comprehensive comparison of five different assay systems: Enzyme-Linked Immunosorbent Assay (ELISA), Chemiluminescence Immunoassay (CLIA), Electro-Chemiluminescence Immunoassay (ECLIA), and a new Particle-Enhanced Turbidimetric Immunoassay (PETIA) for SARS-CoV-2. Furthermore, we also evaluated the suitability of N-, S1- and RBD-antigens for quantifying the SARS-CoV-2 specific immune response. Linearity and precision, overall sensitivity and specificity of the assays, stability of samples, and cross-reactivity of general viral responses, as well as common coronaviruses, were assessed. Moreover, the reactivity of all tests to seroconversion and different sample matrices was quantified. All five assays showed good overall agreement, with 76% and 87% similarity for negative and positive samples, respectively. In conclusion, all evaluated methods showed a high consistency of results and suitability for the robust quantification of the SARS-CoV-2-derived immune response.
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Affiliation(s)
- Alexander Spaeth
- MVZ Medizinische Labore Dessau Kassel GmbH, Bauhüttenstraße 6, 06847 Dessau-Roßlau, Germany; (A.S.); (J.B.); (M.B.)
| | - Thomas Masetto
- Institut für Molekulare Medizin I, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (T.M.); (C.P.)
- DiaSys Diagnostic Systems GmbH, Alte Straße 9, 65558 Holzheim, Germany; (L.W.); (C.K.)
| | - Jessica Brehm
- MVZ Medizinische Labore Dessau Kassel GmbH, Bauhüttenstraße 6, 06847 Dessau-Roßlau, Germany; (A.S.); (J.B.); (M.B.)
| | - Leoni Wey
- DiaSys Diagnostic Systems GmbH, Alte Straße 9, 65558 Holzheim, Germany; (L.W.); (C.K.)
- Hochschule Fresenius, University of Applied Sciences, Limburger Straße 2, 65510 Idstein, Germany
| | - Christian Kochem
- DiaSys Diagnostic Systems GmbH, Alte Straße 9, 65558 Holzheim, Germany; (L.W.); (C.K.)
| | - Martin Brehm
- MVZ Medizinische Labore Dessau Kassel GmbH, Bauhüttenstraße 6, 06847 Dessau-Roßlau, Germany; (A.S.); (J.B.); (M.B.)
| | - Christoph Peter
- Institut für Molekulare Medizin I, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany; (T.M.); (C.P.)
| | - Matthias Grimmler
- DiaSys Diagnostic Systems GmbH, Alte Straße 9, 65558 Holzheim, Germany; (L.W.); (C.K.)
- Hochschule Fresenius, University of Applied Sciences, Limburger Straße 2, 65510 Idstein, Germany
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19
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Poma AB, Thu TTM, Tri LTM, Nguyen HL, Li MS. Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations. J Phys Chem B 2021; 125:7628-7637. [PMID: 34253022 PMCID: PMC8389904 DOI: 10.1021/acs.jpcb.1c02322] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/25/2021] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder and one of the main causes of dementia. The disease is associated with amyloid beta (Aβ) peptide aggregation forming initial clusters and then fibril structure and plaques. Other neurodegenerative diseases such as type 2 diabetes, amyotrophic lateral sclerosis, and Parkinson's disease follow a similar mechanism. Therefore, inhibition of Aβ aggregation is considered an effective way to prevent AD. Recent experiments have provided evidence that oligomers are more toxic agents than mature fibrils, prompting researchers to investigate various factors that may influence their properties. One of these factors is nanomechanical stability, which plays an important role in the self-assembly of Aβ and possibly other proteins. This stability is also likely to be related to cell toxicity. In this work, we compare the mechanical stability of Aβ-tetramers and fibrillar structures using a structure-based coarse-grained (CG) approach and all-atom molecular dynamics simulation. Our results support the evidence for an increase in mechanical stability during the Aβ fibrillization process, which is consistent with in vitro AFM characterization of Aβ42 oligomers. Namely, using a CG model, we showed that the Young modulus of tetramers is lower than that of fibrils and, as follows from the experiment, is about 1 GPa. Hydrogen bonds are the dominant contribution to the detachment of one chain from the Aβ fibril fragment. They tend to be more organized along the pulling direction, whereas in the Aβ tetramers no preference is observed.
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Affiliation(s)
- Adolfo B. Poma
- Institute
of Fundamental Technological Research, Polish
Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
- International
Center for Research on Innovative Biobased Materials (ICRI-BioM)—International
Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Tran Thi Minh Thu
- Institute
for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Faculty
of Materials Science and Technology, Ho
Chi Minh City University of Science - VNUHCM, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Lam Tang Minh Tri
- Faculty
of Materials Science and Technology, Ho
Chi Minh City University of Science - VNUHCM, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Hoang Linh Nguyen
- Institute
for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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20
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Li ZL, Buck M. Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2. Biophys J 2021; 120:2828-2837. [PMID: 34087218 PMCID: PMC8169233 DOI: 10.1016/j.bpj.2021.05.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/30/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. The Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (residues (res.) 1-685) and the S2 (res. 686-1273) domains by furin protease. Nrp1 predominantly binds to the C-terminal RRAR amino acid motif (res. 682-685) of the S1 domain. In this study, we firstly modeled the association of an Nrp1 protein (consisting of domains a2-b1-b2) with the Spike protein. Next, we studied the separation of S2 from the S1 domain, with and without Nrp1 bound, by utilizing molecular dynamics pulling simulations. During the separation, Nrp1 stabilizes the S1 C-terminal region (res. 640-685) and thereby assists the detachment of S2 N-terminal region (res. 686-700). Without Nrp1 bound, S1 tends to become stretched, whereas the bound Nrp1 stimulates an earlier separation of S2 from the S1 domain. The liberated S2 domain is known to mediate the fusion of virus and host membranes; thus, Nrp1 likely increases virus infectivity by facilitating the S1 and S2 separation. We further analyzed the possible topological structure of the SARS-CoV-2 Spike protein when bound with Nrp1 and angiotensin-converting enzyme 2 (ACE2). Understanding of such an Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future Nrp1-ACE2 targeted combination therapy.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, School of Medicine, Cleveland, Ohio
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Cleveland, Ohio; Department of Pharmacology, School of Medicine, Cleveland, Ohio; Department of Neurosciences, School of Medicine, Cleveland, Ohio; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, Ohio.
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21
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Giron CC, Laaksonen A, Barroso da Silva FL. Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:694347. [PMID: 35047936 PMCID: PMC8757851 DOI: 10.3389/fmedt.2021.694347] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/31/2021] [Indexed: 12/23/2022] Open
Abstract
The COVID-19 pandemic has spread worldwide. However, as soon as the first vaccines-the only scientifically verified and efficient therapeutic option thus far-were released, mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged, raising doubts about their efficiency. This study aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor-binding domain (RBD) and angiotensin-converting enzyme II (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state, in which the virus can interact with the cellular receptor, ACE2, rather than due to alterations in the complexation RBD-ACE2, since the difference observed in the free energy values was small (although more attractive in general). Conversely, the South African/Beta variant (B.1.351), compared with the SARS-CoV-2 wild type (wt), is much more stable in the opened state with one or two RBDs in the up position than in the closed state with three RBDs in the down position favoring the infection. Such results contribute to understanding the natural history of disease and indicate possible strategies for developing new therapeutic molecules and adjusting the vaccine doses for higher B-cell antibody production.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil
| | - Aatto Laaksonen
- Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Division of Energy Science, Department of Engineering Sciences and Mathematics, Luleå University of Technology, Luleå, Sweden
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
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22
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Lazarevic I, Pravica V, Miljanovic D, Cupic M. Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far? Viruses 2021; 13:1192. [PMID: 34206453 PMCID: PMC8310325 DOI: 10.3390/v13071192] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/15/2021] [Accepted: 06/19/2021] [Indexed: 12/29/2022] Open
Abstract
Despite the slow evolutionary rate of SARS-CoV-2 relative to other RNA viruses, its massive and rapid transmission during the COVID-19 pandemic has enabled it to acquire significant genetic diversity since it first entered the human population. This led to the emergence of numerous variants, some of them recently being labeled "variants of concern" (VOC), due to their potential impact on transmission, morbidity/mortality, and the evasion of neutralization by antibodies elicited by infection, vaccination, or therapeutic application. The potential to evade neutralization is the result of diversity of the target epitopes generated by the accumulation of mutations in the spike protein. While three globally recognized VOCs (Alpha or B.1.1.7, Beta or B.1.351, and Gamma or P.1) remain sensitive to neutralization albeit at reduced levels by the sera of convalescent individuals and recipients of several anti-COVID19 vaccines, the effect of spike variability is much more evident on the neutralization capacity of monoclonal antibodies. The newly recognized VOC Delta or lineage B.1.617.2, as well as locally accepted VOCs (Epsilon or B.1.427/29-US and B1.1.7 with the E484K-UK) are indicating the necessity of close monitoring of new variants on a global level. The VOCs characteristics, their mutational patterns, and the role mutations play in immune evasion are summarized in this review.
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Affiliation(s)
- Ivana Lazarevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (V.P.); (D.M.); (M.C.)
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23
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Combination of rRT-PCR and Anti-Nucleocapsid/Anti-Spike Antibodies to Characterize Specimens with Very Low Viral SARs-CoV-2 Load: A Real-Life Experience. Microorganisms 2021; 9:microorganisms9061263. [PMID: 34200837 PMCID: PMC8230444 DOI: 10.3390/microorganisms9061263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 11/17/2022] Open
Abstract
The objective of the present study was to evaluate the true positivity among people, whose results of initial testing of nasopharyngeal swabs (NPS) showed a very low viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Seventy-seven people detected with low viral loads of SARs-CoV-2 in nasopharyngeal samples (Ct ≥ 35) were enrolled in the study. For this purpose, a second NPS was collected for rRT-PCR (real-time reverse transcription polymerase chain reaction) combined with a pair of serum samples for detection of anti-nucleocapsid (anti-N) and anti-spike (anti-S) antibodies. In 8 people, subsequent examinations indicated an increase in viral loads, thereafter, followed by an increase of anti-N and anti-S antibodies, findings compatible with an early stage of COVID-19 infection. In 9 people, who already had increased anti-N antibodies, subsequent examination showed a decrease or absence of viral load and an increase in antibodies, indicative of a late stage of COVID-19 infection. In 60 people, subsequent examination showed absence of infection (as indicated by absence of viral load and antibodies). We propose that the combination of a second NPS and one serum-specimen, both taken three days after the first NPS, helps significantly to avoid false-positive results.
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24
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Shaheen A. Can ketone bodies inactivate coronavirus spike protein? The potential of biocidal agents against SARS-CoV-2. Bioessays 2021; 43:e2000312. [PMID: 33857328 PMCID: PMC8250295 DOI: 10.1002/bies.202000312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
Biocidal agents such as formaldehyde and glutaraldehyde are able to inactivate several coronaviruses including SARS-CoV-2. In this article, an insight into one mechanism for the inactivation of these viruses by those two agents is presented, based on analysis of previous observations during electron microscopic examination of several members of the orthocoronavirinae subfamily, including the new virus SARS-CoV-2. This inactivation is proposed to occur through Schiff base reaction-induced conformational changes in the spike glycoprotein leading to its disruption or breakage, which can prevent binding of the virus to cellular receptors. Also, a new prophylactic and therapeutic measure against SARS-CoV-2 using acetoacetate is proposed, suggesting that it could similarly break the viral spike through Schiff base reaction with lysines of the spike protein. This measure needs to be confirmed experimentally before consideration. In addition, a new line of research is proposed to help find a broad-spectrum antivirus against several members of this subfamily.
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Affiliation(s)
- Alaa Shaheen
- Shiwah Al Gharbeyah Medical Center, AgaDakahliaEgypt
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25
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Nguyen K, Chakraborty S, Mansbach RA, Korber B, Gnanakaran S. Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Viruses 2021; 13:927. [PMID: 34067878 PMCID: PMC8156887 DOI: 10.3390/v13050927] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 01/01/2023] Open
Abstract
COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike and ACE2 are densely glycosylated, and it is unclear how distinctive glycan types may modulate the interaction of RBD and ACE2. Detailed understanding of these determinants is key for the development of novel therapeutic strategies. To this end, we perform extensive all-atom simulations of the (i) RBD-ACE2 complex without glycans, (ii) RBD-ACE2 with oligomannose MAN9 glycans in ACE2, and (iii) RBD-ACE2 with complex FA2 glycans in ACE2. These simulations identify the key residues at the RBD-ACE2 interface that form contacts with higher probabilities, thus providing a quantitative evaluation that complements recent structural studies. Notably, we find that this RBD-ACE2 contact signature is not altered by the presence of different glycoforms, suggesting that RBD-ACE2 interaction is robust. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. Furthermore, our simulations reveal how the glycan on Asn90 of ACE2 can play a distinct role in the binding and unbinding of RBD. Finally, an energetics analysis shows that MAN9 glycans on ACE2 decrease RBD-ACE2 affinity, while FA2 glycans lead to enhanced binding of the complex. Together, our results provide a more comprehensive picture of the detailed interplay between virus and human receptor, which is much needed for the discovery of effective treatments that aim at modulating the physical-chemical properties of this virus.
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Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
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26
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González-Puelma J, Aldridge J, Montes de Oca M, Pinto M, Uribe-Paredes R, Fernández-Goycoolea J, Alvarez-Saravia D, Álvarez H, Encina G, Weitzel T, Muñoz R, Olivera-Nappa Á, Pantano S, Navarrete MA. Mutation in a SARS-CoV-2 Haplotype from Sub-Antarctic Chile Reveals New Insights into the Spike's Dynamics. Viruses 2021; 13:883. [PMID: 34064904 PMCID: PMC8151058 DOI: 10.3390/v13050883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of SARS-CoV-2 variants, as observed with the D614G spike protein mutant and, more recently, with B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1) lineages, represent a continuous threat and might lead to strains of higher infectivity and/or virulence. We report on the occurrence of a SARS-CoV-2 haplotype with nine mutations including D614G/T307I double-mutation of the spike. This variant expanded and completely replaced previous lineages within a short period in the subantarctic Magallanes Region, southern Chile. The rapid lineage shift was accompanied by a significant increase of cases, resulting in one of the highest incidence rates worldwide. Comparative coarse-grained molecular dynamic simulations indicated that T307I and D614G belong to a previously unrecognized dynamic domain, interfering with the mobility of the receptor binding domain of the spike. The T307I mutation showed a synergistic effect with the D614G. Continuous surveillance of new mutations and molecular analyses of such variations are important tools to understand the molecular mechanisms defining infectivity and virulence of current and future SARS-CoV-2 strains.
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Affiliation(s)
- Jorge González-Puelma
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Jacqueline Aldridge
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Marco Montes de Oca
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | - Mónica Pinto
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.A.); (M.M.d.O.); (R.U.-P.)
| | | | - Diego Alvarez-Saravia
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Hermy Álvarez
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
| | - Gonzalo Encina
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610658, Chile;
- Instituto de Ciencias e Innovación en Medicina (ICIM), Universidad del Desarrollo, Santiago 7610658, Chile
| | - Rodrigo Muñoz
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Enfermedades Infecciosas, Hospital Clínico de Magallanes, Punta Arenas 6210005, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago 8370456, Chile;
- Facultad de Ciencias, Físicas y Matemáticas, Universidad de Chile, Santiago 8370456, Chile
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Marcelo A. Navarrete
- Escuela de Medicina, Universidad de Magallanes, Punta Arenas 6210427, Chile; (J.G.-P.); (M.P.); (D.A.-S.); (H.Á.); (R.M.)
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas 6210005, Chile
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27
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Paramashivam S, Dhiraviam KN. Computational insights into the identification of a potent matrix metalloproteinase inhibitor from Indigofera aspalathoides to control cancer metastasis. 3 Biotech 2021; 11:206. [PMID: 33927994 PMCID: PMC8026800 DOI: 10.1007/s13205-021-02731-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 03/10/2021] [Indexed: 10/21/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are the major proteolytic enzymes which assist in regulating the metastatic process by degrading the extracellular matrix proteins. In this study, we have investigated the anti-metastatic potential of major bioactive compounds in the medicinal plant Indigofera aspalathoides targeting matrix metalloproteinases (MMP2 & MMP9) and it's in silico pharmacokinetic profiles using computational studies. Indigofera aspalathoides (Sivanar vembu in Tamil) is a renowned medicinal herb in traditional Indian medicine which contains indigocarpan, mucronulatol, indigocarpan diacetate, erythroxydiol X and erythroxydiol Y as the major constituents. The 3-dimensional structure of MMP2 and MMP9 was designed by using I-tasser and Modeller and it was validated by PROCHECK. The structures of mucronulatol and indigocarpan have been retrieved from PubChem and indigocarpan diacetate, erythroxydiol X & Y were drawn by using Chemdraw Ultra 6.0. Batimastat was used as a positive control. Molecular docking was performed by using AutoDock 4.2 tools and AutoDock vina, an open-source program which signifies an effective interaction between the phytoligands and MMP2 & MMP9. From the results, AutoDock 4.2 have showed that indigocarpan possesses strong binding energy (ΔG) of - 7.68 kcal/mol towards MMP2 and - 6.35 kcal/mol towards MMP9, whereas batimastat showed binding energy (ΔG) of - 6.34 kcal/mol for MMP2 and - 5.66 kcal/mol for MMP9, meanwhile the results from AutoDock vina indicates that indigocarpan possesses strong binding energy (ΔG) of - 8.0 kcal/mol towards MMP2 and - 8.2 kcal/mol towards MMP9, whereas batimastat showed binding energy (ΔG) of - 7.2 kcal/mol for MMP2 and - 7.6 kcal/mol for MMP9. Also, the ADME and toxicity results suggest that the indigocarpan compound possesses a druggable pharmacokinetic potentiality and does not have carcinogenicity and Ames mutagenesis compared with other phytoligands. Hence, it is evident from our results that both AutoDock platforms strongly revealed that the phytoligand, indigocarpan possesses strong inhibitory activity against MMP2 and MMP9 to control cancer metastasis. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02731-w.
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Affiliation(s)
- SathishKumar Paramashivam
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, 625021 Tamilnadu India
| | - Kannan Narayanan Dhiraviam
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, 625021 Tamilnadu India
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Oliva R, Shaikh AR, Petta A, Vangone A, Cavallo L. D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect. Molecules 2021; 26:molecules26092622. [PMID: 33946306 PMCID: PMC8124767 DOI: 10.3390/molecules26092622] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
The crown of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constituted by its spike (S) glycoprotein. S protein mediates the SARS-CoV-2 entry into the host cells. The “fusion core” of the heptad repeat 1 (HR1) on S plays a crucial role in the virus infectivity, as it is part of a key membrane fusion architecture. While SARS-CoV-2 was becoming a global threat, scientists have been accumulating data on the virus at an impressive pace, both in terms of genomic sequences and of three-dimensional structures. On 15 February 2021, from the SARS-CoV-2 genomic sequences in the GISAID resource, we collected 415,673 complete S protein sequences and identified all the mutations occurring in the HR1 fusion core. This is a 21-residue segment, which, in the post-fusion conformation of the protein, gives many strong interactions with the heptad repeat 2, bringing viral and cellular membranes in proximity for fusion. We investigated the frequency and structural effect of novel mutations accumulated over time in such a crucial region for the virus infectivity. Three mutations were quite frequent, occurring in over 0.1% of the total sequences. These were S929T, D936Y, and S949F, all in the N-terminal half of the HR1 fusion core segment and particularly spread in Europe and USA. The most frequent of them, D936Y, was present in 17% of sequences from Finland and 12% of sequences from Sweden. In the post-fusion conformation of the unmutated S protein, D936 is involved in an inter-monomer salt bridge with R1185. We investigated the effect of the D936Y mutation on the pre-fusion and post-fusion state of the protein by using molecular dynamics, showing how it especially affects the latter one.
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Affiliation(s)
- Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
- Correspondence:
| | - Abdul Rajjak Shaikh
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (A.R.S.); (L.C.)
| | - Andrea Petta
- Dipartimento di Informatica ed Applicazioni, University of Salerno, Via Papa Paolo Giovanni II, I-84048 Fisciano, Italy;
| | - Anna Vangone
- Roche Innovation Center Munich, Pharma Research and Early Development, Large Molecule Research, Nonnenwald 2, 82377 Penzberg, Germany;
| | - Luigi Cavallo
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (A.R.S.); (L.C.)
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Smaoui MR, Yahyaoui H. Unraveling the stability landscape of mutations in the SARS-CoV-2 receptor-binding domain. Sci Rep 2021; 11:9166. [PMID: 33911163 PMCID: PMC8080587 DOI: 10.1038/s41598-021-88696-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
The interaction between the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein and the ACE2 enzyme is believed to be the entry point of the virus into various cells in the body, including the lungs, heart, liver, and kidneys. The current focus of several therapeutic design efforts explores attempts at affecting the binding potential between the two proteins to limit the activity of the virus and disease progression. In this work, we analyze the stability of the spike protein under all possible single-point mutations in the RBD and computationally explore mutations that can affect the binding with the ACE2 enzyme. We unravel the mutation landscape of the receptor region and assess the toxicity potential of single and multi-point mutations, generating insights for future vaccine efforts on mutations that might further stabilize the spike protein and increase its infectivity. We developed a tool, called SpikeMutator, to construct full atomic protein structures of the mutant spike proteins and shared a database of 3800 single-point mutant structures. We analyzed the recent 65,000 reported spike sequences across the globe and observed the emergence of stable multi-point mutant structures. Using the landscape, we searched through 7.5 million possible 2-point mutation combinations and report that the (R355D K424E) mutation produces one of the strongest spike proteins that therapeutic efforts should investigate for the sake of developing effective vaccines.
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Affiliation(s)
| | - Hamdi Yahyaoui
- Computer Science Department, Kuwait University, Kuwait, State of Kuwait
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Forouzesh N, Mishra N. An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor. Molecules 2021; 26:2383. [PMID: 33923909 PMCID: PMC8074138 DOI: 10.3390/molecules26082383] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022] Open
Abstract
The binding free energy calculation of protein-ligand complexes is necessary for research into virus-host interactions and the relevant applications in drug discovery. However, many current computational methods of such calculations are either inefficient or inaccurate in practice. Utilizing implicit solvent models in the molecular mechanics generalized Born surface area (MM/GBSA) framework allows for efficient calculations without significant loss of accuracy. Here, GBNSR6, a new flavor of the generalized Born model, is employed in the MM/GBSA framework for measuring the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor. A computational protocol is developed based on the widely studied Ras-Raf complex, which has similar binding free energy to SARS-CoV-2/ACE2. Two options for representing the dielectric boundary of the complexes are evaluated: one based on the standard Bondi radii and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein-ligand binding. Predictions based on the two radii sets provide upper and lower bounds on the experimental references: -14.7(ΔGbindBondi)<-10.6(ΔGbindExp.)<-4.1(ΔGbindOPT1) kcal/mol. The consensus estimates of the two bounds show quantitative agreement with the experiment values. This work also presents a novel truncation method and computational strategies for efficient entropy calculations with normal mode analysis. Interestingly, it is observed that a significant decrease in the number of snapshots does not affect the accuracy of entropy calculation, while it does lower computation time appreciably. The proposed MM/GBSA protocol can be used to study the binding mechanism of new variants of SARS-CoV-2, as well as other relevant structures.
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Affiliation(s)
- Negin Forouzesh
- Department of Computer Science, California State University, Los Angeles, CA 90032, USA
| | - Nikita Mishra
- Department of Chemistry and Biochemistry, California State University, Los Angeles, CA 90032, USA;
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Yadav R, Chaudhary JK, Jain N, Chaudhary PK, Khanra S, Dhamija P, Sharma A, Kumar A, Handu S. Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19. Cells 2021; 10:cells10040821. [PMID: 33917481 PMCID: PMC8067447 DOI: 10.3390/cells10040821] [Citation(s) in RCA: 241] [Impact Index Per Article: 80.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with varied consequences in terms of death and debilitation. Strikingly, novel coronavirus (2019-nCoV), later renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and found to be the causative agent of coronavirus disease-19 (COVID-19), shows 88% of sequence identity with bat-SL-CoVZC45 and bat-SL-CoVZXC21, 79% with SARS-CoV and 50% with MERS-CoV, respectively. Despite key amino acid residual variability, there is an incredible structural similarity between the receptor binding domain (RBD) of spike protein (S) of SARS-CoV-2 and SARS-CoV. During infection, spike protein of SARS-CoV-2 compared to SARS-CoV displays 10-20 times greater affinity for its cognate host cell receptor, angiotensin-converting enzyme 2 (ACE2), leading proteolytic cleavage of S protein by transmembrane protease serine 2 (TMPRSS2). Following cellular entry, the ORF-1a and ORF-1ab, located downstream to 5' end of + ssRNA genome, undergo translation, thereby forming two large polyproteins, pp1a and pp1ab. These polyproteins, following protease-induced cleavage and molecular assembly, form functional viral RNA polymerase, also referred to as replicase. Thereafter, uninterrupted orchestrated replication-transcription molecular events lead to the synthesis of multiple nested sets of subgenomic mRNAs (sgRNAs), which are finally translated to several structural and accessory proteins participating in structure formation and various molecular functions of virus, respectively. These multiple structural proteins assemble and encapsulate genomic RNA (gRNA), resulting in numerous viral progenies, which eventually exit the host cell, and spread infection to rest of the body. In this review, we primarily focus on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection.
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Affiliation(s)
- Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
- Correspondence: ; Tel.: +91-94-1415-3849
| | | | - Neeraj Jain
- Department of Medical Oncology & Hematology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India;
| | - Pankaj Kumar Chaudhary
- Molecular Biology & Proteomics Laboratory, Department of Biotechnology, Indian Institute of Technology (IIT), Roorkee 247667, India;
| | - Supriya Khanra
- Uttaranchal Institute of Pharmaceutical Sciences, Dehradun 248007, India;
| | - Puneet Dhamija
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
| | - Ambika Sharma
- Department of Biochemistry, U.P. Pt. Deen Dayal Upadhyaya Veterinary Science University, Mathura 281001, India;
| | - Ashish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh 249203, India;
| | - Shailendra Handu
- Department of Pharmacology, All India Institute of Medical Sciences (AIIMS), Rishikesh 249203, India; (P.D.); (S.H.)
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Yan Y, Pang Y, Lyu Z, Wang R, Wu X, You C, Zhao H, Manickam S, Lester E, Wu T, Pang CH. The COVID-19 Vaccines: Recent Development, Challenges and Prospects. Vaccines (Basel) 2021; 9:349. [PMID: 33916489 PMCID: PMC8067284 DOI: 10.3390/vaccines9040349] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022] Open
Abstract
The highly infectious coronavirus disease 2019 (COVID-19) associated with the pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to become a global pandemic. At present, the world is relying mainly on containment and hygiene-related measures, as well as repurposed drugs to control the outbreak. The development of COVID-19 vaccines is crucial for the world to return to pre-pandemic normalcy, and a collective global effort has been invested into protection against SARS-CoV-2. As of March 2021, thirteen vaccines have been approved for application whilst over 90 vaccine candidates are under clinical trials. This review focuses on the development of COVID-19 vaccines and highlights the efficacy and vaccination reactions of the authorised vaccines. The mechanisms, storage, and dosage specification of vaccine candidates at the advanced stage of development are also critically reviewed together with considerations for potential challenges. Whilst the development of a vaccine is, in general, in its infancy, current progress is promising. However, the world population will have to continue to adapt to the "new normal" and practice social distancing and hygienic measures, at least until effective vaccines are available to the general public.
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Affiliation(s)
- Yuxin Yan
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China; (Y.Y.); (Z.L.); (T.W.)
| | - Yoongxin Pang
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
| | - Zhuoyi Lyu
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China; (Y.Y.); (Z.L.); (T.W.)
| | - Ruiqi Wang
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
| | - Xinyun Wu
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
| | - Chong You
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China;
| | - Haitao Zhao
- MITMECHE, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Sivakumar Manickam
- Petroleum and Chemical Engineering, Faculty of Engineering, Universiti Teknologi Brunei, Bandar Seri Begawan BE1410, Brunei;
| | - Edward Lester
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Tao Wu
- Department of Chemical and Environmental Engineering, University of Nottingham Ningbo China, Ningbo 315100, China; (Y.Y.); (Z.L.); (T.W.)
- Key Laboratory for Carbonaceous Wastes Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo 315100, China
| | - Cheng Heng Pang
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China; (Y.P.); (R.W.); (X.W.)
- Municipal Key Laboratory of Clean Energy Conversion Technologies, University of Nottingham Ningbo China, Ningbo 315100, China
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Abouelela ME, Assaf HK, Abdelhamid RA, Elkhyat ES, Sayed AM, Oszako T, Belbahri L, El Zowalaty AE, Abdelkader MSA. Identification of Potential SARS-CoV-2 Main Protease and Spike Protein Inhibitors from the Genus Aloe: An In Silico Study for Drug Development. Molecules 2021; 26:1767. [PMID: 33801151 PMCID: PMC8004122 DOI: 10.3390/molecules26061767] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/22/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) disease is a global rapidly spreading virus showing very high rates of complications and mortality. Till now, there is no effective specific treatment for the disease. Aloe is a rich source of isolated phytoconstituents that have an enormous range of biological activities. Since there are no available experimental techniques to examine these compounds for antiviral activity against SARS-CoV-2, we employed an in silico approach involving molecular docking, dynamics simulation, and binding free energy calculation using SARS-CoV-2 essential proteins as main protease and spike protein to identify lead compounds from Aloe that may help in novel drug discovery. Results retrieved from docking and molecular dynamics simulation suggested a number of promising inhibitors from Aloe. Root mean square deviation (RMSD) and root mean square fluctuation (RMSF) calculations indicated that compounds 132, 134, and 159 were the best scoring compounds against main protease, while compounds 115, 120, and 131 were the best scoring ones against spike glycoprotein. Compounds 120 and 131 were able to achieve significant stability and binding free energies during molecular dynamics simulation. In addition, the highest scoring compounds were investigated for their pharmacokinetic properties and drug-likeness. The Aloe compounds are promising active phytoconstituents for drug development for SARS-CoV-2.
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Affiliation(s)
- Mohamed E. Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Hamdy K. Assaf
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Reda A. Abdelhamid
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Ehab S. Elkhyat
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut-Branch, Assiut 71524, Egypt; (M.E.A.); (H.K.A.); (R.A.A.); (E.S.E.)
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt;
| | - Tomasz Oszako
- Department of Forest Protection, Forest Research Institute, 05-090 Sekocin Stary, Poland;
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 2000 Neuchatel, Switzerland
| | - Ahmed E. El Zowalaty
- Sahlgrenska Center for Cancer Research, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
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Orrù G, Scano A, Fais S, Loddo M, Carta MG, Steri GC, Santus S, Cappai R, Ferrando ML, Coghe F. Evaluation of " Caterina assay": An Alternative Tool to the Commercialized Kits Used for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Identification. Pathogens 2021; 10:325. [PMID: 33802049 PMCID: PMC7998653 DOI: 10.3390/pathogens10030325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Here we describe the first molecular test developed in the early stage of the pandemic to diagnose the first cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Sardinian patients in February-March 2020, when diagnostic certified methodology had not yet been adopted by clinical microbiology laboratories. The "Caterina assay" is a SYBR®Green real-time reverse-transcription polymerase chain reaction (rRT-PCR), designed to detect the nucleocapsid phosphoprotein (N) gene that exhibits high discriminative variation RNA sequence among bat and human coronaviruses. The molecular method was applied to detect SARS-CoV-2 in nasal swabs collected from 2110 suspected cases. The study article describes the first molecular test developed in the early stage of the declared pandemic to identify the coronavirus disease 2019 (COVID-19) in Sardinian patients in February-March 2020, when a diagnostic certified methodology had not yet been adopted by clinical microbiology laboratories. The assay presented high specificity and sensitivity (with a detection limit ≥50 viral genomes/μL). No false-positives were detected, as confirmed by the comparison with two certified commercial kits. Although other validated molecular methods are currently in use, the Caterina assay still represents a valid and low-cost detection procedure that could be applied in countries with limited economic resources.
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Affiliation(s)
- Germano Orrù
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Alessandra Scano
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Sara Fais
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
| | - Miriam Loddo
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Mauro Giovanni Carta
- Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy;
| | - Giorgio Carlo Steri
- Azienda per la Tutela della Salute (ATS), Aree Socio-Sanitarie Locali (ASSL) of Cagliari, 09131 Cagliari, Italy; (G.C.S.); (S.S.)
| | - Simonetta Santus
- Azienda per la Tutela della Salute (ATS), Aree Socio-Sanitarie Locali (ASSL) of Cagliari, 09131 Cagliari, Italy; (G.C.S.); (S.S.)
| | - Riccardo Cappai
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
| | - Maria Laura Ferrando
- Department of Surgical Sciences, Molecular Biology Service (MBS), University of Cagliari, 09124 Cagliari, Italy; (A.S.); (S.F.); (M.L.F.)
| | - Ferdinando Coghe
- Dipartimento Servizi di Diagnosi e Cura, Azienda Ospedaliero-Universitaria di Cagliari (A.O.U.), University of Cagliari, 09024 Cagliari, Italy; (M.L.); (R.C.); (F.C.)
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Singh J, Samal J, Kumar V, Sharma J, Agrawal U, Ehtesham NZ, Sundar D, Rahman SA, Hira S, Hasnain SE. Structure-Function Analyses of New SARS-CoV-2 Variants B.1.1.7, B.1.351 and B.1.1.28.1: Clinical, Diagnostic, Therapeutic and Public Health Implications. Viruses 2021; 13:439. [PMID: 33803400 PMCID: PMC8000172 DOI: 10.3390/v13030439] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/28/2021] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) has accumulated multiple mutations during its global circulation. Recently, three SARS-CoV-2 lineages, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) and B.1.1.28.1 (P.1), have emerged in the United Kingdom, South Africa and Brazil, respectively. Here, we have presented global viewpoint on implications of emerging SARS-CoV-2 variants based on structural-function impact of crucial mutations occurring in its spike (S), ORF8 and nucleocapsid (N) proteins. While the N501Y mutation was observed in all three lineages, the 501Y.V1 and P.1 accumulated a different set of mutations in the S protein. The missense mutational effects were predicted through a COVID-19 dedicated resource followed by atomistic molecular dynamics simulations. Current findings indicate that some mutations in the S protein might lead to higher affinity with host receptors and resistance against antibodies, but not all are due to different antibody binding (epitope) regions. Mutations may, however, result in diagnostic tests failures and possible interference with binding of newly identified anti-viral candidates against SARS-CoV-2, likely necessitating roll out of recurring "flu-like shots" annually for tackling COVID-19. The functional relevance of these mutations has been described in terms of modulation of host tropism, antibody resistance, diagnostic sensitivity and therapeutic candidates. Besides global economic losses, post-vaccine reinfections with emerging variants can have significant clinical, therapeutic and public health impacts.
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Affiliation(s)
- Jasdeep Singh
- JH-Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India;
| | - Jasmine Samal
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Vipul Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India;
| | - Jyoti Sharma
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Usha Agrawal
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Nasreen Z. Ehtesham
- ICMR National Institute of Pathology, Safdarjung Hospital Campus, New Delhi 110029, India; (J.S.); (J.S.); (U.A.); (N.Z.E.)
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India;
| | - Syed Asad Rahman
- BioInception Pvt. Ltd., Swift House Ground Floor, 18 Hoffmanns Way, Chelmsford, Essex CM1 1GU, UK
| | - Subhash Hira
- Department of Global Health, University of Washington-Seattle, Seattle, WA 98195, USA
| | - Seyed E. Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India;
- Dr Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Prof. C.R. Rao Road, Gachibowli, Hyderabad 500049, India
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Akhter J, Quéromès G, Pillai K, Kepenekian V, Badar S, Mekkawy AH, Frobert E, Valle SJ, Morris DL. The Combination of Bromelain and Acetylcysteine (BromAc) Synergistically Inactivates SARS-CoV-2. Viruses 2021; 13:v13030425. [PMID: 33800932 PMCID: PMC7999995 DOI: 10.3390/v13030425] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection is the cause of a worldwide pandemic, currently with limited therapeutic options. The spike glycoprotein and envelope protein of SARS-CoV-2, containing disulfide bridges for stabilization, represent an attractive target as they are essential for binding to the ACE2 receptor in host cells present in the nasal mucosa. Bromelain and Acetylcysteine (BromAc) has synergistic action against glycoproteins by breakage of glycosidic linkages and disulfide bonds. We sought to determine the effect of BromAc on the spike and envelope proteins and its potential to reduce infectivity in host cells. Recombinant spike and envelope SARS-CoV-2 proteins were disrupted by BromAc. Spike and envelope protein disulfide bonds were reduced by Acetylcysteine. In in vitro whole virus culture of both wild-type and spike mutants, SARS-CoV-2 demonstrated a concentration-dependent inactivation from BromAc treatment but not from single agents. Clinical testing through nasal administration in patients with early SARS-CoV-2 infection is imminent.
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Affiliation(s)
- Javed Akhter
- Department of Surgery, St. George Hospital, Sydney, NSW 2217, Australia; (J.A.); (V.K.); (S.B.); (A.H.M.); (S.J.V.)
- Mucpharm Pty Ltd., Sydney, NSW 2217, Australia;
| | - Grégory Quéromès
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (G.Q.); (E.F.)
| | | | - Vahan Kepenekian
- Department of Surgery, St. George Hospital, Sydney, NSW 2217, Australia; (J.A.); (V.K.); (S.B.); (A.H.M.); (S.J.V.)
- Hospices Civils de Lyon, EMR 3738 (CICLY), Lyon 1 Université, F-69921 Lyon, France
| | - Samina Badar
- Department of Surgery, St. George Hospital, Sydney, NSW 2217, Australia; (J.A.); (V.K.); (S.B.); (A.H.M.); (S.J.V.)
- St. George & Sutherland Clinical School, University of New South Wales, Sydney, NSW 2217, Australia
| | - Ahmed H. Mekkawy
- Department of Surgery, St. George Hospital, Sydney, NSW 2217, Australia; (J.A.); (V.K.); (S.B.); (A.H.M.); (S.J.V.)
- Mucpharm Pty Ltd., Sydney, NSW 2217, Australia;
- St. George & Sutherland Clinical School, University of New South Wales, Sydney, NSW 2217, Australia
| | - Emilie Frobert
- CIRI, Centre International de Recherche en Infectiologie, Team VirPatH, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (G.Q.); (E.F.)
- Laboratoire de Virologie, Institut des Agents Infectieux (IAI), Hospices Civils de Lyon, Groupement Hospitalier Nord, F-69004 Lyon, France
| | - Sarah J. Valle
- Department of Surgery, St. George Hospital, Sydney, NSW 2217, Australia; (J.A.); (V.K.); (S.B.); (A.H.M.); (S.J.V.)
- Mucpharm Pty Ltd., Sydney, NSW 2217, Australia;
- St. George & Sutherland Clinical School, University of New South Wales, Sydney, NSW 2217, Australia
| | - David L. Morris
- Department of Surgery, St. George Hospital, Sydney, NSW 2217, Australia; (J.A.); (V.K.); (S.B.); (A.H.M.); (S.J.V.)
- Mucpharm Pty Ltd., Sydney, NSW 2217, Australia;
- St. George & Sutherland Clinical School, University of New South Wales, Sydney, NSW 2217, Australia
- Correspondence: ; Tel.: +61-(02)-91132590
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Kishimoto M, Uemura K, Sanaki T, Sato A, Hall WW, Kariwa H, Orba Y, Sawa H, Sasaki M. TMPRSS11D and TMPRSS13 Activate the SARS-CoV-2 Spike Protein. Viruses 2021; 13:v13030384. [PMID: 33671076 PMCID: PMC8001073 DOI: 10.3390/v13030384] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/14/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) utilizes host proteases, including a plasma membrane-associated transmembrane protease, serine 2 (TMPRSS2) to cleave and activate the virus spike protein to facilitate cellular entry. Although TMPRSS2 is a well-characterized type II transmembrane serine protease (TTSP), the role of other TTSPs on the replication of SARS-CoV-2 remains to be elucidated. Here, we have screened 12 TTSPs using human angiotensin-converting enzyme 2-expressing HEK293T (293T-ACE2) cells and Vero E6 cells and demonstrated that exogenous expression of TMPRSS11D and TMPRSS13 enhanced cellular uptake and subsequent replication of SARS-CoV-2. In addition, SARS-CoV-1 and SARS-CoV-2 share the same TTSPs in the viral entry process. Our study demonstrates the impact of host TTSPs on infection of SARS-CoV-2, which may have implications for cell and tissue tropism, for pathogenicity, and potentially for vaccine development.
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Affiliation(s)
- Mai Kishimoto
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan; (M.K.); (Y.O.); (H.S.)
| | - Kentaro Uemura
- Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan; (K.U.); (T.S.); (A.S.)
- Division of Anti-Virus Drug Research, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, N12 W6, Kita-ku, Sapporo 060-0812, Japan
| | - Takao Sanaki
- Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan; (K.U.); (T.S.); (A.S.)
- Division of Anti-Virus Drug Research, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiko Sato
- Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan; (K.U.); (T.S.); (A.S.)
- Division of Anti-Virus Drug Research, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - William W. Hall
- National Virus Reference Laboratory, School of Medicine, University College Dublin, DO4V1W8 Dublin, Ireland;
- Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, DO4V1W8 Dublin, Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Global Virus Network, 725 West Lombard St, Room S413, Baltimore, MD 21201, USA
| | - Hiroaki Kariwa
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, N18 W9, Kita-ku, Sapporo 060-0818, Japan;
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan; (M.K.); (Y.O.); (H.S.)
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan; (M.K.); (Y.O.); (H.S.)
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Global Virus Network, 725 West Lombard St, Room S413, Baltimore, MD 21201, USA
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan; (M.K.); (Y.O.); (H.S.)
- Correspondence: ; Tel.: +81-11-70-69513
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Lapaillerie D, Charlier C, Fernandes HS, Sousa SF, Lesbats P, Weigel P, Favereaux A, Guyonnet-Duperat V, Parissi V. In Silico, In Vitro and In Cellulo Models for Monitoring SARS-CoV-2 Spike/Human ACE2 Complex, Viral Entry and Cell Fusion. Viruses 2021; 13:365. [PMID: 33669132 PMCID: PMC7996581 DOI: 10.3390/v13030365] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 01/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the recent coronavirus disease 2019 (COVID-19) pandemic. Productive SARS-CoV-2 infection relies on viral entry into cells expressing angiotensin-converting enzyme 2 (ACE2). Indeed, viral entry into cells is mostly mediated by the early interaction between the viral spike protein S and its ACE2 receptor. The S/ACE2 complex is, thus, the first contact point between the incoming virus and its cellular target; consequently, it has been considered an attractive therapeutic target. To further characterize this interaction and the cellular processes engaged in the entry step of the virus, we set up various in silico, in vitro and in cellulo approaches that allowed us to specifically monitor the S/ACE2 association. We report here a computational model of the SARS-CoV-2 S/ACE2 complex, as well as its biochemical and biophysical monitoring using pulldown, AlphaLISA and biolayer interferometry (BLI) binding assays. This led us to determine the kinetic parameters of the S/ACE2 association and dissociation steps. In parallel to these in vitro approaches, we developed in cellulo transduction assays using SARS-CoV-2 pseudotyped lentiviral vectors and HEK293T-ACE2 cell lines generated in-house. This allowed us to recapitulate the early replication stage of the infection mediated by the S/ACE2 interaction and to detect cell fusion induced by the interaction. Finally, a cell imaging system was set up to directly monitor the S/ACE2 interaction in a cellular context and a flow cytometry assay was developed to quantify this association at the cell surface. Together, these different approaches are available for both basic and clinical research, aiming to characterize the entry step of the original SARS-CoV-2 strain and its variants as well as to investigate the possible chemical modulation of this interaction. All these models will help in identifying new antiviral agents and new chemical tools for dissecting the virus entry step.
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Affiliation(s)
- Delphine Lapaillerie
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 33076 Bordeaux, France; (D.L.); (P.L.)
| | - Cathy Charlier
- IMPACT Platform “Interactions Moléculaires Puces ACTivités”, UMR CNRS 6286 UFIP, Université de Nantes, F-44000 Nantes, France; (C.C.); (P.W.)
| | - Henrique S. Fernandes
- UCIBIO@REQUIMTE, BioSIM -Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal; (H.S.F.); (S.F.S.)
| | - Sergio F. Sousa
- UCIBIO@REQUIMTE, BioSIM -Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal; (H.S.F.); (S.F.S.)
| | - Paul Lesbats
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 33076 Bordeaux, France; (D.L.); (P.L.)
| | - Pierre Weigel
- IMPACT Platform “Interactions Moléculaires Puces ACTivités”, UMR CNRS 6286 UFIP, Université de Nantes, F-44000 Nantes, France; (C.C.); (P.W.)
| | - Alexandre Favereaux
- Interdisciplinary Institute for Neuroscience (IINS-CNRS UMR 5297), Centre Broca Nouvelle Aquitaine, 33076 Bordeaux, France;
| | - Véronique Guyonnet-Duperat
- Vect’UB, vectorology platform, INSERM US05—CNRS UMS 3427-TBM-Core, Université de Bordeaux, 33000 Bordeaux, France;
| | - Vincent Parissi
- Fundamental Microbiology and Pathogenicity Lab (MFP), UMR 5234 CNRS-University of Bordeaux, SFR TransBioMed, 33076 Bordeaux, France; (D.L.); (P.L.)
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Mahmood MI, Poma AB, Okazaki KI. Optimizing Gō-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane. Front Mol Biosci 2021; 8:619381. [PMID: 33693028 PMCID: PMC7937874 DOI: 10.3389/fmolb.2021.619381] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/14/2021] [Indexed: 12/31/2022] Open
Abstract
Coarse-grained (CG) molecular dynamics (MD) simulations allow us to access much larger length and time scales than atomistic MD simulations, providing an attractive alternative to the conventional simulations. Based on the well-known MARTINI CG force field, the recently developed Gō-MARTINI model for proteins describes large-amplitude structural dynamics, which has not been possible with the commonly used elastic network model. Using the Gō-MARTINI model, we conduct MD simulations of the F-BAR Pacsin1 protein on lipid membrane. We observe that structural changes of the non-globular protein are largely dependent on the definition of the native contacts in the Gō model. To address this issue, we introduced a simple cutoff scheme and tuned the cutoff distance of the native contacts and the interaction strength of the Lennard-Jones potentials in the Gō-MARTINI model. With the optimized Gō-MARTINI model, we show that it reproduces structural fluctuations of the Pacsin1 dimer from atomistic simulations. We also show that two Pacsin1 dimers properly assemble through lateral interaction on the lipid membrane. Our work presents a first step towards describing membrane remodeling processes in the Gō-MARTINI CG framework by simulating a crucial step of protein assembly on the membrane.
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Affiliation(s)
- Md Iqbal Mahmood
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
| | - Adolfo B Poma
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland
| | - Kei-Ichi Okazaki
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan
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40
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Vilar S, Isom DG. One Year of SARS-CoV-2: How Much Has the Virus Changed? BIOLOGY 2021; 10:91. [PMID: 33530355 PMCID: PMC7911924 DOI: 10.3390/biology10020091] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide crisis with profound effects on both public health and the economy. In order to combat the COVID-19 pandemic, research groups have shared viral genome sequence data through the Global Initiative on Sharing All Influenza Data (GISAID). Over the past year, ≈290,000 full SARS-CoV-2 proteome sequences have been deposited in the GISAID. Here, we used these sequences to assess the rate of nonsynonymous mutants over the entire viral proteome. Our analysis shows that SARS-CoV-2 proteins are mutating at substantially different rates, with most of the viral proteins exhibiting little mutational variability. As anticipated, our calculations capture previously reported mutations that arose in the first months of the pandemic, such as D614G (Spike), P323L (NSP12), and R203K/G204R (Nucleocapsid), but they also identify more recent mutations, such as A222V and L18F (Spike) and A220V (Nucleocapsid), among others. Our comprehensive temporal and geographical analyses show two distinct periods with different proteome mutation rates: December 2019 to July 2020 and August to December 2020. Notably, some mutation rates differ by geography, primarily during the latter half of 2020 in Europe. Furthermore, our structure-based molecular analysis provides an exhaustive assessment of SARS-CoV-2 mutation rates in the context of the current set of 3D structures available for SARS-CoV-2 proteins. This emerging sequence-to-structure insight is beginning to illuminate the site-specific mutational (in)tolerance of SARS-CoV-2 proteins as the virus continues to spread around the globe.
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Affiliation(s)
- Santiago Vilar
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Daniel G. Isom
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
- Institute for Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
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Li ZL, Buck M. Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.06.425627. [PMID: 33442700 PMCID: PMC7805474 DOI: 10.1101/2021.01.06.425627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. As the Spike protein of SARS-CoV-2 is cleaved into the S1 and the S2 domain by furin protease, Nrp1 binds to the newly created C-terminal RRAR amino acid sequence of the S1 domain. In this study, we model the association of a Nrp1 (a2-b1-b2) protein with the Spike protein computationally and analyze the topological constraints in the SARS-CoV-2 Spike protein for binding with Nrp1 and ACE2. Importantly, we study the exit mechanism of S2 from the S1 domain with the assistance of ACE2 as well as Nrp1 by molecular dynamics pulling simulations. In the presence of Nrp1, by binding the S1 more strongly to the host membrane, there is a high probability of S2 being pulled out, rather than S1 being stretched. Thus, Nrp1 binding could stimulate the exit of S2 from the S1 domain, which will likely increase virus infectivity as the liberated S2 domain mediates the fusion of virus and host membranes. Understanding of such a Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future combination therapy.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Department of Pharmacology, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Department of Neurosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
- Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, U. S. A
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