901
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Kyriakopoulos AM, Papaefthymiou A, Georgilas N, Doulberis M, Kountouras J. The Potential Role of Super Spread Events in SARS-COV-2 Pandemic; a Narrative Review. ARCHIVES OF ACADEMIC EMERGENCY MEDICINE 2020; 8:e74. [PMID: 33134970 PMCID: PMC7587986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Coronaviruses, members of Coronaviridae family, cause extensive epidemics of vast diseases like severe acute respiratory syndrome (SARS) and Coronavirus Disease-19 (COVID-19) in animals and humans. Super spread events (SSEs) potentiate early outbreak of the disease and its constant spread in later stages. Viral recombination events within species and across hosts lead to natural selection based on advanced infectivity and resistance. In this review, the importance of containment of SSEs was investigated with emphasis on stopping COVID-19 spread and its socio-economic consequences. A comprehensive search was conducted among literature available in multiple electronic sources to find articles that addressed the "potential role of SSEs on severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) pandemic" and were published before 20th of August 2020. Overall, ninety-eight articles were found eligible and reviewed. Specific screening strategies within potential super spreading host groups can also help to efficiently manage severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) epidemics, in contrast to the partially effective general restriction measures. The effect of SSEs on previous SARS epidemics has been documented in detail. However, the respective potential impact of SSEs on SARS-COV-2 outbreak is composed and presented in the current review, thereby implying the warranted effort required for effective SSE preventive strategies, which may lead to overt global community health benefits. This is crucial for SARS-COV-2 pandemic containment as the vaccine(s) development process will take considerable time to safely establish its potential usefulness for future clinical usage.
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Affiliation(s)
- Anthony M. Kyriakopoulos
- Department of Research and Development, Nasco AD Biotechnology Laboratory, Piraeus 18536, Greece. ,Corresponding author: Anthony M. Kyriakopoulos; Department of Research and Development, Nasco AD Biotechnology Laboratory, 11 Sachtouri Str, Piraeus 18536, Greece. , Fax : 00309210818032
| | - Apostolis Papaefthymiou
- Department of Gastroenterology, University Hospital of Larisa, Larisa 41110, Greece.,Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 54642 Macedonia, Greece
| | - Nikolaos Georgilas
- Department of Nephrology, Agios Pavlos Hospital of Thessaloniki, Thessaloniki 55134, Macedonia, Greece
| | - Michael Doulberis
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 54642 Macedonia, Greece.,Division of Gastroenterology and Hepatology, University Medical Department Kantonsspital Aarau, Aarau 5001, Switzerland
| | - Jannis Kountouras
- Department of Internal Medicine, Second Medical Clinic, Ippokration Hospital, Aristotle University of Thessaloniki, Thessaloniki, 54642 Macedonia, Greece
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902
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Perišić O. Recognition of Potential COVID-19 Drug Treatments through the Study of Existing Protein-Drug and Protein-Protein Structures: An Analysis of Kinetically Active Residues. Biomolecules 2020; 10:biom10091346. [PMID: 32967116 PMCID: PMC7565175 DOI: 10.3390/biom10091346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 01/18/2023] Open
Abstract
We report the results of our in silico study of approved drugs as potential treatments for COVID-19. The study is based on the analysis of normal modes of proteins. The drugs studied include chloroquine, ivermectin, remdesivir, sofosbuvir, boceprevir, and α-difluoromethylornithine (DMFO). We applied the tools we developed and standard tools used in the structural biology community. Our results indicate that small molecules selectively bind to stable, kinetically active residues and residues adjoining them on the surface of proteins and inside protein pockets, and that some prefer hydrophobic sites over other active sites. Our approach is not restricted to viruses and can facilitate rational drug design, as well as improve our understanding of molecular interactions, in general.
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Affiliation(s)
- Ognjen Perišić
- Big Blue Genomics, Vojvode Brane 32, 11000 Belgrade, Serbia
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903
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Xiao T, Lu J, Zhang J, Johnson RI, McKay LGA, Storm N, Lavine CL, Peng H, Cai Y, Rits-Volloch S, Lu S, Quinlan BD, Farzan M, Seaman MS, Griffiths A, Chen B. A trimeric human angiotensin-converting enzyme 2 as an anti-SARS-CoV-2 agent in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32995768 DOI: 10.1101/2020.09.18.301952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Effective intervention strategies are urgently needed to control the COVID-19 pandemic. Human angiotensin-converting enzyme 2 (ACE2) is a carboxypeptidase that forms a dimer and serves as the cellular receptor for SARS-CoV-2. It is also a key negative regulator of the renin-angiotensin system (RAS), conserved in mammals, which modulates vascular functions. We report here the properties of a trimeric ACE2 variant, created by a structure-based approach, with binding affinity of ~60 pM for the spike (S) protein of SARS-CoV-2, while preserving the wildtype peptidase activity as well as the ability to block activation of angiotensin II receptor type 1 in the RAS. Moreover, the engineered ACE2 potently inhibits infection of SARS-CoV-2 in cell culture. These results suggest that engineered, trimeric ACE2 may be a promising anti-SARS-CoV-2 agent for treating COVID-19.
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904
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Shannon A, Selisko B, Le NTT, Huchting J, Touret F, Piorkowski G, Fattorini V, Ferron F, Decroly E, Meier C, Coutard B, Peersen O, Canard B. Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis. Nat Commun 2020; 11:4682. [PMID: 32943628 PMCID: PMC7499305 DOI: 10.1038/s41467-020-18463-z] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. We demonstrate here that Favipiravir predominantly exerts an antiviral effect through lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.
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Affiliation(s)
- Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Barbara Selisko
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Nhung-Thi-Tuyet Le
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Johanna Huchting
- Faculty of Sciences, Department of Chemistry, Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Véronique Fattorini
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Etienne Decroly
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France
| | - Chris Meier
- Faculty of Sciences, Department of Chemistry, Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, D-20146, Hamburg, Germany
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Olve Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA.
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix-Marseille Université, UMR 7257, 13009, Marseille, France.
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905
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Tyagi A, Nigam S, Chauhan RS. A Concise Review of Baseline Facts of SARS‐CoV‐2 for Interdisciplinary Research. ChemistrySelect 2020. [DOI: 10.1002/slct.202002420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Adish Tyagi
- Chemistry Division Bhabha Atomic Research Centre Trombay Mumbai 400085 INDIA
| | - Sandeep Nigam
- Chemistry Division Bhabha Atomic Research Centre Trombay Mumbai 400085 INDIA
| | - Rohit Singh Chauhan
- Chemistry Department K. J. Somaiya College of Science and Commerce Mumbai 400077 India
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906
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Mohamed TA, Elshamy AI, Ibrahim MAA, Zellagui A, Moustafa MF, Abdelrahman AHM, Ohta S, Pare PW, Hegazy MEF. Carotane sesquiterpenes from Ferula vesceritensis: in silico analysis as SARS-CoV-2 binding inhibitors. RSC Adv 2020; 10:34541-34548. [PMID: 35514418 PMCID: PMC9056801 DOI: 10.1039/d0ra06901a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 09/06/2020] [Indexed: 11/21/2022] Open
Abstract
Two sesquiterpenes, 8α-anisate-dauc-4-ene-3,9-dione (webiol anisate) (1) and 10α-acetoxy-6α-benzoate-jaeschkeanadiol (2) as well as, ten known analogues (3-10), and two sesquiterpene coumarins (11-12) were isolated from an organic root extract of Ferula vesceritensis (Fam. Apiaceae). Chemical structures were elucidated based on IR, 1D- and 2D-NMR and HRMS, spectroscopic analyses. With molecular overlap observed between two protease inhibitors that are being examined as anti-COVID-19 drugs, and sesquiterpenes isolated here, metabolite molecular docking calculations were made using the main protease (Mpro), which is required for viral multiplication as well as RNA-dependent RNA polymerase (RdRp). In silico binding-inhibition analysis predicted that select F. vesceritensis sesquiterpenes can bind to these enzymes required for viral replication. Structures of the isolated constituents were also consistent with the chemo-systematic grouping of F. vesceritensis secondary metabolites with other Ferula species.
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Affiliation(s)
- Tarik A Mohamed
- Chemistry of Medicinal Plants Department, National Research Centre 33 El-Bohouth St., Dokki Giza 12622 Egypt +20-23337093
| | - Abdelsamed I Elshamy
- Chemistry of Natural Compounds Department, National Research Centre 33 El Bohouth St., Dokki Giza 12622 Egypt
| | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Ammar Zellagui
- Laboratory of Biomolecule and Plant Breeding, Life Science and Nature Department, Faculty of Exact Science and Life Science and Nature, University of Larbi Ben Mhidi 4000 Oum El Bouaghi Algeria
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University 9004 Abha Kingdom of Saudi Arabia
- Department of Botany & Microbiology, Faculty of Science, South Valley University Qena Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Shinji Ohta
- Graduate School of Integrated Sciences for Life, Hiroshima University 1-7-1 Kagamiyama Higashi-Hiroshima 739-8521 Japan
| | - Paul W Pare
- Department of Chemistry and Biochemistry, Texas Tech University Lubbock TX 79409 USA +1 806 742 1289
| | - Mohamed-Elamir F Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre 33 El-Bohouth St., Dokki Giza 12622 Egypt +20-23337093
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907
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Li S, Li S, Disoma C, Zheng R, Zhou M, Razzaq A, Liu P, Zhou Y, Dong Z, Du A, Peng J, Hu L, Huang J, Feng P, Jiang T, Xia Z. SARS‐CoV‐2: Mechanism of infection and emerging technologies for future prospects. Rev Med Virol 2020; 31:e2168. [DOI: 10.1002/rmv.2168] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/23/2020] [Accepted: 08/30/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Shiqin Li
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Sijia Li
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Cyrollah Disoma
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Rong Zheng
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Mei Zhou
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Aroona Razzaq
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Pinjia Liu
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Yuzheng Zhou
- Department of Cell Biology School of Life Sciences Central South University Changsha China
- Section of Infection and Immunity Herman Ostrow School of Dentistry University of Southern California Los Angeles California USA
| | - Zijun Dong
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Ashuai Du
- Department of Cell Biology School of Life Sciences Central South University Changsha China
| | - Jian Peng
- Department of General Surgery Xiangya Hospital Central South University Changsha China
| | - Liqiang Hu
- The First Hospital of Changsha University of South China Changsha China
| | - Jufang Huang
- Department of Anatomy and Neurobiology School of Basic Medical Sciences Central South University Changsha China
- School of Life Sciences Central South University Changsha China
| | - Pinghui Feng
- Section of Infection and Immunity Herman Ostrow School of Dentistry University of Southern California Los Angeles California USA
| | - Taijiao Jiang
- Center for Systems Medicine Institute of Basic Medical Sciences Chinese Academy of Medical Sciences & Peking Union Medical College Beijing China
- Suzhou Institute of Systems Medicine Suzhou Jiangsu China
| | - Zanxian Xia
- Department of Cell Biology School of Life Sciences Central South University Changsha China
- Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics School of Life Sciences Hunan Key Laboratory of Animal Models for Human Diseases Central South University Changsha China
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908
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Mutlu O, Ugurel OM, Sariyer E, Ata O, Inci TG, Ugurel E, Kocer S, Turgut-Balik D. Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach. J Biomol Struct Dyn 2020; 40:918-930. [PMID: 32933378 PMCID: PMC7544933 DOI: 10.1080/07391102.2020.1819882] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In this study, the Nsp12–Nsp8 complex of SARS-CoV-2 was targeted with structure-based and computer-aided drug design approach because of its vital role in viral replication. Sequence analysis of RNA-dependent RNA polymerase (Nsp12) sequences from 30,366 different isolates were analysed for possible mutations. FDA-approved and investigational drugs were screened for interaction with both mutant and wild-type Nsp12–Nsp8 interfaces. Sequence analysis revealed that 70.42% of Nsp12 sequences showed conserved P323L mutation, located in the Nsp8 binding cleft. Compounds were screened for interface interaction, any with XP GScores lower than −7.0 kcal/mol were considered as possible interface inhibitors. RX-3117 (fluorocyclopentenyl cytosine) and Nebivolol had the highest binding affinities in both mutant and wild-type enzymes, therefore they were selected and resultant protein–ligand complexes were simulated for analysis of stability over 100 ns. Although the selected ligands had partial mobility in the binding cavity, they were not removed from the binding pocket after 100 ns. The ligand RX-3117 remained in the same position in the binding pocket of the mutant and wild-type enzyme after 100 ns MD simulation. However, the ligand Nebivolol folded and embedded in the binding pocket of mutant Nsp12 protein. Overall, FDA-approved and investigational drugs are able to bind to the Nsp12–Nsp8 interaction interface and prevent the formation of the Nsp12–Nsp8 complex. Interruption of viral replication by drugs proposed in this study should be further tested to pave the way for in vivo studies towards the treatment of COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Ozal Mutlu
- Faculty of Arts and Sciences, Department of Biology, Marmara University, Istanbul, Turkey
| | - Osman Mutluhan Ugurel
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey.,School of Engineering and Natural Science, Department of Basic Science, Altinbas University, Istanbul, Turkey
| | - Emrah Sariyer
- Vocational School of Health Services, Medical Laboratory Techniques, Artvin Coruh University, Artvin, Turkey
| | - Oguz Ata
- School of Engineering and Natural Science, Department of Software Engineering, Altinbas University, Istanbul, Turkey
| | - Tugba Gul Inci
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Erennur Ugurel
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Sinem Kocer
- Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, Istanbul Yeni Yuzyil University, Istanbul, Turkey
| | - Dilek Turgut-Balik
- Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
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909
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Chiotos K, Hayes M, Kimberlin DW, Jones SB, James SH, Pinninti SG, Yarbrough A, Abzug MJ, MacBrayne CE, Soma VL, Dulek DE, Vora SB, Waghmare A, Wolf J, Olivero R, Grapentine S, Wattier RL, Bio L, Cross SJ, Dillman NO, Downes KJ, Oliveira CR, Timberlake K, Young J, Orscheln RC, Tamma PD, Schwenk HT, Zachariah P, Aldrich ML, Goldman DL, Groves HE, Rajapakse NS, Lamb GS, Tribble AC, Hersh AL, Thorell EA, Denison MR, Ratner AJ, Newland JG, Nakamura MM. Multicenter Interim Guidance on Use of Antivirals for Children With Coronavirus Disease 2019/Severe Acute Respiratory Syndrome Coronavirus 2. J Pediatric Infect Dis Soc 2020; 10:34-48. [PMID: 32918548 PMCID: PMC7543452 DOI: 10.1093/jpids/piaa115] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Although coronavirus disease 2019 (COVID-19) is a mild infection in most children, a small proportion develop severe or critical illness. Data describing agents with potential antiviral activity continue to expand such that updated guidance is needed regarding use of these agents in children. METHODS A panel of pediatric infectious diseases physicians and pharmacists from 20 geographically diverse North American institutions was convened. Through a series of teleconferences and web-based surveys, a set of guidance statements was developed and refined based on review of the best available evidence and expert opinion. RESULTS Given the typically mild course of COVID-19 in children, supportive care alone is suggested for most cases. For children with severe illness, defined as a supplemental oxygen requirement without need for noninvasive or invasive mechanical ventilation or extracorporeal membrane oxygenation (ECMO), remdesivir is suggested, preferably as part of a clinical trial if available. Remdesivir should also be considered for critically ill children requiring invasive or noninvasive mechanical ventilation or ECMO. A duration of 5 days is appropriate for most patients. The panel recommends against the use of hydroxychloroquine or lopinavir-ritonavir (or other protease inhibitors) for COVID-19 in children. CONCLUSIONS Antiviral therapy for COVID-19 is not necessary for the great majority of pediatric patients. For children with severe or critical disease, this guidance offers an approach for decision-making regarding use of remdesivir.
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Affiliation(s)
- Kathleen Chiotos
- Division of Critical Care Medicine, Department of Anesthesia and Critical Care Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Division of Infectious Diseases, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Antimicrobial Stewardship Program, Children’s Hospital of Philadelphia, Philadelphia, United States,Corresponding Author: Kathleen Chiotos, MD, Roberts Center for Pediatric Research, 2716 South Street, Room 10292, Philadelphia, PA 19146,
| | - Molly Hayes
- Antimicrobial Stewardship Program, Children’s Hospital of Philadelphia, Philadelphia, United States
| | - David W Kimberlin
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Sarah B Jones
- Department of Pharmacy, Boston Children’s Hospital, Boston, MA, United States,Antimicrobial Stewardship Program, Boston Children’s Hospital, Boston, MA, United States
| | - Scott H James
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Swetha G Pinninti
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - April Yarbrough
- Department of Pharmacy, Children’s of Alabama, Birmingham, AL, United States
| | - Mark J Abzug
- Division of Infectious Diseases, Department of Pediatrics, University of Colorado School of Medicine and Children’s Hospital Colorado, Aurora, CO, United States
| | | | - Vijaya L Soma
- Division of Infectious Diseases, Department of Pediatrics, New York University Grossman School of Medicine and Hassenfeld Children’s Hospital, New York, NY, United States
| | - Daniel E Dulek
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University and Monroe Carell Jr. Children’s Hospital, Nashville, TN, United States
| | - Surabhi B Vora
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, WA, United States
| | - Alpana Waghmare
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, WA, United States,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Rosemary Olivero
- Section of Infectious Diseases, Department of Pediatrics and Human Development, Helen DeVos Children's Hospital of Spectrum Health, Michigan State College of Human Medicine, Grand Rapids, MI, United States
| | - Steven Grapentine
- Department of Pharmacy, UCSF Benioff Children’s Hospital, San Francisco, CA, United States
| | - Rachel L Wattier
- Division of Infectious Diseases and Global Health, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Laura Bio
- Department of Pharmacy, Lucile Packard Children’s Hospital Stanford, Stanford, United States
| | - Shane J Cross
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Nicholas O Dillman
- Department of Pharmacy, CS Mott Children’s Hospital, Ann Arbor, MI, United States
| | - Kevin J Downes
- Division of Infectious Diseases, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Carlos R Oliveira
- Yale University School of Medicine, Yale University, New Haven, CT, United States
| | | | - Jennifer Young
- Department of Pharmacy, St. Louis Children’s Hospital, St. Louis, MO, United States
| | - Rachel C Orscheln
- Division of Infectious Diseases, Department of Pediatrics, Washington University and St. Louis Children’s Hospital, St. Louis, MO, United States
| | - Pranita D Tamma
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hayden T Schwenk
- Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine & Lucile Packard Children’s Hospital Stanford, Stanford, CA, United States
| | - Philip Zachariah
- Division of Infectious Diseases, Department of Pediatrics, Columbia University, New York, NY, United States
| | - Margaret L Aldrich
- Division of Infectious Diseases, Department of Pediatrics, Children’s Hospital at Montefiore, New York, NY, United States
| | - David L Goldman
- Division of Infectious Diseases, Department of Pediatrics, Children’s Hospital at Montefiore, New York, NY, United States
| | - Helen E Groves
- Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, Toronto, Canada
| | - Nipunie S Rajapakse
- Division of Pediatric Infectious Diseases, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, United States
| | - Gabriella S Lamb
- Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
| | - Alison C Tribble
- Department of Pediatrics, Division of Infectious Diseases, University of Michigan and CS Mott Children’s Hospital, Ann Arbor, MI, United States
| | - Adam L Hersh
- Division of Infectious Diseases, Department of Pediatrics, University of Utah and Primary Children’s Hospital, Salt Lake City, UT, United States
| | - Emily A Thorell
- Division of Infectious Diseases, Department of Pediatrics, University of Utah and Primary Children’s Hospital, Salt Lake City, UT, United States
| | - Mark R Denison
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University and Monroe Carell Jr. Children’s Hospital, Nashville, TN, United States
| | - Adam J Ratner
- Division of Infectious Diseases, Department of Pediatrics, New York University Grossman School of Medicine and Hassenfeld Children’s Hospital, New York, NY, United States,Department of Microbiology, New York University Grossman School of Medicine, New York, NY, United States
| | - Jason G Newland
- Division of Infectious Diseases, Department of Pediatrics, Washington University and St. Louis Children’s Hospital, St. Louis, MO, United States
| | - Mari M Nakamura
- Antimicrobial Stewardship Program, Boston Children’s Hospital, Boston, MA, United States,Division of Infectious Diseases, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States,Alternate Corresponding Author: Mari M. Nakamura, MD, MPH, Antimicrobial Stewardship Program, Boston Children’s Hospital, 300 Longwood Avenue, Mailstop BCH 3052, Boston, MA 02115, 617-355-1561,
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910
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Hartenian E, Nandakumar D, Lari A, Ly M, Tucker JM, Glaunsinger BA. The molecular virology of coronaviruses. J Biol Chem 2020; 295:12910-12934. [PMID: 32661197 PMCID: PMC7489918 DOI: 10.1074/jbc.rev120.013930] [Citation(s) in RCA: 302] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/13/2020] [Indexed: 12/14/2022] Open
Abstract
Few human pathogens have been the focus of as much concentrated worldwide attention as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of COVID-19. Its emergence into the human population and ensuing pandemic came on the heels of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), two other highly pathogenic coronavirus spillovers, which collectively have reshaped our view of a virus family previously associated primarily with the common cold. It has placed intense pressure on the collective scientific community to develop therapeutics and vaccines, whose engineering relies on a detailed understanding of coronavirus biology. Here, we present the molecular virology of coronavirus infection, including its entry into cells, its remarkably sophisticated gene expression and replication mechanisms, its extensive remodeling of the intracellular environment, and its multifaceted immune evasion strategies. We highlight aspects of the viral life cycle that may be amenable to antiviral targeting as well as key features of its biology that await discovery.
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Affiliation(s)
- Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Divya Nandakumar
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Azra Lari
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Michael Ly
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Jessica M Tucker
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Britt A Glaunsinger
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Department of Plant and Microbial Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA.
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911
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Mansour MA, AboulMagd AM, Abdel-Rahman HM. Quinazoline-Schiff base conjugates: in silico study and ADMET predictions as multi-target inhibitors of coronavirus (SARS-CoV-2) proteins. RSC Adv 2020; 10:34033-34045. [PMID: 35519053 PMCID: PMC9056799 DOI: 10.1039/d0ra06424f] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022] Open
Abstract
The 2019 coronavirus (COVID-19) pandemic is spreading worldwide, with a dramatic increase in death without any effective therapeutic treatment available up to now. We previously reported quinazoline-trihydroxyphenyl Schiff base conjugates as phosphodiesterase 4B (PDE 4B) inhibitors (an enzyme that plays an essential role in the early stages of COVID-19 pneumonia). Additionally, the structural similarity between these conjugates and identified anti-severe acute respiratory syndrome (SARS)-coronavirus (CoV)-2 flavonoids inspired us to in silico study their possible binding interactions with essential SARS-CoV-2 proteins. Thus, this study provides an insight into the potential bindings between quinazoline-Schiff base conjugates and SARS-CoV-2 proteins, including spike glycoprotein (SGp), main protease (Mpro) and RNA-dependent RNA polymerase (RdRp), to offer an opportunity to find an effective therapy. Besides this, based on the role that COVID-19 plays in iron dysmetabolism, the conjugate trihydroxyphenyl moiety should be reconsidered as an iron chelator. Moreover, molecular dynamics simulations of quinazoline derivative Ic bound to the mentioned targets were carried out. Finally, ADMET calculations were performed for the studied compounds to predict their pharmacokinetic profiles.
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Affiliation(s)
- Mostafa A Mansour
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University (NUB) Beni-Suef Egypt
| | - Asmaa M AboulMagd
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University (NUB) Beni-Suef Egypt
| | - Hamdy M Abdel-Rahman
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University (NUB) Beni-Suef Egypt
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
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912
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Banerjee A, Sarkar R, Mitra S, Lo M, Dutta S, Chawla-Sarkar M. The Novel Coronavirus Enigma: Phylogeny and Analyses of Coevolving Mutations Among the SARS-CoV-2 Viruses Circulating in India. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2020; 1:e20735. [PMID: 33496683 PMCID: PMC7720937 DOI: 10.2196/20735] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/25/2020] [Accepted: 08/24/2020] [Indexed: 01/15/2023]
Abstract
BACKGROUND The RNA genome of the emerging novel coronavirus is rapidly mutating, and its human-to-human transmission rate is increasing. Hence, temporal dissection of their evolutionary dynamics, the nature of variations among different strains, and understanding the single nucleotide polymorphisms in the endemic settings are crucial. Delineating the heterogeneous genomic constellations of this novel virus will help us understand its complex behavior in a particular geographical region. OBJECTIVE This is a comprehensive analysis of 95 Indian SARS-CoV-2 genome sequences available from the Global Initiative on Sharing All Influenza Data (GISAID) repository during the first 6 months of 2020 (January through June). Evolutionary dynamics, gene-specific phylogeny, and the emergence of the novel coevolving mutations in 9 structural and nonstructural genes among circulating SARS-CoV-2 strains across 12 different Indian states were analyzed. METHODS A total of 95 SARS-CoV-2 nucleotide sequences submitted from India were downloaded from the GISAID database. Molecular Evolutionary Genetics Analysis, version X software was used to construct the 9 phylogenetic dendrograms based on nucleotide sequences of the SARS-CoV-2 genes. Analyses of the coevolving mutations were done in comparison to the prototype SARS-CoV-2 from Wuhan, China. The secondary structure of the RNA-dependent RNA polymerase/nonstructural protein NSP12 was predicted with respect to the novel A97V mutation. RESULTS Phylogenetic analyses revealed the evolution of "genome-type clusters" and adaptive selection of "L"-type SARS-CoV-2 strains with genetic closeness to the bat severe acute respiratory syndrome-like coronaviruses. These strains were distant to pangolin or Middle East respiratory syndrome-related coronavirus strains. With regard to the novel coevolving mutations, 2 groups have been seen circulating in India at present, the "major group" (66/95, 69.4%) and the "minor group" (21/95, 22.1%) , harboring 4 and 5 coexisting mutations, respectively. The "major group" mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6 gene), were unique to the Indian isolates. CONCLUSIONS This study highlights the rapidly evolving SARS-CoV-2 virus and the cocirculation of multiple clades and subclades. This comprehensive study is a potential resource for monitoring the novel mutations in the viral genome, interpreting changes in viral pathogenesis, and designing vaccines or other therapeutics.
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Affiliation(s)
- Anindita Banerjee
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases Kolkata India
| | - Rakesh Sarkar
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases Kolkata India
| | - Suvrotoa Mitra
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases Kolkata India
| | - Mahadeb Lo
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases Kolkata India
| | - Shanta Dutta
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases Kolkata India
| | - Mamta Chawla-Sarkar
- Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases Kolkata India
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913
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Jiang Y, Yin W, Xu HE. RNA-dependent RNA polymerase: Structure, mechanism, and drug discovery for COVID-19. Biochem Biophys Res Commun 2020; 538:47-53. [PMID: 32943188 PMCID: PMC7473028 DOI: 10.1016/j.bbrc.2020.08.116] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global pandemic. Although great efforts have been made to develop effective therapeutic interventions, only the nucleotide analog remdesivir was approved for emergency use against COVID-19. Remdesivir targets the RNA-dependent RNA polymerase (RdRp), an essential enzyme for viral RNA replication and a promising drug target for COVID-19. Recently, several structures of RdRp in complex with substrate RNA and remdesivir were reported, providing insights into the mechanisms of RNA recognition by RdRp. These structures also reveal the mechanism of RdRp inhibition by nucleotide inhibitors and offer a molecular template for the development of RdRp-targeting drugs. This review discusses the recognition mechanism of RNA and nucleotide inhibitor by RdRp, and its implication in drug discovery.
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Affiliation(s)
- Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Wanchao Yin
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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914
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Ladner JT, Larsen BB, Bowers JR, Hepp CM, Bolyen E, Folkerts M, Sheridan K, Pfeiffer A, Yaglom H, Lemmer D, Sahl JW, Kaelin EA, Maqsood R, Bokulich NA, Quirk G, Watts TD, Komatsu KK, Waddell V, Lim ES, Caporaso JG, Engelthaler DM, Worobey M, Keim P. An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona. mBio 2020; 11:e02107-20. [PMID: 32887735 PMCID: PMC7474171 DOI: 10.1128/mbio.02107-20] [Citation(s) in RCA: 25] [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: 07/28/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020.IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest undetected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.
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Affiliation(s)
- Jason T Ladner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Jolene R Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Crystal M Hepp
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, USA
| | - Evan Bolyen
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Megan Folkerts
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Krystal Sheridan
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ashlyn Pfeiffer
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Hayley Yaglom
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Darrin Lemmer
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Emily A Kaelin
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Tempe, Arizona, USA
| | - Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Tempe, Arizona, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Grace Quirk
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Thomas D Watts
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | | | - Victor Waddell
- Bureau of Laboratory Services, Arizona Department of Health Services, Phoenix, Arizona, USA
| | - Efrem S Lim
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Tempe, Arizona, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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915
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Robson F, Khan KS, Le TK, Paris C, Demirbag S, Barfuss P, Rocchi P, Ng WL. Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting. Mol Cell 2020; 79:710-727. [PMID: 32853546 PMCID: PMC7402271 DOI: 10.1016/j.molcel.2020.07.027] [Citation(s) in RCA: 249] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 01/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) that is wreaking havoc on worldwide public health and economies has heightened awareness about the lack of effective antiviral treatments for human coronaviruses (CoVs). Many current antivirals, notably nucleoside analogs (NAs), exert their effect by incorporation into viral genomes and subsequent disruption of viral replication and fidelity. The development of anti-CoV drugs has long been hindered by the capacity of CoVs to proofread and remove mismatched nucleotides during genome replication and transcription. Here, we review the molecular basis of the CoV proofreading complex and evaluate its potential as a drug target. We also consider existing nucleoside analogs and novel genomic techniques as potential anti-CoV therapeutics that could be used individually or in combination to target the proofreading mechanism.
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Affiliation(s)
- Fran Robson
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Khadija Shahed Khan
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Thi Khanh Le
- Life Science Department, University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam; Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Clément Paris
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Sinem Demirbag
- Faculty of Engineering and Natural Sciences, Sabanci University, İstanbul, Turkey
| | - Peter Barfuss
- Université Paris-Est, Cermics (ENPC), INRIA, 77455 Marne-la-Vallée, France
| | - Palma Rocchi
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes, Marseille, France
| | - Wai-Lung Ng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
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916
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Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight. PLoS One 2020; 15:e0238344. [PMID: 32881907 PMCID: PMC7470274 DOI: 10.1371/journal.pone.0238344] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/14/2020] [Indexed: 12/20/2022] Open
Abstract
A novel severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) causing COVID-19 pandemic in humans, recently emerged and has exported in more than 200 countries as a result of rapid spread. In this study, we have made an attempt to investigate the SARS-CoV-2 genome reported from 13 different countries, identification of mutations in major coronavirus proteins of these different SARS-CoV-2 genomes and compared with SARS-CoV. These thirteen complete genome sequences of SARS-CoV-2 showed high identity (>99%) to each other, while they shared 82% identity with SARS-CoV. Here, we performed a very systematic mutational analysis of SARS-CoV-2 genomes from different geographical locations, which enabled us to identify numerous unique features of this viral genome. This includes several important country-specific unique mutations in the major proteins of SARS-CoV-2 namely, replicase polyprotein, spike glycoprotein, envelope protein and nucleocapsid protein. Indian strain showed mutation in spike glycoprotein at R408I and in replicase polyprotein at I671T, P2144S and A2798V,. While the spike protein of Spain & South Korea carried F797C and S221W mutation, respectively. Likewise, several important country specific mutations were analyzed. The effect of mutations of these major proteins were also investigated using various in silico approaches. Main protease (Mpro), the therapeutic target protein of SARS with maximum reported inhibitors, was thoroughly investigated and the effect of mutation on the binding affinity and structural dynamics of Mpro was studied. It was found that the R60C mutation in Mpro affects the protein dynamics, thereby, affecting the binding of inhibitor within its active site. The implications of mutation on structural characteristics were determined. The information provided in this manuscript holds great potential in further scientific research towards the design of potential vaccine candidates/small molecular inhibitor against COVID19.
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917
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Elkarhat Z, Charoute H, Elkhattabi L, Barakat A, Rouba H. Potential inhibitors of SARS-cov-2 RNA dependent RNA polymerase protein: molecular docking, molecular dynamics simulations and MM-PBSA analyses. J Biomol Struct Dyn 2020; 40:361-374. [PMID: 32873176 DOI: 10.1080/07391102.2020.1813628] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The SARS-cov-2 RNA dependent RNA polymerase (nsp12) is a crucial viral enzyme that catalyzes the replication of RNA from RNA templates. The fixation of some ligands in the active site may alter the viral life cycle. The aim of the present study is to identify the conservation level of nsp12 motifs (A-G), using consurf server, and discover their interactions with rifabutin, rifampicin, rifapentin, sorangicin A, streptolydigin, myxopyronin B, VXR and VRX using AutoDockTools-1.5.6, Gromacs 2018.2 and g-mmpbsa. Thus, the most of amino acids residues located in nsp12 protein Motifs (A-G) were predicted as highly conserved. The binding energies of streptolydigin, VXR, rifabutin, rifapentine, VRX, sorangicin A, myxopyronin B and rifampicin with nsp12 protein are -8.11, -8.23, -7.14, -6.94, -6.55, -5.46, -5.33 and -5.26 kcal/mol, respectively. In the other hand, the binding energies of ligand in the same order with nsp7-nsp8-nsp12 complex are -7.23, -7.08, -7.21, -7, -6.59, -8.73, -5.52, -5.87 kcal/mol, respectively. All ligands interact with at least two nsp12 motifs. The molecular dynamics simulation of nsp12-streptolydigin and nsp12-VXR complexes shows that these two complexes are stable and the number of hydrogen bonds as a function of time, after 30 ns of simulation, varies between 0 and 6 for nsp12-streptolydigin complex and between 0 and 4 for nsp12-VXR complex. The average of free binding energies obtained using g_mmpbsa, after 30 ns of simulation, is -191.982 Kj/mol for nsp12-streptolydigin complex and -153.583 Kj/mol for nsp12-VXR complex. Our results suggest that these ligands may be used as inhibitors of SARS-cov-2 nsp12 protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zouhair Elkarhat
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hicham Charoute
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Lamiae Elkhattabi
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, Département de la Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco
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918
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Zhu G, Zhu C, Zhu Y, Sun F. Minireview of progress in the structural study of SARS-CoV-2 proteins. CURRENT RESEARCH IN MICROBIAL SCIENCES 2020; 1:53-61. [PMID: 33236001 PMCID: PMC7323663 DOI: 10.1016/j.crmicr.2020.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/18/2023] Open
Abstract
A severe form of pneumonia, named coronavirus disease 2019 (COVID-19) by the World Health Organization, broke out in China and rapidly developed into a global pandemic, with millions of cases and hundreds of thousands of deaths reported globally. The novel coronavirus, which was designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified as the etiological agent of COVID-19. On the basis of experience accumulated following previous SARS-CoV and MERS-CoV outbreaks and research, a series of studies have been conducted rapidly, and major progress has been achieved with regard to the understanding of the phylogeny and genomic organization of SARS-CoV-2 in addition its molecular mechanisms of infection and replication. In the present review, we summarized crucial developments in the elucidation of the structure and function of key SARS-CoV-2 proteins, especially the main protease, RNA-dependent RNA polymerase, spike glycoprotein, and nucleocapsid protein. Results of studies on their associated inhibitors and drugs have also been highlighted.
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Key Words
- 3CLpro, 3C-like protease
- 6-HB, six-helix bundle
- ACE2, angiotensin-converting enzyme 2
- COVID-19
- COVID-19, coronavirus disease 2019
- CatB/L, cysteine proteases-cathepsin B and L
- Drug-screening
- E protein, Envelope protein
- Genome-encoded proteins
- HR1, heptad repeat 1
- HR2, heptad repeat 2
- M protein, Membrane protein
- MERS-CoV, the Middle Eastern respiratory syndrome coronavirus
- Mpro, Main protease
- N protein, Nucleocapsid protein
- NSP, non-structural protein
- ORF, Open reading frame
- PD, peptidase domain
- RBD, receptor-binding domain
- RBM, receptor-binding motif
- RMP, The remdesivir monophosphate
- RdRp, RNA-dependent RNA polymerase
- S protein, Spike glycoprotein
- SARS-CoV, severe acute respiratory syndrome coronavirus
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- Structure-based screening
- gRNA, genomic RNA
- sgRNA, subgenomic RNA
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Affiliation(s)
- Guoliang Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunmei Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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919
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Hightower LE, Santoro MG. Coronaviruses and stress: from cellular to global. Cell Stress Chaperones 2020; 25:701-705. [PMID: 32889638 PMCID: PMC7474501 DOI: 10.1007/s12192-020-01155-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2020] [Indexed: 12/12/2022] Open
Abstract
Near the end of 2019, SARS-CoV-2, a novel highly contagious coronavirus phylogenetically related to the SARS virus, entered the human population with lethal consequences. This special issue devoted to the resulting disease COVID-19 was not planned but instead the articles accumulated organically as researchers in the cell stress response field noticed similarities among the pathophysiology of COVID-19 infections and the responses that they studied in contexts unrelated to viral infection. We preface the issue with an introductory article which begins with a brief review of the structure and biology of SARS-CoV-2. As we collected and compared the COVID-19 articles, several shared themes emerged. In the second part of the introduction, each article is summarized briefly and the common themes that link each into a spontaneously arising chain of ideas and hypotheses are emphasized. These themes include growing evidence of molecular mimicry among the viral proteins and the proteins of patients. The realization that much of the consequences of such immune mimicry may play out on the plasma membrane of vascular endothelial cells raised the specter of autoimmune-induced vascular endothelial damage in multiple organs. Proposals of new therapeutic approaches have coalesced around the theme of inducing protection of the vascular endothelium. New chemical treatments that are proposed include stannous chloride, inducers of the gasotransmitter hydrogen sulfide such as sodium thiosulfate and inducers of the cytoprotective stress protein heme oxygenase. Oxygen delivered by ventilators is already in extensive use to provide life support for patients with severe COVID-19. Two articles propose to advance the use of oxygen to the level of a therapeutic treatment early in the detection of the virus in infected patients by delivering oxygen under elevated pressure in hyperbaric chambers. At elevated blood plasma concentrations, hyperbaric oxygen is capable of achieving results far beyond the capability of ventilators as it promotes the activation of transcription factors that control the establishment of inducible cellular defense systems.
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Affiliation(s)
- Lawrence E Hightower
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA.
| | - M Gabriella Santoro
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Institute of Translational Pharmacology, CNR, Rome, Italy
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920
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Alamri MA, Altharawi A, Alabbas AB, Alossaimi MA, Alqahtani SM. Structure-based virtual screening and molecular dynamics of phytochemicals derived from Saudi medicinal plants to identify potential COVID-19 therapeutics. ARAB J CHEM 2020; 13:7224-7234. [PMID: 34909058 PMCID: PMC7415226 DOI: 10.1016/j.arabjc.2020.08.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/02/2020] [Indexed: 01/26/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has affected almost every country in the world by causing a global pandemic with a high mortality rate. Lack of an effective vaccine and/or antiviral drugs against SARS-CoV-2, the causative agent, has severely hampered the response to this novel coronavirus. Natural products have long been used in traditional medicines to treat various diseases, and purified phytochemicals from medicinal plants provide a valuable scaffold for the discovery of new drug leads. In the present study, we performed a computational screening of an in-house database composed of ~1000 phytochemicals derived from traditional Saudi medicinal plants with recognised antiviral activity. Structure-based virtual screening was carried out against three druggable SARS-CoV-2 targets, viral RNA-dependent RNA polymerase (RdRp), 3-chymotrypsin-like cysteine protease (3CLpro) and papain like protease (PLpro) to identify putative inhibitors that could facilitate the development of potential anti-COVID-19 drug candidates. Computational analyses identified three compounds inhibiting each target, with binding affinity scores ranging from -9.9 to -6.5 kcal/mol. Among these, luteolin 7-rutinoside, chrysophanol 8-(6-galloylglucoside) and kaempferol 7-(6″-galloylglucoside) bound efficiently to RdRp, while chrysophanol 8-(6-galloylglucoside), 3,4,5-tri-O-galloylquinic acid and mulberrofuran G interacted strongly with 3CLpro, and withanolide A, isocodonocarpine and calonysterone bound tightly to PLpro. These potential drug candidates will be subjected to further in vitro and in vivo studies and may assist the development of effective anti-COVID-19 drugs.
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921
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Machhi J, Herskovitz J, Senan AM, Dutta D, Nath B, Oleynikov MD, Blomberg WR, Meigs DD, Hasan M, Patel M, Kline P, Chang RCC, Chang L, Gendelman HE, Kevadiya BD. The Natural History, Pathobiology, and Clinical Manifestations of SARS-CoV-2 Infections. J Neuroimmune Pharmacol 2020; 15:359-386. [PMID: 32696264 PMCID: PMC7373339 DOI: 10.1007/s11481-020-09944-5] [Citation(s) in RCA: 319] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of coronavirus disease 2019 (COVID-19). SARS-CoV-2, is a positive-sense single-stranded RNA virus with epithelial cell and respiratory system proclivity. Like its predecessor, SARS-CoV, COVID-19 can lead to life-threatening disease. Due to wide geographic impact affecting an extremely high proportion of the world population it was defined by the World Health Organization as a global public health pandemic. The infection is known to readily spread from person-to-person. This occurs through liquid droplets by cough, sneeze, hand-to-mouth-to-eye contact and through contaminated hard surfaces. Close human proximity accelerates SARS-CoV-2 spread. COVID-19 is a systemic disease that can move beyond the lungs by blood-based dissemination to affect multiple organs. These organs include the kidney, liver, muscles, nervous system, and spleen. The primary cause of SARS-CoV-2 mortality is acute respiratory distress syndrome initiated by epithelial infection and alveolar macrophage activation in the lungs. The early cell-based portal for viral entry is through the angiotensin-converting enzyme 2 receptor. Viral origins are zoonotic with genomic linkages to the bat coronaviruses but without an identifiable intermediate animal reservoir. There are currently few therapeutic options, and while many are being tested, although none are effective in curtailing the death rates. There is no available vaccine yet. Intense global efforts have targeted research into a better understanding of the epidemiology, molecular biology, pharmacology, and pathobiology of SARS-CoV-2. These fields of study will provide the insights directed to curtailing this disease outbreak with intense international impact. Graphical Abstract.
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Affiliation(s)
- Jatin Machhi
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Jonathan Herskovitz
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ahmed M Senan
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 20095, China
| | - Debashis Dutta
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Barnali Nath
- Viral Immunology Lab, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Maxim D Oleynikov
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Wilson R Blomberg
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Douglas D Meigs
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Mahmudul Hasan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Milankumar Patel
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Peter Kline
- SARS-CoV-2 Patient Survivor, Chicago, IL, 60204, USA
| | - Raymond Chuen-Chung Chang
- Laboratory of Neurodegenerative Diseases, School of Biomedical Sciences, LKS Faculty of Medicine, and State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Linda Chang
- University of Maryland, School of Medicine, Baltimore, MD, 21201, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA.
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA.
- Interventional Regenerative Medicine and Imaging Laboratory, Department of Radiology, Stanford University, Palo Alto, CA, 94304, USA.
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922
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Amin SA, Jha T. Fight against novel coronavirus: A perspective of medicinal chemists. Eur J Med Chem 2020; 201:112559. [PMID: 32563814 PMCID: PMC7289749 DOI: 10.1016/j.ejmech.2020.112559] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022]
Abstract
The ongoing novel coronavirus disease (COVID-19) pandemic makes us painfully perceive that our bullet shells are blank so far for fighting against severe human coronavirus (HCoV). In spite of vast research work, it is crystal clear that the evident does not warrant the commercial blossoming of anti-HCoV drugs. In this circumstance, drug repurposing and/or screening of databases are the only fastest option. This study is an initiative to recapitulate the medicinal chemistry of severe acute respiratory syndrome (SARS)-CoV-2 (SARS-CoV-2). The aim is to present an exquisite delineation of the current research from the perspective of a medicinal chemist to allow the rapid development of anti-SARS-CoV-2 agents.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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923
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Shi W, Lv J, Lin L. Coagulopathy in COVID-19: Focus on vascular thrombotic events. J Mol Cell Cardiol 2020; 146:32-40. [PMID: 32681845 PMCID: PMC7362808 DOI: 10.1016/j.yjmcc.2020.07.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/28/2020] [Accepted: 07/11/2020] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 causes a phenotype of pneumonia with diverse manifestation, which is termed as coronavirus disease 2019 (COVID-19). An impressive high transmission rate allows COVID-19 conferring enormous challenge for clinicians worldwide, and developing to a pandemic level. Combined with a series of complications, a part of COVID-19 patients progress into severe cases, which critically contributes to the risk of fatality. To date, coagulopathy has been found as a prominent feature of COVID-19 and severe coagulation dysfunction may be associated with poor prognosis. Coagulopathy in COVID-19 may predispose patients to hypercoagulability-related disorders including thrombosis and even fatal vascular events. Inflammatory storm, uncontrolled inflammation-mediated endothelial injury and renin angiotensin system (RAS) dysregulation are the potential mechanisms. Ongoing efforts made to develop promising therapies provide several potential strategies for hypercoagulability in COVID-19. In this review, we introduce the clinical features of coagulation and the increased vascular thrombotic risk conferred by coagulopathy according to present reports about COVID-19. The potential underlying mechanisms and emerging therapeutic avenues are discussed, emphasizing an urgent need for effective interventions.
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Affiliation(s)
- Wei Shi
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
| | - Jiagao Lv
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
| | - Li Lin
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China.
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924
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Fan S, Xiao D, Wang Y, Liu L, Zhou X, Zhong W. Research progress on repositioning drugs and specific therapeutic drugs for SARS-CoV-2. Future Med Chem 2020; 12:1565-1578. [PMID: 32638628 PMCID: PMC7341957 DOI: 10.4155/fmc-2020-0158] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 has been widely spread around the world and COVID-19 was declared a global pandemic by the WHO. Limited clinically effective antiviral drugs are available now. The development of anti-SARS-CoV-2 drugs has become an urgent work worldwide. At present, potential therapeutic targets and drugs for SARS-CoV-2 are continuously reported, and many repositioning drugs are undergoing extensive clinical research, including remdesivir and chloroquine. On the other hand, structures of many important viral target proteins and host target proteins, including that of RdRp and Mpro were constantly reported, which greatly promoted structure-based drug design. This paper summarizes the current research progress and challenges in the development of anti-SARS-CoV-2 drugs, and proposes novel short-term and long-term drug research strategies.
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Affiliation(s)
- Shiyong Fan
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Dian Xiao
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Yanming Wang
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Lianqi Liu
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Xinbo Zhou
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
| | - Wu Zhong
- National Engineering Research Center For The Emergency Drug, Beijing Institute of Pharmacology & Toxicology, Beijing, 100850, China
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925
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Hecel A, Ostrowska M, Stokowa-Sołtys K, Wątły J, Dudek D, Miller A, Potocki S, Matera-Witkiewicz A, Dominguez-Martin A, Kozłowski H, Rowińska-Żyrek M. Zinc(II)-The Overlooked Éminence Grise of Chloroquine's Fight against COVID-19? Pharmaceuticals (Basel) 2020; 13:E228. [PMID: 32882888 PMCID: PMC7558363 DOI: 10.3390/ph13090228] [Citation(s) in RCA: 17] [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: 08/03/2020] [Revised: 08/28/2020] [Accepted: 08/29/2020] [Indexed: 12/24/2022] Open
Abstract
Zn(II) is an inhibitor of SARS-CoV-2's RNA-dependent RNA polymerase, and chloroquine and hydroxychloroquine are Zn(II) ionophores-this statement gives a curious mind a lot to think about. We show results of the first clinical trials on chloroquine (CQ) and hydroxychloroquine (HCQ) in the treatment of COVID-19, as well as earlier reports on the anticoronaviral properties of these two compounds and of Zn(II) itself. Other FDA-approved Zn(II) ionophores are given a decent amount of attention and are thought of as possible COVID-19 therapeutics.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
| | - Małgorzata Ostrowska
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
| | - Kamila Stokowa-Sołtys
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
| | - Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
| | - Dorota Dudek
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
| | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
| | - Agnieszka Matera-Witkiewicz
- Screening Laboratory of Biological Activity Tests and Collection of Biological Material, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland;
| | - Alicia Dominguez-Martin
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada, E-18071 Granada, Spain;
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
- Department of Physiotherapy, Opole Medical School, Katowicka 68, 40-060 Opole, Poland
| | - Magdalena Rowińska-Żyrek
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wroclaw, Poland; (A.H.); (M.O.); (K.S.-S.); (J.W.); (D.D.); (A.M.); (S.P.); (H.K.)
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926
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Joshi S, Joshi M, Degani MS. Tackling SARS-CoV-2: proposed targets and repurposed drugs. Future Med Chem 2020; 12:1579-1601. [PMID: 32564623 PMCID: PMC7307730 DOI: 10.4155/fmc-2020-0147] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/03/2020] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 pandemic, declared as a global health emergency by the WHO in February 2020, has currently infected more than 6 million people with fatalities near 371,000 and increasing exponentially, in absence of vaccines and drugs. The pathogenesis of SARS-CoV-2 is still being elucidated. Identifying potential targets and repurposing drugs as therapeutic options is the need of the hour. In this review, we focus on potential druggable targets and suitable therapeutics, currently being explored in clinical trials, to treat SARS-CoV-2 infection. A brief understanding of the complex interactions of both viral as well as host targets, and the possible repurposed drug candidates are described with an emphasis on understanding the mechanisms at the molecular level.
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Affiliation(s)
- Siddhi Joshi
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
| | - Maithili Joshi
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
| | - Mariam S Degani
- Department of Pharmaceutical Sciences & Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Mumbai, 400019, Maharashtra, India
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927
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Cuadrado A, Pajares M, Benito C, Jiménez-Villegas J, Escoll M, Fernández-Ginés R, Garcia Yagüe AJ, Lastra D, Manda G, Rojo AI, Dinkova-Kostova AT. Can Activation of NRF2 Be a Strategy against COVID-19? Trends Pharmacol Sci 2020; 41:598-610. [PMID: 32711925 PMCID: PMC7359808 DOI: 10.1016/j.tips.2020.07.003] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 01/08/2023]
Abstract
Acute respiratory distress syndrome (ARDS) caused by SARS-CoV-2 is largely the result of a dysregulated host response, followed by damage to alveolar cells and lung fibrosis. Exacerbated proinflammatory cytokines release (cytokine storm) and loss of T lymphocytes (leukopenia) characterize the most aggressive presentation. We propose that a multifaceted anti-inflammatory strategy based on pharmacological activation of nuclear factor erythroid 2 p45-related factor 2 (NRF2) can be deployed against the virus. The strategy provides robust cytoprotection by restoring redox and protein homeostasis, promoting resolution of inflammation, and facilitating repair. NRF2 activators such as sulforaphane and bardoxolone methyl are already in clinical trials. The safety and efficacy information of these modulators in humans, together with their well-documented cytoprotective and anti-inflammatory effects in preclinical models, highlight the potential of this armamentarium for deployment to the battlefield against COVID-19.
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Affiliation(s)
- Antonio Cuadrado
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain; Department of Cellular and Molecular Medicine, Victor Babes National Institute of Pathology, Bucharest, Romania.
| | - Marta Pajares
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - Cristina Benito
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - José Jiménez-Villegas
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - Maribel Escoll
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - Raquel Fernández-Ginés
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - Angel J Garcia Yagüe
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - Diego Lastra
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - Gina Manda
- Department of Cellular and Molecular Medicine, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Ana I Rojo
- Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid (UAM), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria la Paz (idiPAZ), Instituto de Investigaciones Biomédicas 'Alberto Sols', Consejo Superior de Investigaciones Científicas (CSIC), UAM, Madrid, Spain
| | - Albena T Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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928
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Pillaiyar T, Wendt LL, Manickam M, Easwaran M. The recent outbreaks of human coronaviruses: A medicinal chemistry perspective. Med Res Rev 2020; 41:72-135. [PMID: 32852058 PMCID: PMC7461420 DOI: 10.1002/med.21724] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/22/2020] [Accepted: 08/08/2020] [Indexed: 01/18/2023]
Abstract
Coronaviruses (CoVs) infect both humans and animals. In humans, CoVs can cause respiratory, kidney, heart, brain, and intestinal infections that can range from mild to lethal. Since the start of the 21st century, three β‐coronaviruses have crossed the species barrier to infect humans: severe‐acute respiratory syndrome (SARS)‐CoV‐1, Middle East respiratory syndrome (MERS)‐CoV, and SARS‐CoV‐2 (2019‐nCoV). These viruses are dangerous and can easily be transmitted from human to human. Therefore, the development of anticoronaviral therapies is urgently needed. However, to date, no approved vaccines or drugs against CoV infections are available. In this review, we focus on the medicinal chemistry efforts toward the development of antiviral agents against SARS‐CoV‐1, MERS‐CoV, SARS‐CoV‐2, targeting biochemical events important for viral replication and its life cycle. These targets include the spike glycoprotein and its host‐receptors for viral entry, proteases that are essential for cleaving polyproteins to produce functional proteins, and RNA‐dependent RNA polymerase for viral RNA replication.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Lukas L Wendt
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Manoj Manickam
- Department of Chemistry, PSG Institute of Technology and Applied Research, Coimbatore, Tamil Nadu, India
| | - Maheswaran Easwaran
- Department of Biomedical Engineering, Sethu Institute of Technology, Virudhunagar, Tamilnadu, India
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929
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Ali A, Vijayan R. Dynamics of the ACE2-SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms. Sci Rep 2020; 10:14214. [PMID: 32848162 PMCID: PMC7449962 DOI: 10.1038/s41598-020-71188-3] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/12/2020] [Indexed: 12/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major public health concern. A handful of static structures now provide molecular insights into how SARS-CoV-2 and SARS-CoV interact with its host target, which is the angiotensin converting enzyme 2 (ACE2). Molecular recognition, binding and function are dynamic processes. To evaluate this, multiple 500 ns or 1 μs all-atom molecular dynamics simulations were performed to better understand the structural stability and interfacial interactions between the receptor binding domain of the spike (S) protein of SARS-CoV-2 and SARS-CoV bound to ACE2. Several contacts were observed to form, break and reform in the interface during the simulations. Our results indicate that SARS-CoV-2 and SARS-CoV utilizes unique strategies to achieve stable binding to ACE2. Several differences were observed between the residues of SARS-CoV-2 and SARS-CoV that consistently interacted with ACE2. Notably, a stable salt bridge between Lys417 of SARS-CoV-2 S protein and Asp30 of ACE2 as well as three stable hydrogen bonds between Tyr449, Gln493 and Gln498 of SARS-CoV-2 and Asp38, Glu35 and Lys353 of ACE2 were observed, which were absent in the ACE2-SARS-CoV interface. Some previously reported residues, which were suggested to enhance the binding affinity of SARS-CoV-2, were not observed to form stable interactions in these simulations. Molecular mechanics-generalized Born surface area based free energy of binding was observed to be higher for SARS-CoV-2 in all simulations. Stable binding to the host receptor is crucial for virus entry. Therefore, special consideration should be given to these stable interactions while designing potential drugs and treatment modalities to target or disrupt this interface.
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Affiliation(s)
- Amanat Ali
- Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, PO Box 15551, Al Ain, United Arab Emirates.
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930
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Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a newly emerging, highly transmissible, and pathogenic coronavirus in humans that has caused global public health emergencies and economic crises. To date, millions of infections and thousands of deaths have been reported worldwide, and the numbers continue to rise. Currently, there is no specific drug or vaccine against this deadly virus; therefore, there is a pressing need to understand the mechanism(s) through which this virus enters the host cell. Viral entry into the host cell is a multistep process in which SARS-CoV-2 utilizes the receptor-binding domain (RBD) of the spike (S) glycoprotein to recognize angiotensin-converting enzyme 2 (ACE2) receptors on the human cells; this initiates host-cell entry by promoting viral-host cell membrane fusion through large-scale conformational changes in the S protein. Receptor recognition and fusion are critical and essential steps of viral infections and are key determinants of the viral host range and cross-species transmission. In this review, we summarize the current knowledge on the origin and evolution of SARS-CoV-2 and the roles of key viral factors. We discuss the structure of RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and its significance in drug discovery and explain the receptor recognition mechanisms of coronaviruses. Further, we provide a comparative analysis of the SARS-CoV and SARS-CoV-2 S proteins and their receptor-binding specificity and discuss the differences in their antigenicity based on biophysical and structural characteristics.
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931
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted the repurposing of drugs on the basis of promising in vitro and therapeutic results with other human coronavirus diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). These repurposed drugs have mainly included remdesivir, favipiravir, lopinavir-ritonavir, ribavirin, interferons, and hydroxychloroquine. The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted the repurposing of drugs on the basis of promising in vitro and therapeutic results with other human coronavirus diseases, such as severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). These repurposed drugs have mainly included remdesivir, favipiravir, lopinavir-ritonavir, ribavirin, interferons, and hydroxychloroquine. Unfortunately, the first open-label, randomized, controlled trials are showing poor efficacy of these repurposed drugs. These results highlight the necessity of identifying and characterizing specific and potent SARS-CoV-2 antivirals.
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932
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Dominguez Andres A, Feng Y, Campos AR, Yin J, Yang CC, James B, Murad R, Kim H, Deshpande AJ, Gordon DE, Krogan N, Pippa R, Ronai ZA. SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32839770 DOI: 10.1101/2020.08.18.256776] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Disrupted antiviral immune responses are associated with severe COVID-19, the disease caused by SAR-CoV-2. Here, we show that the 73-amino-acid protein encoded by ORF9c of the viral genome contains a putative transmembrane domain, interacts with membrane proteins in multiple cellular compartments, and impairs antiviral processes in a lung epithelial cell line. Proteomic, interactome, and transcriptomic analyses, combined with bioinformatic analysis, revealed that expression of only this highly unstable small viral protein impaired interferon signaling, antigen presentation, and complement signaling, while inducing IL-6 signaling. Furthermore, we showed that interfering with ORF9c degradation by either proteasome inhibition or inhibition of the ATPase VCP blunted the effects of ORF9c. Our study indicated that ORF9c enables immune evasion and coordinates cellular changes essential for the SARS-CoV-2 life cycle. One-sentence summary SARS-CoV-2 ORF9c is the first human coronavirus protein localized to membrane, suppressing antiviral response, resembling full viral infection.
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933
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Saha RP, Sharma AR, Singh MK, Samanta S, Bhakta S, Mandal S, Bhattacharya M, Lee SS, Chakraborty C. Repurposing Drugs, Ongoing Vaccine, and New Therapeutic Development Initiatives Against COVID-19. Front Pharmacol 2020; 11:1258. [PMID: 32973505 PMCID: PMC7466451 DOI: 10.3389/fphar.2020.01258] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/30/2020] [Indexed: 12/15/2022] Open
Abstract
As the COVID-19 is still growing throughout the globe, a thorough investigation into the specific immunopathology of SARS-CoV-2, its interaction with the host immune system and pathogen evasion mechanism may provide a clear picture of how the pathogen can breach the host immune defenses in elderly patients and patients with comorbid conditions. Such studies will also reveal the underlying mechanism of how children and young patients can withstand the disease better. The study of the immune defense mechanisms and the prolonged immune memory from patients population with convalescent plasma may help in designing a suitable vaccine candidate not only for the current outbreak but also for similar outbreaks in the future. The vital drug candidates, which are being tested as potential vaccines or therapeutics against COVID-19, include live attenuated vaccine, inactivated or killed vaccine, subunit vaccine, antibodies, interferon treatment, repurposing existing drugs, and nucleic acid-based vaccines. Several organizations around the world have fast-tracked the development of a COVID-19 vaccine, and some drugs already went to phase III of clinical trials. Hence, here, we have tried to take a quick glimpse of the development stages of vaccines or therapeutic approaches to treat this deadly disease.
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Affiliation(s)
- Rudra P. Saha
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | - Manoj K. Singh
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Saikat Samanta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Swarnav Bhakta
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Snehasish Mandal
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
| | - Manojit Bhattacharya
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science & Biotechnology, Adamas University, Kolkata, India
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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934
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Narayanan N, Nair DT. Vitamin B12 may inhibit RNA-dependent-RNA polymerase activity of nsp12 from the SARS-CoV-2 virus. IUBMB Life 2020; 72:2112-2120. [PMID: 32812340 PMCID: PMC7461454 DOI: 10.1002/iub.2359] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 01/18/2023]
Abstract
SARS‐CoV‐2 is the causative agent for the ongoing COVID19 pandemic, and this virus belongs to the Coronaviridae family. Like other members of this family, the virus possesses a positive‐sense single‐stranded RNA genome. The genome encodes for the nsp12 protein, which houses the RNA‐dependent‐RNA polymerase (RdRP) activity responsible for the replication of the viral genome. A homology model of nsp12 was prepared using the structure of the SARS nsp12 (6NUR) as a model. The model was used to carry out in silico screening to identify molecules among natural products, or Food and Drug Administration‐approved drugs that can potentially inhibit the activity of nsp12. This exercise showed that vitamin B12 (methylcobalamin) may bind to the active site of the nsp12 protein. A model of the nsp12 in complex with substrate RNA and incoming NTP showed that vitamin B12 binding site overlaps with that of the incoming nucleotide. A comparison of the calculated energies of binding for RNA plus NTP and methylcobalamin suggested that the vitamin may bind to the active site of nsp12 with significant affinity. It is, therefore, possible that methylcobalamin binding may prevent association with RNA and NTP and thus inhibit the RdRP activity of nsp12. Overall, our computational studies suggest that methylcobalamin form of vitamin B12 may serve as an effective inhibitor of the nsp12 protein.
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Affiliation(s)
- Naveen Narayanan
- Laboratory of Genomic Integrity and Evolution, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, India.,Manipal Academy of Higher Education, Manipal, India
| | - Deepak T Nair
- Laboratory of Genomic Integrity and Evolution, Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, India
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935
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Asif M, Saleem M, Saadullah M, Yaseen HS, Al Zarzour R. COVID-19 and therapy with essential oils having antiviral, anti-inflammatory, and immunomodulatory properties. Inflammopharmacology 2020; 28:1153-1161. [PMID: 32803479 PMCID: PMC7427755 DOI: 10.1007/s10787-020-00744-0] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease of 2019 (COVID-19) has emerged as a global health threat. Unfortunately, there are very limited approved drugs available with established efficacy against the SARs-CoV-2 virus and its inflammatory complications. Vaccine development is actively being researched, but it may take over a year to become available to general public. Certain medications, for example, dexamethasone, antimalarials (chloroquine/hydroxychloroquine), antiviral (remdesivir), and IL-6 receptor blocking monoclonal antibodies (tocilizumab), are used in various combinations as off-label medications to treat COVID-19. Essential oils (EOs) have long been known to have anti-inflammatory, immunomodulatory, bronchodilatory, and antiviral properties and are being proposed to have activity against SARC-CoV-2 virus. Owing to their lipophilic nature, EOs are advocated to penetrate viral membranes easily leading to membrane disruption. Moreover, EOs contain multiple active phytochemicals that can act synergistically on multiple stages of viral replication and also induce positive effects on host respiratory system including bronchodilation and mucus lysis. At present, only computer-aided docking and few in vitro studies are available which show anti-SARC-CoV-2 activities of EOs. In this review, role of EOs in the prevention and treatment of COVID-19 is discussed. A discussion on possible side effects associated with EOs as well as anti-corona virus claims made by EOs manufacturers are also highlighted. Based on the current knowledge a chemo-herbal (EOs) combination of the drugs could be a more feasible and effective approach to combat this viral pandemic.![]()
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Affiliation(s)
- Muhammad Asif
- Department of Pharmacology, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.
| | - Mohammad Saleem
- Punjab University College of Pharmacy, University of the Punjab, Lahore, Pakistan
| | - Malik Saadullah
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Hafiza Sidra Yaseen
- Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Raghdaa Al Zarzour
- Discipline of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden Penang, Malaysia
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936
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Procacci P, Macchiagodena M, Pagliai M, Guarnieri G, Iannone F. Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulations. Chem Commun (Camb) 2020; 56:8854-8856. [PMID: 32633733 DOI: 10.1039/d0cc03558k] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Using a combination of enhanced sampling molecular dynamics techniques and non-equilibrium alchemical transformations with full atomistic details, we have shown that hydroxychloroquine (HCQ) may act as a mild inhibitor of important functional proteins for SARS-CoV2 replication, with potency increasing in the series PLpro, 3CLpro, RdRp. By analyzing the bound state configurations, we were able to improve the potency for the 3CLpro target, designing a novel HCQ-inspired compound, named PMP329, with predicted nanomolar activity. If confirmed in vitro, our results provide a molecular rationale for the use of HCQ or of strictly related derivatives in the treatment of Covid-19.
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Affiliation(s)
- Piero Procacci
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino (FI), I-50019, Italy.
| | - Marina Macchiagodena
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino (FI), I-50019, Italy.
| | - Marco Pagliai
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino (FI), I-50019, Italy.
| | - Guido Guarnieri
- ENEA, Portici Research Centre, DTE-ICT-HPC P.le E. Fermi, 1, Portici (NA), I-80055, Italy.
| | - Francesco Iannone
- ENEA, Portici Research Centre, DTE-ICT-HPC P.le E. Fermi, 1, Portici (NA), I-80055, Italy.
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937
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Wang R, Chen J, Gao K, Hozumi Y, Yin C, Wei GW. Characterizing SARS-CoV-2 mutations in the United States. RESEARCH SQUARE 2020:rs.3.rs-49671. [PMID: 32818213 PMCID: PMC7430589 DOI: 10.21203/rs.3.rs-49671/v1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been mutating since it was first sequenced in early January 2020. The genetic variants have developed into a few distinct clusters with different properties. Since the United States (US) has the highest number of viral infected patients globally, it is essential to understand the US SARS-CoV-2. Using genotyping, sequence-alignment, time-evolution, k-means clustering, protein-folding stability, algebraic topology, and network theory, we reveal that the US SARS-CoV-2 has four substrains and five top US SARS-CoV-2 mutations were first detected in China (2 cases), Singapore (2 cases), and the United Kingdom (1 case). The next three top US SARS-CoV-2 mutations were first detected in the US. These eight top mutations belong to two disconnected groups. The first group consisting of 5 concurrent mutations is prevailing, while the other group with three concurrent mutations gradually fades out. We identify that one of the top mutations, 27964C>T-(S24L) on ORF8, has an unusually strong gender dependence. Based on the analysis of all mutations on the spike protein, we further uncover that three of four US SASR-CoV-2 substrains become more infectious. Our study calls for effective viral control and containing strategies in the US.
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Affiliation(s)
- Rui Wang
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Kaifu Gao
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Yuta Hozumi
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Changchuan Yin
- Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, MI 48824, USA
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938
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Sternberg A, McKee DL, Naujokat C. Novel Drugs Targeting the SARS-CoV-2/COVID-19 Machinery. Curr Top Med Chem 2020; 20:1423-1433. [PMID: 32416679 DOI: 10.2174/1568026620999200517043137] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 12/13/2022]
Abstract
Like other human pathogenic viruses, coronavirus SARS-CoV-2 employs sophisticated macromolecular machines for viral host cell entry, genome replication and protein processing. Such machinery encompasses SARS-CoV-2 envelope spike (S) glycoprotein required for host cell entry by binding to the ACE2 receptor, viral RNA-dependent RNA polymerase (RdRp) and 3-chymotrypsin-like main protease (3Clpro/Mpro). Under the pressure of the accelerating COVID-19 pandemic caused by the outbreak of SARS-CoV-2 in Wuhan, China in December 2019, novel and repurposed drugs were recently designed and identified for targeting the SARS-CoV-2 reproduction machinery, with the aim to limit the spread of SARS-CoV-2 and morbidity and mortality due to the COVID-19 pandemic.
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Affiliation(s)
- Ariane Sternberg
- Center and Network for Targeted Oncology, Muehlackerweg 8, D-69239 Heidelberg, Germany
| | | | - Cord Naujokat
- Institute of Immunology, University of Heidelberg, Im Neuenheimer Feld 305, D-69120 Heidelberg, Germany
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939
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Russo A, Minichini C, Starace M, Astorri R, Calò F, Coppola N. Current Status of Laboratory Diagnosis for COVID-19: A Narrative Review. Infect Drug Resist 2020; 13:2657-2665. [PMID: 32801804 PMCID: PMC7413717 DOI: 10.2147/idr.s264020] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/05/2020] [Indexed: 12/22/2022] Open
Abstract
The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the related disease (COVID-19) has spread rapidly to pandemic proportions, increasing the demands on healthcare systems for the containment and management of COVID-19. One of the critical issues to be addressed is the improvement in laboratory diagnosis and screening of large portions of the population to stop the virus spreading. Currently, the laboratory diagnosis of SARS-CoV-2 infection and the related disease is based on the research of viral RNA with rt-PCR methods in upper and lower respiratory airways. Serological tests to detect SARS-CoV-2 antibodies could help physicians and healthcare workers to support COVID-19 diagnosis and follow-up and perform population screening. Our review, using MEDLINE and EMBASE, summarizes the current knowledge of direct and serological tests performed to research RNA, antigens, or antibodies for SARS-CoV-2, evaluating the advantages and drawbacks for specific tests.
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Affiliation(s)
- Antonio Russo
- Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Carmine Minichini
- Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Mario Starace
- Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Roberta Astorri
- Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Federica Calò
- Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, Infectious Diseases Unit, University of Campania Luigi Vanvitelli, Naples, Italy
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940
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Kumar P, Pandey R, Sharma P, Dhar MS, A. V, Uppili B, Vashisht H, Wadhwa S, Tyagi N, Fatihi S, Sharma U, Singh P, Lall H, Datta M, Gupta P, Saini N, Tewari A, Nandi B, Kumar D, Bag S, Gahlot D, Rathore S, Jatana N, Jaiswal V, Gogia H, Madan P, Singh S, Singh P, Dash D, Bala M, Kabra S, Singh S, Mukerji M, Thukral L, Faruq M, Agrawal A, Rakshit P. Integrated genomic view of SARS-CoV-2 in India. Wellcome Open Res 2020; 5:184. [PMID: 32995557 PMCID: PMC7506191 DOI: 10.12688/wellcomeopenres.16119.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2020] [Indexed: 01/12/2023] Open
Abstract
Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
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Affiliation(s)
- Pramod Kumar
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Rajesh Pandey
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Pooja Sharma
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Mahesh S. Dhar
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Vivekanand A.
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Bharathram Uppili
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Himanshu Vashisht
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Saruchi Wadhwa
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Nishu Tyagi
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Saman Fatihi
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Uma Sharma
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Priyanka Singh
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Hemlata Lall
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Meena Datta
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Poonam Gupta
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Nidhi Saini
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Aarti Tewari
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Bibhash Nandi
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Dhirendra Kumar
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Satyabrata Bag
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Deepanshi Gahlot
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Surabhi Rathore
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Nidhi Jatana
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Varun Jaiswal
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Hema Gogia
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Preeti Madan
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Simrita Singh
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Prateek Singh
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Debasis Dash
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Manju Bala
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Sandhya Kabra
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Sujeet Singh
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
| | - Mitali Mukerji
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Lipi Thukral
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Mohammed Faruq
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Anurag Agrawal
- Department of Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, Delhi, 110007, India
| | - Partha Rakshit
- Biotechnology Division, National Centre for Disease Control, Delhi, Delhi, 110054, India
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941
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Artika IM, Dewantari AK, Wiyatno A. Molecular biology of coronaviruses: current knowledge. Heliyon 2020; 6:e04743. [PMID: 32835122 PMCID: PMC7430346 DOI: 10.1016/j.heliyon.2020.e04743] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.
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Affiliation(s)
- I. Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680, Indonesia
| | - Aghnianditya Kresno Dewantari
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
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942
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Ojha R, Gupta N, Naik B, Singh S, Verma VK, Prusty D, Prajapati VK. High throughput and comprehensive approach to develop multiepitope vaccine against minacious COVID-19. Eur J Pharm Sci 2020; 151:105375. [PMID: 32417398 PMCID: PMC7224663 DOI: 10.1016/j.ejps.2020.105375] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
Abstract
The ongoing enigmatic COVID-19 outbreak, first reported from Wuhan, China, on last day of the year 2019, which has spread to 213 countries, territories/areas till 28th April 2020, threatens hundreds of thousands human souls. This devastating viral infection has stimulated the urgent development of viable vaccine against COVID-19 across the research institutes around the globe. The World Health Organization (WHO) has also confirmed that the recent pandemic is causing Public Health Emergency of International apprehension. Moreover, the earlier two pathogenic SARS-CoV and MERS-CoV and many others yet to be identified pose a universal menace. Here, in this piece of work, we have utilized an in silico structural biology and advanced immunoinformatic strategies to devise a multi-epitope subunit vaccine against ongoing COVID-19 infection. The engineered vaccine sequence is adjuvanted with ß-3 defensin and comprised of B-cell epitopes, HTL epitopes and CTL epitopes. This is very likely that the vaccine will be able to elicit the strong immune response. Further, specific binding of the engineered vaccine and immune cell receptor TLR3 was estimated by molecular interaction studies. Strong interaction in the binding groove as well as good docking scores affirmed the stringency of engineered vaccine. The interaction is stable with minimal deviation in root-mean square deviation and root-mean-square fluctuation was confirmed by the molecular dynamics simulation experiment. The immune-simulation by C-ImmSim server, which mimics the natural immune environment, yielded more potent immune response data of B-cells, Th cells, Tc cells and IgG for vaccine. The encouraging data obtained from the various in-silico works indicated this vaccine as an effective therapeutic against COVID-19.
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Affiliation(s)
- Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Nidhi Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Vijay Kumar Verma
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India.
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943
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Jockusch S, Tao C, Li X, Anderson TK, Chien M, Kumar S, Russo JJ, Kirchdoerfer RN, Ju J. A library of nucleotide analogues terminate RNA synthesis catalyzed by polymerases of coronaviruses that cause SARS and COVID-19. Antiviral Res 2020; 180:104857. [PMID: 32562705 PMCID: PMC7299870 DOI: 10.1016/j.antiviral.2020.104857] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/30/2020] [Accepted: 06/12/2020] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2, a member of the coronavirus family, is responsible for the current COVID-19 worldwide pandemic. We previously demonstrated that five nucleotide analogues inhibit the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), including the active triphosphate forms of Sofosbuvir, Alovudine, Zidovudine, Tenofovir alafenamide and Emtricitabine. We report here the evaluation of a library of nucleoside triphosphate analogues with a variety of structural and chemical features as inhibitors of the RdRps of SARS-CoV and SARS-CoV-2. These features include modifications on the sugar (2' or 3' modifications, carbocyclic, acyclic, or dideoxynucleotides) or on the base. The goal is to identify nucleotide analogues that not only terminate RNA synthesis catalyzed by these coronavirus RdRps, but also have the potential to resist the viruses' exonuclease activity. We examined these nucleotide analogues for their ability to be incorporated by the RdRps in the polymerase reaction and to prevent further incorporation. While all 11 molecules tested displayed incorporation, 6 exhibited immediate termination of the polymerase reaction (triphosphates of Carbovir, Ganciclovir, Stavudine and Entecavir; 3'-OMe-UTP and Biotin-16-dUTP), 2 showed delayed termination (Cidofovir diphosphate and 2'-OMe-UTP), and 3 did not terminate the polymerase reaction (2'-F-dUTP, 2'-NH2-dUTP and Desthiobiotin-16-UTP). The coronaviruses possess an exonuclease that apparently requires a 2'-OH at the 3'-terminus of the growing RNA strand for proofreading. In this study, all nucleoside triphosphate analogues evaluated form Watson-Crick-like base pairs. The nucleotide analogues demonstrating termination either lack a 2'-OH, have a blocked 2'-OH, or show delayed termination. Thus, these nucleotide analogues are of interest for further investigation to evaluate whether they can evade the viral exonuclease activity. Prodrugs of five of these nucleotide analogues (Cidofovir, Abacavir, Valganciclovir/Ganciclovir, Stavudine and Entecavir) are FDA-approved medications for treatment of other viral infections, and their safety profiles are well established. After demonstrating potency in inhibiting viral replication in cell culture, candidate molecules can be rapidly evaluated as potential therapies for COVID-19.
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Affiliation(s)
- Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Thomas K Anderson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA; Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA; Department of Pharmacology, Columbia University, New York, NY, 10027, USA.
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944
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Tiwari V, Beer JC, Sankaranarayanan NV, Swanson-Mungerson M, Desai UR. Discovering small-molecule therapeutics against SARS-CoV-2. Drug Discov Today 2020; 25:1535-1544. [PMID: 32574699 PMCID: PMC7305878 DOI: 10.1016/j.drudis.2020.06.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/19/2020] [Accepted: 06/16/2020] [Indexed: 02/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global health pandemic. The lack of effective treatments, coupled with its etiology, has resulted in more than 400,000 deaths at the time of writing. The SARS-CoV-2 genome is highly homologous to that of SARS-CoV, the causative agent behind the 2003 SARS outbreak. Based on prior reports, clinicians have pursued the off-label use of several antiviral drugs, while the scientific community has responded by seeking agents against traditional targets, especially viral proteases. However, several avenues remain unexplored, including disrupting E and M protein oligomerization, outcompeting host glycan-virus interactions, interfering with the heparan sulfate proteoglycans-virus interaction, and others. In this review, we highlight some of these opportunities while summarizing the drugs currently in use against coronavirus 2019 (COVID-19).
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Affiliation(s)
- Vaibhav Tiwari
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University Downers Grove, IL 6051, USA; Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA.
| | - Jacob C Beer
- Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Nehru Viji Sankaranarayanan
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 2321, USA
| | - Michelle Swanson-Mungerson
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University Downers Grove, IL 6051, USA; Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA 2321, USA.
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945
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Nitulescu GM, Paunescu H, Moschos SA, Petrakis D, Nitulescu G, Ion GND, Spandidos DA, Nikolouzakis TK, Drakoulis N, Tsatsakis A. Comprehensive analysis of drugs to treat SARS‑CoV‑2 infection: Mechanistic insights into current COVID‑19 therapies (Review). Int J Mol Med 2020; 46:467-488. [PMID: 32468014 PMCID: PMC7307820 DOI: 10.3892/ijmm.2020.4608] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
The major impact produced by the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) focused many researchers attention to find treatments that can suppress transmission or ameliorate the disease. Despite the very fast and large flow of scientific data on possible treatment solutions, none have yet demonstrated unequivocal clinical utility against coronavirus disease 2019 (COVID‑19). This work represents an exhaustive and critical review of all available data on potential treatments for COVID‑19, highlighting their mechanistic characteristics and the strategy development rationale. Drug repurposing, also known as drug repositioning, and target based methods are the most used strategies to advance therapeutic solutions into clinical practice. Current in silico, in vitro and in vivo evidence regarding proposed treatments are summarized providing strong support for future research efforts.
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Affiliation(s)
| | - Horia Paunescu
- Faculty of Medicine, ′Carol Davila′ University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Sterghios A. Moschos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University
- PulmoBioMed Ltd., Newcastle-Upon-Tyne NE1 8ST, UK
| | | | | | | | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion
| | | | - Nikolaos Drakoulis
- Research Group of Clinical Pharmacology and Pharmacogenomics, Faculty of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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946
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Mirza MU, Froeyen M. Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase. J Pharm Anal 2020; 10:320-328. [PMID: 32346490 PMCID: PMC7187848 DOI: 10.1016/j.jpha.2020.04.008] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/23/2020] [Accepted: 04/26/2020] [Indexed: 01/07/2023] Open
Abstract
Recently emerged SARS-CoV-2 caused a major outbreak of coronavirus disease 2019 (COVID-19) and instigated a widespread fear, threatening global health safety. To date, no licensed antiviral drugs or vaccines are available against COVID-19 although several clinical trials are under way to test possible therapies. During this urgent situation, computational drug discovery methods provide an alternative to tiresome high-throughput screening, particularly in the hit-to-lead-optimization stage. Identification of small molecules that specifically target viral replication apparatus has indicated the highest potential towards antiviral drug discovery. In this work, we present potential compounds that specifically target SARS-CoV-2 vital proteins, including the main protease, Nsp12 RNA polymerase and Nsp13 helicase. An integrative virtual screening and molecular dynamics simulations approach has facilitated the identification of potential binding modes and favourable molecular interaction profile of corresponding compounds. Moreover, the identification of structurally important binding site residues in conserved motifs located inside the active site highlights relative importance of ligand binding based on residual energy decomposition analysis. Although the current study lacks experimental validation, the structural information obtained from this computational study has paved way for the design of targeted inhibitors to combat COVID-19 outbreak.
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Affiliation(s)
- Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000, Leuven, Belgium
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947
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In silico ADMET and molecular docking study on searching potential inhibitors from limonoids and triterpenoids for COVID-19. Comput Biol Med 2020; 124:103936. [PMID: 32738628 PMCID: PMC7386496 DOI: 10.1016/j.compbiomed.2020.103936] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/26/2020] [Accepted: 07/26/2020] [Indexed: 01/25/2023]
Abstract
Virtual screening of phytochemicals was performed through molecular docking, simulations, in silico ADMET and drug-likeness prediction to identify the potential hits that can inhibit the effects of SARS-CoV-2. Considering the published literature on medicinal importance, 154 phytochemicals with analogous structure from limonoids and triterpenoids were selected to search potential inhibitors for the five therapeutic protein targets of SARS-CoV-2, i.e., 3CLpro (main protease), PLpro (papain-like protease), SGp-RBD (spike glycoprotein-receptor binding domain), RdRp (RNA dependent RNA polymerase) and ACE2 (angiotensin-converting enzyme 2). The in silico computational results revealed that the phytochemicals such as glycyrrhizic acid, limonin, 7-deacetyl-7-benzoylgedunin, maslinic acid, corosolic acid, obacunone and ursolic acid were found to be effective against the target proteins of SARS-CoV-2. The protein-ligand interaction study revealed that these phytochemicals bind with the amino acid residues at the active site of the target proteins. Therefore, the core structure of these potential hits can be used for further lead optimization to design drugs for SARS-CoV-2. Also, the medicinal plants containing these phytochemicals like licorice, neem, tulsi, citrus and olives can be used to formulate suitable therapeutic approaches in traditional medicines. 154 limonoids and triterpenoids were screened computationally to search potential inhibitors for COVID-19. Phytochemicals were screened by molecular docking, in silico ADMET and drug-likeness prediction. Docking studies of phytochemicals were performed with five therapeutic protein targets of SARS-CoV-2. 7 potential phytochemicals were proposed as potential hits against the SARS-CoV-2. Proposed phytochemicals are found mainly in neem, tulsi, citrus, licorice and olives.
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948
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Kumar R, Verma H, Singhvi N, Sood U, Gupta V, Singh M, Kumari R, Hira P, Nagar S, Talwar C, Nayyar N, Anand S, Rawat CD, Verma M, Negi RK, Singh Y, Lal R. Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution. mSystems 2020; 5:e00505-20. [PMID: 32723797 PMCID: PMC7394360 DOI: 10.1128/msystems.00505-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) that started in Wuhan, China, in December 2019 has spread worldwide, emerging as a global pandemic. The severe respiratory pneumonia caused by novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has so far claimed more than 0.38 million lives and has impacted human lives worldwide. However, as the novel SARS-CoV-2 virus displays high transmission rates, the underlying genomic severity is required to be fully understood. We studied the complete genomes of 95 SARS-CoV-2 strains from different geographical regions worldwide to uncover the pattern of the spread of the virus. We show that there is no direct transmission pattern of the virus among neighboring countries, suggesting that its spread is a result of travel of infected humans to different countries. We revealed unique single nucleotide polymorphisms (SNPs) in nonstructural protein 13 (nsp13), nsp14, nsp15, and nsp16 (ORF1b polyproteins) and in the S-protein within 10 viral isolates from the United States. These viral proteins are involved in RNA replication and binding with the human receptors, indicating that the viral variants that are circulating in the population of the United States are different from those circulating in the populations of other countries. In addition, we found an amino acid addition in nsp16 (mRNA cap-1 methyltransferase) of a U.S. isolate (GenBank accession no. MT188341.1) leading to a shift in the amino acid frame from position 2540 onward. Through comparative structural analysis of the wild-type and mutant proteins, we showed that this addition of a phenylalanine residue renders the protein in the mutant less stable, which might affect mRNA cap-1 methyltransferase function. We further analyzed the SARS-CoV-2-human interactome, which revealed that the interferon signaling pathway is targeted by orf1ab during infection and that it also interacts with NF-κB-repressing factor (NKRF), which is a potential regulator of interleukin-8 (IL-8). We propose that targeting this interaction may subsequently improve the health condition of COVID-19 patients. Our analysis also emphasized that SARS-CoV-2 manipulates spliceosome machinery during infection; hence, targeting splicing might affect viral replication. In conclusion, the replicative machinery of SARS-CoV-2 is targeting interferon and the notch signaling pathway along with spliceosome machinery to evade host challenges.IMPORTANCE The COVID-19 pandemic continues to storm the world, with over 6.5 million cases worldwide. The severity of the disease varies with the territories and is mainly influenced by population density and age factor. In this study, we analyzed the transmission pattern of 95 SARS-CoV-2 genomes isolated from 11 different countries. Our study also revealed several nonsynonymous mutations in ORF1b and S-proteins and the impact on their structural stability. Our analysis showed the manipulation of host system by viral proteins through SARS-CoV-2-human protein interactome, which can be useful to understand the impact of virus on human health.
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Affiliation(s)
- Roshan Kumar
- P.G. Department of Zoology, Magadh University, Bodh Gaya, Bihar, India
| | - Helianthous Verma
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | | | - Utkarsh Sood
- The Energy and Resources Institute, New Delhi, India
| | - Vipin Gupta
- PhiXGen Private Limited, Gurugram, Haryana, India
| | - Mona Singh
- PhiXGen Private Limited, Gurugram, Haryana, India
| | - Rashmi Kumari
- Department of Zoology, College of Commerce, Arts & Science, Patliputra University, Patna, Bihar, India
| | - Princy Hira
- Department of Zoology, Maitreyi College, University of Delhi, New Delhi, India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, India
| | - Namita Nayyar
- Department of Zoology, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Shailly Anand
- Department of Zoology, Deen Dayal Upadhyaya College, University of Delhi, New Delhi, India
| | - Charu Dogra Rawat
- Department of Zoology, Ramjas College, University of Delhi, Delhi, India
| | - Mansi Verma
- Department of Zoology, Sri Venkateswara College, University of Delhi, New Delhi, India
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India
| | - Rup Lal
- The Energy and Resources Institute, New Delhi, India
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949
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Ahmad M, Dwivedy A, Mariadasse R, Tiwari S, Kar D, Jeyakanthan J, Biswal BK. Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase. ACS OMEGA 2020; 5:18356-18366. [PMID: 32743211 PMCID: PMC7391942 DOI: 10.1021/acsomega.0c02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 05/08/2023]
Abstract
The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2.
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Affiliation(s)
- Mohammed Ahmad
- National
Institute of Immunology, New Delhi 110067, India
| | | | - Richard Mariadasse
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
| | - Satish Tiwari
- National
Institute of Immunology, New Delhi 110067, India
| | - Deepsikha Kar
- National
Institute of Immunology, New Delhi 110067, India
| | - Jeyaraman Jeyakanthan
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
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950
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Yadav R, Imran M, Dhamija P, Chaurasia DK, Handu S. Virtual screening, ADMET prediction and dynamics simulation of potential compounds targeting the main protease of SARS-CoV-2. J Biomol Struct Dyn 2020; 39:6617-6632. [PMID: 32715956 PMCID: PMC7441774 DOI: 10.1080/07391102.2020.1796812] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The coronavirus disease-2019 caused by a novel SARS CoV-2 virus has emerged as a global
threat. Still, no drugs are available for its treatment. The main protease is the most
conserved structure responsible for the posttranslational processing of non-structural
polyproteins of this virus. Therefore, it can be the potential target for drug discovery
against SARS CoV-2. Twenty-one thousand two hundred and seven chemical compounds used for
sequential virtual screening studies including coronavirus screening compounds (Life
Chemical database) and antiviral compounds (Asinex database). The Schrodinger suite 2019
employed for high throughput screening, molecular docking and MM-GBSA through the Glide
module. Subsequently, 23 compounds were selected in the phase first selection criteria for
re-docking with AutoDock and iDock followed by ADMET prediction. The drug-likeness
predicted through Lipinski’s rule of five, Veber’s rule and Muegge’s rule. Finally, three
ligands were selected for molecular dynamics simulation studies over 150 ns against the
main protease of the SARS CoV-2. They showed promising docking scores on Glide, iDock and
AutoDock Vina algorithms (ligand F2679-0163: −10.75, −10.29 and −9.2; ligand F6355-0442:
−9.38, −8.61 and −7.6; ligand 8250: −9.795, −7.94 and −7.5), respectively. The RMSD
parameter remained stable at 2.5 Å for all the three ligands for 150 ns. The high RMSF
fluctuations, RoG of around 22 Å and the binding free energy were favorable in each case.
The hydrogen bond interactions of 8250, F6355-0442 and F2679-0163 were six, five and
three, respectively. These compounds can be further explored for in vitro experimental validation against SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Mohammed Imran
- Department of Pharmacology, College of Medicine, Shaqra University, Shaqra, Kingdom of Saudi Arabia
| | - Puneet Dhamija
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Dheeraj Kumar Chaurasia
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology, Delhi, India
| | - Shailendra Handu
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
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