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Vázquez-Valadez VH, Hernández-Serda A, Jiménez-Cabiedes MF, Aguirre-Vidal P, González-Tapia I, Carreño-Vargas L, Alarcón-López YA, Espejel-Fuentes A, Martínez-Soriano P, Lugo Álvarez M, Velázquez-Sánchez AM, Markarian NM, Angeles E, Abrahamyan L. Evaluation of Inhibitory Activity In Silico of In-House Thiomorpholine Compounds between the ACE2 Receptor and S1 Subunit of SARS-CoV-2 Spike. Pathogens 2021; 10:1208. [PMID: 34578240 PMCID: PMC8468748 DOI: 10.3390/pathogens10091208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/22/2022] Open
Abstract
At the end of 2019, the world was struck by the COVID-19 pandemic, which resulted in dire repercussions of unimaginable proportions. From the beginning, the international scientific community employed several strategies to tackle the spread of this disease. Most notably, these consisted of the development of a COVID-19 vaccine and the discovery of antiviral agents through the repositioning of already known drugs with methods such as de novo design. Previously, methylthiomorphic compounds, designed by our group as antihypertensive agents, have been shown to display an affinity with the ACE2 (angiotensin converting enzyme) receptor, a key mechanism required for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) entry into target cells. Therefore, the objective of this work consists of evaluating, in silico, the inhibitory activity of these compounds between the ACE2 receptor and the S1 subunit of the SARS-CoV-2 spike protein. Supported by the advances of different research groups on the structure of the coronavirus spike and the interaction of the latter with its receptor, ACE2, we carried out a computational study that examined the effect of in-house designed compounds on the inhibition of said interaction. Our results indicate that the polyphenol LQM322 is one of the candidates that should be considered as a possible anti-COVID-19 agent.
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Affiliation(s)
- Victor H. Vázquez-Valadez
- Departamento de Ciencias Biológicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico;
| | - Alejandro Hernández-Serda
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Ma. Fernanda Jiménez-Cabiedes
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Pablo Aguirre-Vidal
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Ingrid González-Tapia
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Laura Carreño-Vargas
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Yoshio A. Alarcón-López
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Andrea Espejel-Fuentes
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Pablo Martínez-Soriano
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Miguel Lugo Álvarez
- Laboratorio de Química Medicinal y Teórica FESC, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (M.F.J.-C.); (P.A.-V.); (I.G.-T.); (L.C.-V.); (Y.A.A.-L.); (A.E.-F.); (M.L.Á.)
| | - Ana María Velázquez-Sánchez
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Nathan Marko Markarian
- Swine and Poultry Infectious Diseases Research Center (CRIPA) and Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
| | - Enrique Angeles
- Departamento de Ciencias Químicas FES Cuautitlán, Universidad Nacional Autónoma de México (UNAM), Av. 1 de Mayo SN Cuautitlán Izcalli, Estado de México, México CP 54750, Mexico; (A.H.-S.); (P.M.-S.); (A.M.V.-S.); (E.A.)
| | - Levon Abrahamyan
- Swine and Poultry Infectious Diseases Research Center (CRIPA) and Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC J2S 2M2, Canada;
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Szemiel AM, Merits A, Orton RJ, MacLean OA, Pinto RM, Wickenhagen A, Lieber G, Turnbull ML, Wang S, Furnon W, Suarez NM, Mair D, da Silva Filipe A, Willett BJ, Wilson SJ, Patel AH, Thomson EC, Palmarini M, Kohl A, Stewart ME. In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. PLoS Pathog 2021; 17:e1009929. [PMID: 34534263 PMCID: PMC8496873 DOI: 10.1371/journal.ppat.1009929] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 10/07/2021] [Accepted: 08/30/2021] [Indexed: 01/18/2023] Open
Abstract
Remdesivir (RDV), a broadly acting nucleoside analogue, is the only FDA approved small molecule antiviral for the treatment of COVID-19 patients. To date, there are no reports identifying SARS-CoV-2 RDV resistance in patients, animal models or in vitro. Here, we selected drug-resistant viral populations by serially passaging SARS-CoV-2 in vitro in the presence of RDV. Using high throughput sequencing, we identified a single mutation in RNA-dependent RNA polymerase (NSP12) at a residue conserved among all coronaviruses in two independently evolved populations displaying decreased RDV sensitivity. Introduction of the NSP12 E802D mutation into our SARS-CoV-2 reverse genetics backbone confirmed its role in decreasing RDV sensitivity in vitro. Substitution of E802 did not affect viral replication or activity of an alternate nucleoside analogue (EIDD2801) but did affect virus fitness in a competition assay. Analysis of the globally circulating SARS-CoV-2 variants (>800,000 sequences) showed no evidence of widespread transmission of RDV-resistant mutants. Surprisingly, we observed an excess of substitutions in spike at corresponding sites identified in the emerging SARS-CoV-2 variants of concern (i.e., H69, E484, N501, H655) indicating that they can arise in vitro in the absence of immune selection. The identification and characterisation of a drug resistant signature within the SARS-CoV-2 genome has implications for clinical management and virus surveillance.
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Affiliation(s)
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Richard J. Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Oscar A. MacLean
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rute Maria Pinto
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arthur Wickenhagen
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Gauthier Lieber
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Matthew L. Turnbull
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sainan Wang
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Nicolas M. Suarez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Daniel Mair
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Brian J. Willett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Sam J. Wilson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Emma C. Thomson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Meredith E. Stewart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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Nejati M, Dehghan* P, Hashempour- Baltork* F, Alizadeh AM, Farshi P, Khosravi- Darani K. Potential Dietary Interventions for COVID-19 Infection Based on the Gut-Immune Axis: An Update Review on Bioactive Component of Macronutrients. Int J Prev Med 2021; 12:105. [PMID: 34729139 PMCID: PMC8505687 DOI: 10.4103/ijpvm.ijpvm_493_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/19/2020] [Indexed: 01/08/2023] Open
Abstract
Recently emerged coronavirus, known as SARS-CoV-2 or Covid-19 is considered as a serious threat for human health. Due to unavailable specific drugs for this virus, there is an urgent need for supportive cares. Epigenetic immune boosting approaches and developing anti-inflammatory agents by gut-associated bioactive macronutrients can be plausible protective cares for COVID-19. Suitable intake of bioactive macronutrients including prebiotics, fatty acids, proteins and branched-chain amino acids may result in anti-viral responses through modulating macrophages and dendritic cells via Toll-like receptors, decreasing viral load, inactivating the enveloped viruses, increasing the anti-inflammatory metabolites and inhibiting the proliferation of microbial organisms. Bioactive macronutrients may help in promotion of immunological responses and recovery acceleration against Covid-19. This review focuses on the mechanisms of bioactive macronutrients and related clinical trials on enveloped viruses with emphasis on gut-microbiome-immune axis. Macronutrients and this axis may be conducive strategies to protect host against the viral infection.
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Affiliation(s)
- Marzieh Nejati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parvin Dehghan*
- Department of Biochemistry and Diet Therapy, Faculty of Nutrition and Food Sciences, Tabriz, University of Medical Sciences, Tabriz, Iran
| | - Fataneh Hashempour- Baltork*
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Adel Mirza Alizadeh
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parastou Farshi
- Food Science Institute, Kansas State University, Manhattan, KS, USA
| | - Kianoush Khosravi- Darani
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Possible therapeutic targets and promising drugs based on unsymmetrical hetaryl-substituted porphyrins to combat SARS-CoV-2. J Pharm Anal 2021; 11:691-698. [PMID: 34377564 PMCID: PMC8340555 DOI: 10.1016/j.jpha.2021.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/15/2021] [Accepted: 08/03/2021] [Indexed: 01/10/2023] Open
Abstract
Coronavirus disease 2019 is a serious disease that causes acute respiratory syndrome and negatively affects the central nervous system. SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) crosses the blood-brain barrier due to the S protein on the surface of the viral particles. Thus, it is important to develop compounds that not only have an inhibitory effect but are also capable of completely deactivating the S-protein function. This study describes the purposeful modification of porphyrins and proposes compounds, asymmetrically hetaryl-substituted porphyrins with benzothiazole, benzoxazole, and N-methylbenzimidazole residues, to deactivate the S-protein functions. Molecular docking of SARS-CoV-2 proteins with hetaryl-substituted porphyrins showed that the viral proteins S-, N-, and nsp13 exhibited the highest binding affinity. Hetaryl-substituted porphyrins form strong complexes (13-14 kcal/mol) with the receptor-binding domain of the S protein, while the distance from the porphyrins to the receptor-binding motif (RBM) does not exceed 20 Å; therefore, RBM can be oxidized by 1O2, which is generated by porphyrin. Hetaryl-substituted porphyrins interact with the nucleocapsid protein in the serine/arginine-rich region, and a number of vulnerable amino acid residues are located in the photooxidation zone. This damage complicates the packaging of viral RNA into new virions. High-energy binding of hetaryl-substituted porphyrins with the N- and C-terminal domains of nsp13 was observed. This binding blocks the action of nsp13 as an enzyme of exoribonuclease and methyltransferase, thereby preventing RNA replication and processing. A procedure for the synthesis of hetaryl-substituted porphyrins was developed, new compounds were obtained, their structures were identified, and their photocatalytic properties were studied.
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Junaid M, Akter Y, Siddika A, Nayeem SMA, Nahrin A, Afrose SS, Ezaj MMA, Alam MS. Nature-derived hit, lead, and drug-like small molecules: Current status and future aspects against key target proteins of Coronaviruses. Mini Rev Med Chem 2021; 22:498-549. [PMID: 34353257 DOI: 10.2174/1389557521666210805113231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND COVID-19 pandemic, the most unprecedented event of the year 2020, has brought millions of scientists worldwide in a single platform to fight against it. Though several drugs are now in the clinical trial, few vaccines available on the market already but the lack of an effect of those is making the situation worse. AIM OF THE STUDY In this review, we demonstrated comprehensive data of natural antiviral products showing activities against different proteins of Human Coronaviruses (HCoV) that are responsible for its pathogenesis. Furthermore, we categorized the compounds into the hit, lead, and drug based on the IC50/EC50 value, drug-likeness, and lead-likeness test to portray their potentiality to be a drug. We also demonstrated the present status of our screened antiviral compounds with respect to clinical trials and reported the lead compounds that can be promoted to clinical trial against COVID-19. METHODS A systematic search strategy was employed focusing on Natural Products (NPs) with proven activity (in vitro, in vivo, or in silico) against human coronaviruses, in general, and data were gathered from databases like PubMed, Web of Science, Google Scholar, SciVerse, and Scopus. Information regarding clinical trials retrieved from the Clinical Trial database. RESULTS Total "245" natural compounds were identified initially from the literature study. Among them, Glycyrrhizin, Caffeic acid, Curcumin is in phase 3, and Tetrandrine, Cyclosporine, Tacrolimus, Everolimus are in phase 4 clinical trial. Except for Glycyrrhizin, all compounds showed activity against COVID-19. CONCLUSIONS In summary, our demonstrated specific small molecules with lead and drug-like capabilities clarified their position in the drug discovery pipeline and proposed their future research against COVID-19.
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Affiliation(s)
- Md Junaid
- Natural Products Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory. Bangladesh
| | - Yeasmin Akter
- Natural Products Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory. Bangladesh
| | - Aysha Siddika
- Natural Products Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory. Bangladesh
| | - S M Abdul Nayeem
- Natural Products Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory. Bangladesh
| | - Afsana Nahrin
- Department of Pharmacy, University of Science and Technology Chittagong. Bangladesh
| | - Syeda Samira Afrose
- Natural Products Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory. Bangladesh
| | - Md Muzahid Ahmed Ezaj
- Natural Products Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory. Bangladesh
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Common Themes in Zoonotic Spillover and Disease Emergence: Lessons Learned from Bat- and Rodent-Borne RNA Viruses. Viruses 2021; 13:v13081509. [PMID: 34452374 PMCID: PMC8402684 DOI: 10.3390/v13081509] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rodents (order Rodentia), followed by bats (order Chiroptera), comprise the largest percentage of living mammals on earth. Thus, it is not surprising that these two orders account for many of the reservoirs of the zoonotic RNA viruses discovered to date. The spillover of these viruses from wildlife to human do not typically result in pandemics but rather geographically confined outbreaks of human infection and disease. While limited geographically, these viruses cause thousands of cases of human disease each year. In this review, we focus on three questions regarding zoonotic viruses that originate in bats and rodents. First, what biological strategies have evolved that allow RNA viruses to reside in bats and rodents? Second, what are the environmental and ecological causes that drive viral spillover? Third, how does virus spillover occur from bats and rodents to humans?
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COVID-19 Pathogenesis: From Molecular Pathway to Vaccine Administration. Biomedicines 2021; 9:biomedicines9080903. [PMID: 34440107 PMCID: PMC8389702 DOI: 10.3390/biomedicines9080903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
The Coronavirus 2 (SARS-CoV-2) infection is a global pandemic that has affected millions of people worldwide. The advent of vaccines has permitted some restitution. Aside from the respiratory complications of the infection, there is also a thrombotic risk attributed to both the disease and the vaccine. There are no reliable data for the risk of thromboembolism in SARS-CoV-2 infection in patients managed out of the hospital setting. A literature review was performed to identify the pathophysiological mechanism of thrombosis from the SARS-CoV-2 infection including the role of Angiotensin-Converting Enzyme receptors. The impact of the vaccine and likely mechanisms of thrombosis following vaccination were also clarified. Finally, the utility of the vaccines available against the multiple variants is also highlighted. The systemic response to SARS-CoV-2 infection is still relatively poorly understood, but several risk factors have been identified. The roll-out of the vaccines worldwide has also allowed the lifting of lockdown measures and a reduction in the spread of the disease. The experience of the SARS-CoV-2 infection, however, has highlighted the crucial role of epidemiological research and the need for ongoing studies within this field.
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Gan HH, Twaddle A, Marchand B, Gunsalus KC. Structural Modeling of the SARS-CoV-2 Spike/Human ACE2 Complex Interface can Identify High-Affinity Variants Associated with Increased Transmissibility. J Mol Biol 2021; 433:167051. [PMID: 33992693 PMCID: PMC8118711 DOI: 10.1016/j.jmb.2021.167051] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic has triggered concerns about the emergence of more infectious and pathogenic viral strains. As a public health measure, efficient screening methods are needed to determine the functional effects of new sequence variants. Here we show that structural modeling of SARS-CoV-2 Spike protein binding to the human ACE2 receptor, the first step in host-cell entry, predicts many novel variant combinations with enhanced binding affinities. By focusing on natural variants at the Spike-hACE2 interface and assessing over 700 mutant complexes, our analysis reveals that high-affinity Spike mutations (including N440K, S443A, G476S, E484R, G502P) tend to cluster near known human ACE2 recognition sites (K31 and K353). These Spike regions are structurally flexible, allowing certain mutations to optimize interface interaction energies. Although most human ACE2 variants tend to weaken binding affinity, they can interact with Spike mutations to generate high-affinity double mutant complexes, suggesting variation in individual susceptibility to infection. Applying structural analysis to highly transmissible variants, we find that circulating point mutations S477N, E484K and N501Y form high-affinity complexes (~40% more than wild-type). By combining predicted affinities and available antibody escape data, we show that fast-spreading viral variants exploit combinatorial mutations possessing both enhanced affinity and antibody resistance, including S477N/E484K, E484K/N501Y and K417T/E484K/N501Y. Thus, three-dimensional modeling of the Spike/hACE2 complex predicts changes in structure and binding affinity that correlate with transmissibility and therefore can help inform future intervention strategies.
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Affiliation(s)
- Hin Hark Gan
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States.
| | - Alan Twaddle
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States; NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Benoit Marchand
- High-Performance Computing, Center for Research Computing, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin C Gunsalus
- Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, United States; NYU Abu Dhabi Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.
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Polydorides S, Archontis G. Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2. Biophys J 2021; 120:2859-2871. [PMID: 33984310 PMCID: PMC8110322 DOI: 10.1016/j.bpj.2021.02.049] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 01/19/2021] [Accepted: 02/15/2021] [Indexed: 01/15/2023] Open
Abstract
The coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is responsible for the coronavirus disease 2019 pandemic, and the closely related SARS-CoV coronavirus enter cells by binding at the human angiotensin converting enzyme 2 (hACE2). The stronger hACE2 affinity of SARS-CoV-2 has been connected with its higher infectivity. In this work, we study hACE2 complexes with the receptor-binding domains (RBDs) of the human SARS-CoV-2 and human SARS-CoV viruses, using all-atom molecular dynamics simulations and computational protein design with a physics-based energy function. The molecular dynamics simulations identify charge-modifying substitutions between the CoV-2 and CoV RBDs, which either increase or decrease the hACE2 affinity of the SARS-CoV-2 RBD. The combined effect of these mutations is small, and the relative affinity is mainly determined by substitutions at residues in contact with hACE2. Many of these findings are in line and interpret recent experiments. Our computational protein design calculations redesign positions 455, 493, 494, and 501 of the SARS-CoV-2 receptor binding motif, which contact hACE2 in the complex and are important for ACE2 recognition. Sampling is enhanced by an adaptive importance sampling Monte Carlo method. Sequences with increased affinity replace CoV-2 glutamine by a negative residue at position 493; serine by a nonpolar or aromatic residue or an asparagine at position 494; and asparagine by valine or threonine at position 501. Substitutions at positions 455 and 501 have a smaller effect on affinity. Substitutions suggested by our design are seen in viral sequences encountered in other species, including bat and pangolin. Our results might be used to identify potential virus strains with higher human infectivity and assist in the design of peptide-based or peptidomimetic compounds with the potential to inhibit SARS-CoV-2 binding at hACE2.
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First Detection of SARS-CoV-2 B.1.1.7 Variant of Concern in an Asymptomatic Dog in Spain. Viruses 2021; 13:v13071379. [PMID: 34372585 PMCID: PMC8310032 DOI: 10.3390/v13071379] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 01/08/2023] Open
Abstract
Natural SARS-CoV-2 infection in pets has been widely documented during the last year. Although the majority of reports suggested that dogs’ susceptibility to the infection is low, little is known about viral pathogenicity and transmissibility in the case of variants of concern, such as B.1.1.7 in this species. Here, as part of a large-scale study on SARS-CoV-2 prevalence in pets in Spain, we have detected the B.1.1.7 variant of concern (VOC) in a dog whose owners were infected with SARS-CoV-2. The animal did not present any symptoms, but viral loads were high in the nasal and rectal swabs. In addition, viral isolation was possible from both swabs, demonstrating that the dog was shedding infectious virus. Seroconversion occurred 23 days after the first sampling. This study documents the first detection of B.1.1.7 VOC in a dog in Spain and emphasizes the importance of performing active surveillance and genomic investigation on infected animals.
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Chen J, Li S, Lei Z, Tang Q, Mo L, Zhao X, Xie F, Zi D, Tan J. Inhibition of SARS-CoV-2 pseudovirus invasion by ACE2 protecting and Spike neutralizing peptides: An alternative approach to COVID19 prevention and therapy. Int J Biol Sci 2021; 17:2957-2969. [PMID: 34345219 PMCID: PMC8326117 DOI: 10.7150/ijbs.61476] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/26/2021] [Indexed: 12/31/2022] Open
Abstract
SARS-CoV-2 invades host cells mainly through the interaction of its spike-protein with host cell membrane ACE2. Various antibodies targeting S-protein have been developed to combat COVID-19 pandemic; however, the potential risk of antibody-dependent enhancement and novel spike mutants-induced neutralization loss or antibody resistance still remain. Alternative preventative agents or therapeutics are still urgently needed. In this study, we designed series of peptides with either ACE2 protecting or Spike-protein neutralizing activities. Molecular docking predicted that, among these peptides, ACE2 protecting peptide AYp28 and Spike-protein neutralizing peptide AYn1 showed strongest intermolecular interaction to ACE2 and Spike-protein, respectively, which were further confirmed by both cell- and non-cell-based in vitro assays. In addition, both peptides inhibited the invasion of pseudotype SARS-CoV-2 into HEK293T/hACE2 cells, either alone or in combination. Moreover, the intranasal administration of AYp28 could partially block pseudovirus invasion in hACE2 transgenic mice. Much more importantly, no significant toxicity was observed in peptides-treated cells. AYp28 showed no impacts on ACE2 function. Taken together, the data from our present study predicted promising preventative and therapeutic values of peptides against COVID-19, and may prove the concept that cocktail containing ACE2 protecting peptides and spike neutralizing peptides could serve as a safe and effective approach for SARS-CoV-2 prevention and therapy.
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Affiliation(s)
- Jiang Chen
- Key Laboratory of Endemic and Ethnic Diseases, Laboratory of Molecular Biology, Ministry of Education, Guizhou Medical University, Guiyang 550004, China
| | - Song Li
- The First Affiliated Hospital of Dalian Medical University, Dalian 116021, China
| | - Zhifeng Lei
- Key Laboratory of Endemic and Ethnic Diseases, Laboratory of Molecular Biology, Ministry of Education, Guizhou Medical University, Guiyang 550004, China
| | - Qinmin Tang
- Key Laboratory of Endemic and Ethnic Diseases, Laboratory of Molecular Biology, Ministry of Education, Guizhou Medical University, Guiyang 550004, China
| | - Ling Mo
- Key Laboratory of Endemic and Ethnic Diseases, Laboratory of Molecular Biology, Ministry of Education, Guizhou Medical University, Guiyang 550004, China
| | - Xing Zhao
- Key Laboratory of Adult Stem Cell Transformation Research, Chinese Academy of Medical Sciences/Stem Cell and Tissue Engineering Research Center, Guizhou Medical University, Guiyang 550004, China
| | - Feifei Xie
- Anyu Biopharmaceutical (Hangzhou) Co., Ltd. 9F, Building I, No. 265, Chengrui Street, Qiantang New District, Hangzhou 310018, China
| | - Dan Zi
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Jun Tan
- Key Laboratory of Endemic and Ethnic Diseases, Laboratory of Molecular Biology, Ministry of Education, Guizhou Medical University, Guiyang 550004, China
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62
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Jokinen EM, Gopinath K, Kurkinen ST, Pentikäinen OT. Detection of Binding Sites on SARS-CoV-2 Spike Protein Receptor-Binding Domain by Molecular Dynamics Simulations in Mixed Solvents. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1281-1289. [PMID: 33914685 PMCID: PMC8791430 DOI: 10.1109/tcbb.2021.3076259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
The novel SARS-CoV-2 uses ACE2 (Angiotensin-Converting Enzyme 2) receptor as an entry point. Insights on S protein receptor-binding domain (RBD) interaction with ACE2 receptor and drug repurposing has accelerated drug discovery for the novel SARS-CoV-2 infection. Finding small molecule binding sites in S protein and ACE2 interface is crucial in search of effective drugs to prevent viral entry. In this study, we employed molecular dynamics simulations in mixed solvents together with virtual screening to identify small molecules that could be potential inhibitors of S protein -ACE2 interaction. Observation of organic probe molecule localization during the simulations revealed multiple sites at the S protein surface related to small molecule, antibody, and ACE2 binding. In addition, a novel conformation of the S protein was discovered that could be stabilized by small molecules to inhibit attachment to ACE2. The most promising binding site on RBD-ACE2 interface was targeted with virtual screening and top-ranked compounds (DB08248, DB02651, DB03714, and DB14826) are suggested for experimental testing. The protocol described here offers an extremely fast method for characterizing key proteins of a novel pathogen and for the identification of compounds that could inhibit or accelerate spreading of the disease.
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63
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Verma J, Subbarao N. Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants' interaction with ACE2 to understand the binding affinity and stability. Virology 2021; 561:107-116. [PMID: 34217923 PMCID: PMC8237243 DOI: 10.1016/j.virol.2021.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/16/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023]
Abstract
The fall of 2020 brought several new variants of SARS-CoV-2 circulating across the globe, and the steadily increasing COVID-19 cases are responsible for the emergence of these variants. All the SARS-CoV-2 variants reported to date have multiple mutations in the spike (S) protein, specifically in the receptor-binding domain (RBD). Here, we employed an integrated computational approach involving structure and sequence based predictions to study the effect of naturally occurring variations in the S-RBD on its stability and ACE2 binding affinity. The hotspot stabilizing residue mutations N501I, N501Y, Q493L, Q493H and K417R, strengthen the RBD-ACE2 complex by modulating the interaction statistics at the interface. Thus, we report here some critical mutations that could increase the binding affinity of the SARS-CoV-2 RBD with ACE2, increasing the viral infectivity and pathogenicity. Understanding the effect of these mutations will help in developing potential vaccines and therapeutics.
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Affiliation(s)
- Jyoti Verma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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64
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Pavlova A, Zhang Z, Acharya A, Lynch DL, Pang YT, Mou Z, Parks JM, Chipot C, Gumbart JC. Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2. J Phys Chem Lett 2021; 12:5494-5502. [PMID: 34086459 PMCID: PMC8204752 DOI: 10.1021/acs.jpclett.1c01494] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 05/06/2023]
Abstract
SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD-ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.
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Affiliation(s)
- Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zijian Zhang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Atanu Acharya
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yui Tik Pang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhongyu Mou
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jerry M. Parks
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Chris Chipot
- Université
de Lorraine, UMR 7019, Laboratoire International Associé
CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-lès-Nancy F-54506, France
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana 61801-3003, Illinois, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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65
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Zhu C, He G, Yin Q, Zeng L, Ye X, Shi Y, Xu W. Molecular biology of the SARs-CoV-2 spike protein: A review of current knowledge. J Med Virol 2021; 93:5729-5741. [PMID: 34125455 PMCID: PMC8427004 DOI: 10.1002/jmv.27132] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022]
Abstract
The global coronavirus disease 2019 (COVID‐19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), has led to an unprecedented worldwide public health emergency. Despite the concerted efforts of the scientific field, by April 25, 2021, SARS‐CoV‐2 had spread to over 192 countries/regions, causing more than 146 million confirmed cases including 31 million deaths. For now, an established treatment for patients with COVID‐19 remains unavailable. The key to tackling this pandemic is to understand the mechanisms underlying its infectivity and pathogenicity. As a predominant focus, the coronavirus spike (S) protein is the key determinant of host range, infectivity, and pathogenesis. Thereby comprehensive understanding of the sophisticated structure of SARS‐CoV‐2 S protein may provide insights into possible intervention strategies to fight this ongoing global pandemic. Herein, we summarize the current knowledge of the molecular structural and functional features of SARS‐CoV‐2 S protein as well as recent updates on the cell entry mechanism of the SARS‐CoV‐2, paving the way for exploring more structure‐guided strategies against SARS‐CoV‐2.
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Affiliation(s)
- Chaogeng Zhu
- Translational Medicine Laboratory of Pancreatic Diseases, Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Guiyun He
- Department of Ophthalmology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Qinqin Yin
- Department of Ophthalmology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Lin Zeng
- Institute of Translational Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Xiangli Ye
- Department of Medical Laboratory Science, School of Medicine, Hunan Normal University, Changsha, China
| | - Yongzhong Shi
- Institute of Translational Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Wei Xu
- Institute of Translational Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
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66
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Ruan Y, Wen H, He X, Wu CI. A theoretical exploration of the origin and early evolution of a pandemic. Sci Bull (Beijing) 2021; 66:1022-1029. [PMID: 33520335 PMCID: PMC7831721 DOI: 10.1016/j.scib.2020.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/15/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022]
Abstract
A virus that can cause a global pandemic must be highly adaptive to human conditions. Such adaptation is not likely to have emerged suddenly but, instead, may have evolved step by step with each step favored by natural selection. It is thus necessary to develop a theory about the origin in order to guide the search. Here, we propose such a model whereby evolution occurs in both the virus and the hosts (where the evolution is somatic; i.e., in the immune system). The hosts comprise three groups - the wild animal hosts, the nearby human population, and farther-away human populations. The theory suggests that the conditions under which the pandemic has initially evolved are: (i) an abundance of wild animals in the place of origin (PL0); (ii) a nearby human population of low density; (iii) frequent and long-term animal-human contacts to permit step-by-step evolution; and (iv) a level of herd immunity in the animal and human hosts. In this model, the evolving virus may have regularly spread out of PL0 although such invasions often fail, leaving sporadic cases of early infections. The place of the first epidemic (PL1), where humans are immunologically naïve to the virus, is likely a distance away from PL0. Finally, this current model is only a first attempt and more theoretical models can be expected to guide the search for the origin of SARS-CoV-2.
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Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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67
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Jelinek HF, Mousa M, Alefishat E, Osman W, Spence I, Bu D, Feng SF, Byrd J, Magni PA, Sahibzada S, Tay GK, Alsafar HS. Evolution, Ecology, and Zoonotic Transmission of Betacoronaviruses: A Review. Front Vet Sci 2021; 8:644414. [PMID: 34095271 PMCID: PMC8173069 DOI: 10.3389/fvets.2021.644414] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Coronavirus infections have been a part of the animal kingdom for millennia. The difference emerging in the twenty-first century is that a greater number of novel coronaviruses are being discovered primarily due to more advanced technology and that a greater number can be transmitted to humans, either directly or via an intermediate host. This has a range of effects from annual infections that are mild to full-blown pandemics. This review compares the zoonotic potential and relationship between MERS, SARS-CoV, and SARS-CoV-2. The role of bats as possible host species and possible intermediate hosts including pangolins, civets, mink, birds, and other mammals are discussed with reference to mutations of the viral genome affecting zoonosis. Ecological, social, cultural, and environmental factors that may play a role in zoonotic transmission are considered with reference to SARS-CoV, MERS, and SARS-CoV-2 and possible future zoonotic events.
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Affiliation(s)
- Herbert F. Jelinek
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Center of Heath Engineering Innovation, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mira Mousa
- Nuffield Department of Women's and Reproduction Health, Oxford University, Oxford, United Kingdom
| | - Eman Alefishat
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, Jordan
| | - Wael Osman
- Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ian Spence
- Discipline of Pharmacology, University of Sydney, Sydney, NSW, Australia
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, China
| | - Samuel F. Feng
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Mathematics, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jason Byrd
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Paola A. Magni
- Discipline of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
- Murdoch University Singapore, King's Centre, Singapore, Singapore
| | - Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Guan K. Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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68
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Zhang X, Han P, Wang H, Xu Y, Li F, Li M, Fan L, Zhang H, Dai Q, Lin H, Qi X, Liang J, Wang X, Yang X. Engineering mesenchymal stromal cells with neutralizing and anti-inflammatory capability against SARS-CoV-2 infection. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 21:754-764. [PMID: 34007862 PMCID: PMC8118700 DOI: 10.1016/j.omtm.2021.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
The emergence of the novel human severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has led to the pandemic of coronavirus disease 2019 (COVID-19), which has markedly affected global health and the economy. Both uncontrolled viral replication and a proinflammatory cytokine storm can cause severe tissue damage in patients with COVID-19. SARS-CoV-2 utilizes angiotensin-converting enzyme 2 (ACE2) as its entry receptor. In this study, we generated ACE2 extracellular domain-Fc and single-chain variable fragment-interleukin 6 (IL-6) single-chain variable fragment against IL-6 receptor (scFv-IL6R)-Fc fusion proteins to differentially neutralize viruses and ameliorate the cytokine storm. The human ACE2 (hACE2)1-740-Fc fusion protein showed a potent inhibitory effect on pseudo-typed SARS-CoV-2 entry and a good safety profile in mice. In addition, scFv-IL6R-Fc strongly blocked IL-6 signal activation. We also established a mesenchymal stromal cell (MSC)-based hACE21-740-Fc and scFv-IL6R-Fc delivery system, which could serve as a potential therapy strategy for urgent clinical needs of patients with COVID-19.
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Affiliation(s)
- Xiaoqing Zhang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Han
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haiyong Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanqin Xu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fanlin Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Min Li
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lilv Fan
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huihui Zhang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Dai
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Lin
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinyue Qi
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Liang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin Wang
- Shanghai Longyao Biotechnology Limited, Shanghai 201203, China
| | - Xuanming Yang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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69
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Clark SA, Clark LE, Pan J, Coscia A, McKay LGA, Shankar S, Johnson RI, Brusic V, Choudhary MC, Regan J, Li JZ, Griffiths A, Abraham J. SARS-CoV-2 evolution in an immunocompromised host reveals shared neutralization escape mechanisms. Cell 2021; 184:2605-2617.e18. [PMID: 33831372 PMCID: PMC7962548 DOI: 10.1016/j.cell.2021.03.027] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/23/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023]
Abstract
Many individuals mount nearly identical antibody responses to SARS-CoV-2. To gain insight into how the viral spike (S) protein receptor-binding domain (RBD) might evolve in response to common antibody responses, we studied mutations occurring during virus evolution in a persistently infected immunocompromised individual. We use antibody Fab/RBD structures to predict, and pseudotypes to confirm, that mutations found in late-stage evolved S variants confer resistance to a common class of SARS-CoV-2 neutralizing antibodies we isolated from a healthy COVID-19 convalescent donor. Resistance extends to the polyclonal serum immunoglobulins of four out of four healthy convalescent donors we tested and to monoclonal antibodies in clinical use. We further show that affinity maturation is unimportant for wild-type virus neutralization but is critical to neutralization breadth. Because the mutations we studied foreshadowed emerging variants that are now circulating across the globe, our results have implications to the long-term efficacy of S-directed countermeasures.
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Affiliation(s)
- Sarah A Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lars E Clark
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Junhua Pan
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Adrian Coscia
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lindsay G A McKay
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Sundaresh Shankar
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca I Johnson
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Vesna Brusic
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Manish C Choudhary
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James Regan
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jonathan Z Li
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
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70
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Obakachi VA, Kushwaha ND, Kushwaha B, Mahlalela MC, Shinde SR, Kehinde I, Karpoormath R. Design and synthesis of pyrazolone-based compounds as potent blockers of SARS-CoV-2 viral entry into the host cells. J Mol Struct 2021; 1241:130665. [PMID: 34007088 PMCID: PMC8118388 DOI: 10.1016/j.molstruc.2021.130665] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 05/09/2021] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 are enveloped positive-stranded RNA viruses that replicate in the cytoplasm. It relies on the fusion of their envelope with the host cell membrane to deliver their nucleocapsid into the host cell. The spike glycoprotein (S) mediates virus entry into cells via the human Angiotensin-converting enzyme 2 (hACE2) protein located on many cell types and tissues' outer surface. This study, therefore, aimed to design and synthesize novel pyrazolone-based compounds as potential inhibitors that would interrupt the interaction between the viral spike protein and the host cell receptor to prevent SARS-CoV 2 entrance into the cell. A series of pyrazolone compounds as potential SARS-CoV-2 inhibitors were designed and synthesized. Employing computational techniques, the inhibitory potentials of the designed compounds against both spike protein and hACE2 were evaluated. Results of the binding free energy from the in-silico analysis, showed that three compounds (7i, 7k and 8f) and six compounds (7b, 7h, 7k, 8d, 8g, and 8h) showed higher and better binding high affinity to SARS-CoV-2 Sgp and hACE-2, respectively compared to the standard drugs cefoperazone (CFZ) and MLN-4760. Furthermore, the outcome of the structural analysis of the two proteins upon binding of the inhibitors showed that the two proteins (SARS-CoV-2 Sgp and hACE-2) were stable, and the structural integrity of the proteins was not compromised. This study suggests pyrazolone-based compounds might be potent blockers of the viral entry into the host cells.
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Affiliation(s)
- Vincent A Obakachi
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Narva Deshwar Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Babita Kushwaha
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mavela Cleopus Mahlalela
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Suraj Raosaheb Shinde
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Idowu Kehinde
- School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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71
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Guler HI, Tatar G, Yildiz O, Belduz AO, Kolayli S. Investigation of potential inhibitor properties of ethanolic propolis extracts against ACE-II receptors for COVID-19 treatment by molecular docking study. Arch Microbiol 2021; 203:3557-3564. [PMID: 33950349 PMCID: PMC8098016 DOI: 10.1007/s00203-021-02351-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 11/28/2022]
Abstract
The angiotensin-converting enzyme (ACE)-related carboxypeptidase, ACE-II, is a type I integral membrane protein of 805 amino acids that contains 1 HEXXH-E zinc binding consensus sequence. ACE-II has been implicated in the regulation of heart function and also as a functional receptor for the coronavirus that causes the severe acute respiratory syndrome (SARS). In this study, the potential of some flavonoids presents in propolis to bind to ACE-II receptors was calculated with in silico. Binding constants of ten flavonoids, caffeic acid, caffeic acid phenethyl ester, chrysin, galangin, myricetin, rutin, hesperetin, pinocembrin, luteolin and quercetin were measured using the AutoDock 4.2 molecular docking program. And also, these binding constants were compared to reference ligand of MLN-4760. The results are shown that rutin has the best inhibition potentials among the studied molecules with high binding energy − 8.04 kcal/mol, and it is followed by myricetin, quercetin, caffeic acid phenethyl ester and hesperetin. However, the reference molecule has binding energy of – 7.24 kcal/mol. In conclusion, the high potential of flavonoids in ethanolic propolis extracts to bind to ACE-II receptors indicates that this natural bee product has high potential for COVID-19 treatment, but this needs to be supported by experimental studies.
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Affiliation(s)
- Halil Ibrahim Guler
- Faculty of Science, Department of Molecular Biology and Genetics, Karadeniz Technical University, 61080, Trabzon, Turkey.
| | - Gizem Tatar
- Faculty of Medicine, Department of Biostatistics and Medical Informatics, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Oktay Yildiz
- Faculty of Pharmacy, Basic Pharmaceutical Sciences, Department of Biochemistry, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Ali Osman Belduz
- Faculty of Science, Department of Biology, Karadeniz Technical University, 61080, Trabzon, Turkey
| | - Sevgi Kolayli
- Faculty of Science, Department of Chemistry, Karadeniz Technical University, 61080, Trabzon, Turkey
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72
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Olarte-Castillo XA, Dos Remédios JF, Heeger F, Hofer H, Karl S, Greenwood AD, East ML. The virus-host interface: Molecular interactions of Alphacoronavirus-1 variants from wild and domestic hosts with mammalian aminopeptidase N. Mol Ecol 2021; 30:2607-2625. [PMID: 33786949 PMCID: PMC8251223 DOI: 10.1111/mec.15910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022]
Abstract
The Alphacoronavirus‐1 species include viruses that infect numerous mammalian species. To better understand the wide host range of these viruses, better knowledge on the molecular determinants of virus–host cell entry mechanisms in wildlife hosts is essential. We investigated Alphacoronavirus‐1 infection in carnivores using long‐term data on Serengeti spotted hyenas (Crocuta crocuta) and molecular analyses guided by the tertiary structure of the viral spike (S) attachment protein's interface with the host receptor aminopeptidase N (APN). We sequenced the complete 3′‐end region of the genome of nine variants from wild African carnivores, plus the APN gene of 15 wild carnivore species. Our results revealed two outbreaks of Alphacoronavirus‐1 infection in spotted hyenas associated with genetically distinct canine coronavirus type II (CCoVII) variants. Within the receptor binding domain (RBD) of the S gene the residues that directly bind to the APN receptor were conserved in all variants studied, even those infecting phylogenetically diverse host taxa. We identified a variable region within RBD located next to a region that directly interacts with the APN receptor. Two residues within this variable region were under positive selection in hyena variants, indicating that both sites were associated with adaptation of CCoVII to spotted hyena APN. Analysis of APN sequences revealed that most residues that interact with the S protein are conserved in wild carnivores, whereas some adjacent residues are highly variable. Of the variable residues, four that are critical for virus–host binding were under positive selection and may modulate the efficiency of virus attachment to carnivore APN.
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Affiliation(s)
- Ximena A Olarte-Castillo
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,ZIBI Interdisciplinary Center for Infection Biology and Immunity, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Felix Heeger
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Stephan Karl
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Marion L East
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,ZIBI Interdisciplinary Center for Infection Biology and Immunity, Humboldt-Universität zu Berlin, Berlin, Germany
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73
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A Virulent PEDV Strain FJzz1 with Genomic Mutations and Deletions at the High Passage Level Was Attenuated in Piglets via Serial Passage In Vitro. Virol Sin 2021; 36:1052-1065. [PMID: 33909220 PMCID: PMC8080196 DOI: 10.1007/s12250-021-00368-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/28/2020] [Indexed: 01/06/2023] Open
Abstract
Highly virulent porcine epidemic diarrhea virus (PEDV) strains re-emerged and circulated in China at the end of 2010, causing significant economic losses in the pork industry worldwide. To understand the genetic dynamics of PEDV during its passage in vitro, the PEDV G2 strain FJzz1 was serially propagated in Vero cells for up to 200 passages. The susceptibility and adaptability of the FJzz1 strain increased gradually as it was serially passaged in vitro. Sequence analysis revealed that amino acid (aa) changes were mainly concentrated in the S glycoprotein, which accounted for 72.22%–85.71% of all aa changes. A continuous aa deletion (55I56G57E → 55K56Δ57Δ) occurred in the N-terminal domain of S1 (S1-NTD). To examine how the aa changes affected its virulence, FJzz1-F20 and FJzz1-F200 were selected to simultaneously evaluate their pathogenicity in suckling piglets. All the piglets in the FJzz1-F20-infected group showed typical diarrhea at 24 h postinfection, and the piglets died successively by 48 h postinfection. However, the clinical signs of the piglets in the FJzz1-F200-infected group were significantly weaker, and no deaths occurred. The FJzz1-F200-infected group also showed a lower level of fecal viral shedding and lower viral loads in the intestinal tissues, and no obvious histopathological lesions. Type I and III interferon were induced in the FJzz1-F200 infection group, together with pro-inflammatory cytokines, such as TNF-α, IL-1β and IL-8. These results indicate that the identified genetic changes may contribute to the attenuation of FJzz1 strain, and the attenuated FJzz1-F200 may have the potential for developing PEDV live-attenuated vaccines.
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74
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Hopp MT, Domingo-Fernández D, Gadiya Y, Detzel MS, Graf R, Schmalohr BF, Kodamullil AT, Imhof D, Hofmann-Apitius M. Linking COVID-19 and Heme-Driven Pathophysiologies: A Combined Computational-Experimental Approach. Biomolecules 2021; 11:biom11050644. [PMID: 33925394 PMCID: PMC8147026 DOI: 10.3390/biom11050644] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 outbreak was declared a worldwide pandemic in 2020. Infection triggers the respiratory tract disease COVID-19, which is accompanied by serious changes in clinical biomarkers such as hemoglobin and interleukins. The same parameters are altered during hemolysis, which is characterized by an increase in labile heme. We present two computational–experimental approaches aimed at analyzing a potential link between heme-related and COVID-19 pathophysiologies. Herein, we performed a detailed analysis of the common pathways induced by heme and SARS-CoV-2 by superimposition of knowledge graphs covering heme biology and COVID-19 pathophysiology. Focus was laid on inflammatory pathways and distinct biomarkers as the linking elements. In a second approach, four COVID-19-related proteins, the host cell proteins ACE2 and TMPRSS2 as well as the viral proteins 7a and S protein were computationally analyzed as potential heme-binding proteins with an experimental validation. The results contribute to the understanding of the progression of COVID-19 infections in patients with different clinical backgrounds and may allow for a more individual diagnosis and therapy in the future.
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Affiliation(s)
- Marie-Thérèse Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Daniel Domingo-Fernández
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
- Enveda Biosciences, Inc., San Francisco, CA 94080, USA
| | - Yojana Gadiya
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
| | - Milena S. Detzel
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Regina Graf
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Benjamin F. Schmalohr
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
| | - Alpha T. Kodamullil
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
- Causality Biomodels, Kinfra Hi-Tech Park, Kalamassery, Cochin, Kerala 683503, India
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany; (M.-T.H.); (M.S.D.); (R.G.); (B.F.S.)
- Correspondence: (D.I.); (M.H.-A.)
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53757 Sankt Augustin, Germany; (D.D.-F.); (Y.G.); (A.T.K.)
- Correspondence: (D.I.); (M.H.-A.)
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75
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Das UN. Bioactive lipid-based therapeutic approach to COVID-19 and other similar infections. Arch Med Sci 2021; 19:1327-1359. [PMID: 37732033 PMCID: PMC10507771 DOI: 10.5114/aoms/135703] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/11/2021] [Indexed: 09/22/2023] Open
Abstract
COVID-19 is caused by SARS-CoV-2 infection. Epithelial and T, NK, and other immunocytes release bioactive lipids especially arachidonic acid (AA) in response to microbial infections to inactivate them and upregulate the immune system. COVID-19 (coronavirus) and other enveloped viruses including severe acute respiratory syndrome (SARS-CoV-1 of 2002-2003) and Middle East respiratory syndrome (MERS; 2012-ongoing) and hepatitis B and C (HBV and HCV) can be inactivated by AA, γ-linolenic acid (GLA, dihomo-GLA (DGLA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), which are precursors to several eicosanoids. Prostaglandin E1, lipoxin A4, resolvins, protectins and maresins enhance phagocytosis of macrophages and leukocytes to clear debris from the site(s) of infection and injury, enhance microbial clearance and wound healing to restore homeostasis. Bioactive lipids modulate the generation of M1 and M2 macrophages and the activity of other immunocytes. Mesenchymal and adipose tissue-derived stem cells secrete LXA4 and other bioactive lipids to bring about their beneficial actions in COVID-19. Bioactive lipids regulate vasomotor tone, inflammation, thrombosis, immune response, inactivate enveloped viruses, regulate T cell proliferation and secretion of cytokines, stem cell survival, proliferation and differentiation, and leukocyte and macrophage functions, JAK kinase activity and neutrophil extracellular traps and thus, have a critical role in COVID-19.
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Affiliation(s)
- Undurti N. Das
- UND Life Sciences, Battle Ground, WA, USA
- Department of Medicine, Omega Hospitals, Gachibowli, Hyderabad, India
- International Research Centre, Biotechnologies of the third Millennium, ITMO University, Saint-Petersburg, Russia
- Department of Biotechnology, Indian Institute of Technology-Hyderabad, Telangana, India
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76
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Malik YS, Ansari MI, Kattoor JJ, Kaushik R, Sircar S, Subbaiyan A, Tiwari R, Dhama K, Ghosh S, Tomar S, Zhang KYJ. Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Brief Bioinform 2021; 22:1006-1022. [PMID: 33377145 PMCID: PMC7953982 DOI: 10.1093/bib/bbaa383] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/31/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.
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Affiliation(s)
| | | | | | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, Japan
| | | | | | - Ruchi Tiwari
- Department of Vet erinary Microbiology, DUVASU, Mathura, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Souvik Ghosh
- Health Center for Zoonoses and Tropical Veterinary Medicine, Basseterre, St. Kitts, West Indies
| | | | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Japan
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77
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Suryamohan K, Diwanji D, Stawiski EW, Gupta R, Miersch S, Liu J, Chen C, Jiang YP, Fellouse FA, Sathirapongsasuti JF, Albers PK, Deepak T, Saberianfar R, Ratan A, Washburn G, Mis M, Santhosh D, Somasekar S, Hiranjith GH, Vargas D, Mohan S, Phalke S, Kuriakose B, Antony A, Ustav M, Schuster SC, Sidhu S, Junutula JR, Jura N, Seshagiri S. Human ACE2 receptor polymorphisms and altered susceptibility to SARS-CoV-2. Commun Biol 2021; 4:475. [PMID: 33846513 PMCID: PMC8041869 DOI: 10.1038/s42003-021-02030-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/23/2021] [Indexed: 01/07/2023] Open
Abstract
COVID-19 is a respiratory illness caused by a novel coronavirus called SARS-CoV-2. The viral spike (S) protein engages the human angiotensin-converting enzyme 2 (ACE2) receptor to invade host cells with ~10-15-fold higher affinity compared to SARS-CoV S-protein, making it highly infectious. Here, we assessed if ACE2 polymorphisms can alter host susceptibility to SARS-CoV-2 by affecting this interaction. We analyzed over 290,000 samples representing >400 population groups from public genomic datasets and identified multiple ACE2 protein-altering variants. Using reported structural data, we identified natural ACE2 variants that could potentially affect virus-host interaction and thereby alter host susceptibility. These include variants S19P, I21V, E23K, K26R, T27A, N64K, T92I, Q102P and H378R that were predicted to increase susceptibility, while variants K31R, N33I, H34R, E35K, E37K, D38V, Y50F, N51S, M62V, K68E, F72V, Y83H, G326E, G352V, D355N, Q388L and D509Y were predicted to be protective variants that show decreased binding to S-protein. Using biochemical assays, we confirmed that K31R and E37K had decreased affinity, and K26R and T92I variants showed increased affinity for S-protein when compared to wildtype ACE2. Consistent with this, soluble ACE2 K26R and T92I were more effective in blocking entry of S-protein pseudotyped virus suggesting that ACE2 variants can modulate susceptibility to SARS-CoV-2.
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Affiliation(s)
- Kushal Suryamohan
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Devan Diwanji
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Eric W Stawiski
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Ravi Gupta
- MedGenome Labs Ltd., Bangalore, Karnataka, India
| | - Shane Miersch
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Jiang Liu
- ModMab Therapeutics, Foster City, CA, USA
| | - Chao Chen
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Frederic A Fellouse
- ModMab Therapeutics, Accelerator for Donnelly Collaboration, University of Toronto, Toronto, ON, Canada
| | | | | | | | - Reza Saberianfar
- ModMab Therapeutics, Accelerator for Donnelly Collaboration, University of Toronto, Toronto, ON, Canada
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Gavin Washburn
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Monika Mis
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | | | | | - G H Hiranjith
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Derek Vargas
- Research and Development Department, MedGenome Inc, Foster City, CA, USA
| | - Sangeetha Mohan
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | - Sameer Phalke
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | | | - Aju Antony
- Department of Molecular Biology, SciGenom Labs Pvt Ltd, Kochi, Kerala, India
| | - Mart Ustav
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sachdev Sidhu
- Department of Molecular Genetics, and the Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | | | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
| | - Somasekar Seshagiri
- ModMab Therapeutics, Foster City, CA, USA.
- SciGenom Research Foundation, Bangalore, Karnataka, India.
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78
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Sepahvandi A, Ghaffari M, Bahmanpour AH, Moztarzadeh F, Zarrintaj P, Uludağ H, Mozafari M. COVID-19: insights into virus-receptor interactions. MOLECULAR BIOMEDICINE 2021; 2:10. [PMID: 34766003 PMCID: PMC8035060 DOI: 10.1186/s43556-021-00033-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/03/2021] [Indexed: 01/03/2023] Open
Abstract
The recent outbreak of Coronavirus Disease 2019 (COVID-19) calls for rapid mobilization of scientists to probe and explore solutions to this deadly disease. A limited understanding of the high transmissibility of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) relative to other coronavirus strains guides a deeper investigation into the virus/receptor interactions. The cutting-edge studies in thermodynamic and kinetic properties of interactions such as protein-protein interplays have been reviewed in many modeling and analysis studies. Highlighting the thermodynamic assessments of biological interactions and emphasizing the boosted transmissibility of SARS-CoV-2 despite its high similarity in structure and sequence with other coronavirus strains is an important and highly valuable investigation that can lead scientists to discover analytical and fundamental approaches in studying virus's interactions. Accordingly, we have attempted to describe the crucial factors such as conformational changes and hydrophobicity particularities that influence on thermodynamic potentials in the SARS-COV-2 S-protein adsorption process. Discussing the thermodynamic potentials and the kinetics of the SARS-CoV-2 S-protein in its interaction with the ACE2 receptors of the host cell is a fundamental approach that would be extremely valuable in designing candidate pharmaceutical agents or exploring alternative treatments.
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Affiliation(s)
- Azadeh Sepahvandi
- Department of Mechanical Engineering College of Engineering and Computing, University of South Carolina, 301 Main St, Columbia, SC 29208 USA
| | - Maryam Ghaffari
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Amir Hossein Bahmanpour
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Fathollah Moztarzadeh
- Biomaterial Group, Faculty of Biomedical Engineering (Center of Excellence), Amirkabir University of Technology, Tehran, Iran
| | - Payam Zarrintaj
- School of Chemical Engineering, Oklahoma State University, 420 Engineering North, Stillwater, OK 74078 USA
| | - Hasan Uludağ
- Department of Chemical and Material Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada
- Department of Biomedical Engineering, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Masoud Mozafari
- Department of Tissue Engineering & Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Currently at: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
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79
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Li JY, Wang Q, Liao CH, Qiu Y, Ge XY. The 442th amino acid residue of the spike protein is critical for the adaptation to bat hosts for SARS-related coronaviruses. Virus Res 2021; 295:198307. [PMID: 33476695 PMCID: PMC7813513 DOI: 10.1016/j.virusres.2021.198307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 11/24/2022]
Abstract
Bats carry diverse severe acute respiratory syndrome-related coronaviruses (SARSr-CoVs). The suspected interspecies transmission of SARSr-CoVs from bats to humans has caused two severe CoV pandemics, the SARS pandemic in 2003 and the recent COVID-19 pandemic. The receptor utilization of SARSr-CoV plays the key role in determining the host range and the interspecies transmission ability of the virus. Both SARS-CoV and SARS-CoV-2 use angiotensin-converting enzyme 2 (ACE2) as their receptor. Previous studies showed that WIV1 strain, the first living coronavirus isolated from bat using ACE2 as its receptor, is the prototype of SARS-CoV. The receptor-binding domain (RBD) in the spike protein (S) of SARS-CoV and WIV1 is responsible for ACE2 binding and medicates the viral entry. Comparing to SARS-CoV, WIV1 has three distinct amino acid residues (442, 472, and 487) in its RBD. This study aimed at exploring whether these three residues could alter the receptor utilization of SARSr-CoVs. We replaced the three residues in SARS-CoV (BJ01 strain) S with their counterparts in WIV1 S, and then evaluated the change of their utilization of bat, civet, and human ACE2s using a lentivirus-based pseudovirus infection system. To further validate the S-ACE2 interactions, the binding affinity between the RBDs of these S proteins and the three ACE2s were verified by flow cytometry. The results showed that the single amino acid substitution Y442S in the RBD of BJ01 S enhanced its utilization of bat ACE2 and its binding affinity to bat ACE2. On the contrary, the reverse substitution in WIV1 S (S442Y) significantly attenuated the pseudovirus utilization of bat, civet and human ACE2s for cell entry, and reduced its binding affinity with the three ACE2s. These results suggest that the S442 is critical for WIV1 adapting to bats as its natural hosts. These findings will enhance our understanding of host adaptations and cross-species infections of coronaviruses, contributing to the prediction and prevention of coronavirus epidemics.
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Affiliation(s)
- Jin-Yan Li
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Qiong Wang
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Ce-Heng Liao
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Ye Qiu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
| | - Xing-Yi Ge
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, 27 Tianma Rd., Changsha, Hunan, 410012, China.
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80
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Kalra RS, Kumar V, Dhanjal JK, Garg S, Li X, Kaul SC, Sundar D, Wadhwa R. COVID19-inhibitory activity of withanolides involves targeting of the host cell surface receptor ACE2: insights from computational and biochemical assays. J Biomol Struct Dyn 2021; 40:7885-7898. [PMID: 33797339 PMCID: PMC8022344 DOI: 10.1080/07391102.2021.1902858] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 outbreak in China in December 2019 and its spread as worldwide pandemic has been a major global health crisis. Extremely high infection and mortality rate has severely affected all sectors of life and derailed the global economy. While drug and vaccine development have been prioritized and have made significant progression, use of phytochemicals and herbal constituents is deemed as a low-cost, safer and readily available alternative. We investigated therapeutic efficacy of eight withanolides (derived from Ashwagandha) against the angiotensin-converting enzyme 2 (ACE2) proteins, a target cell surface receptor for SARS-CoV-2 and report results on the (i) computational analyses including binding affinity and stable interactions with ACE2, occupancy of ACE2 residues in making polar and nonpolar interactions with different withanolides/ligands and (2) in vitro mRNA and protein analyses using human cancer (A549, MCF7 and HSC3) cells. We found that among all withanolides, Withaferin-A, Withanone, Withanoside-IV and Withanoside-V significantly inhibited the ACE2 expression. Analysis of withanolides-rich aqueous extracts derived from Ashwagandha leaves and stem showed a higher ACE2 inhibitory potency of stem-derived extracts. Taken together, we demonstrated the inhibitory potency of Ashwagandha withanolides and its aqueous extracts against ACE2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Rajkumar Singh Kalra
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Vipul Kumar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Jaspreet Kaur Dhanjal
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Sukant Garg
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Xiaoshuai Li
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Sunil C Kaul
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, India
| | - Renu Wadhwa
- Cellular and Molecular Biotechnology Research Institute, AIST-INDIA DAILAB, DBT-AIST International Center for Translational & Environmental Research (DAICENTER), National Institute of Advanced Industrial Science & Technology (AIST), Japan
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81
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Park C, Lee J, Hassan ZU, Ku KB, Kim SJ, Kim HG, Park EC, Park GS, Park D, Baek SH, Park D, Lee J, Jeon S, Kim S, Lee CS, Yoo HM, Kim S. Comparison of Digital PCR and Quantitative PCR with Various SARS-CoV-2 Primer-Probe Sets. J Microbiol Biotechnol 2021; 31:358-367. [PMID: 33397829 PMCID: PMC9705847 DOI: 10.4014/jmb.2009.09006] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/09/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022]
Abstract
The World Health Organization (WHO) has declared the coronavirus disease 2019 (COVID-19) as an international health emergency. Current diagnostic tests are based on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method, which is the gold standard test that involves the amplification of viral RNA. However, the RT-qPCR assay has limitations in terms of sensitivity and quantification. In this study, we tested both qPCR and droplet digital PCR (ddPCR) to detect low amounts of viral RNA. The cycle threshold (CT) of the viral RNA by RT-PCR significantly varied according to the sequences of the primer and probe sets with in vitro transcript (IVT) RNA or viral RNA as templates, whereas the copy number of the viral RNA by ddPCR was effectively quantified with IVT RNA, cultured viral RNA, and RNA from clinical samples. Furthermore, the clinical samples were assayed via both methods, and the sensitivity of the ddPCR was determined to be equal to or more than that of the RT-qPCR. However, the ddPCR assay is more suitable for determining the copy number of reference materials. These findings suggest that the qPCR assay with the ddPCR defined reference materials could be used as a highly sensitive and compatible diagnostic method for viral RNA detection.
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Affiliation(s)
- Changwoo Park
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea,National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Jina Lee
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea,College of Pharmacy, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Zohaib ul Hassan
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Keun Bon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Hong Gi Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Edmond Changkyun Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Republic of Korea,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Republic of Korea
| | - Gun-Soo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea,Research Group of Food Processing, Korea Food Research Institute, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Daeui Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea,Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Republic of Korea
| | - Seung-Hwa Baek
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea,Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Republic of Korea
| | - Dongju Park
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea,Department of Biological Science, Chungnam National University College of Bioscience and Biotechnology, Daejeon 34134, Republic of Korea
| | - Jihye Lee
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Sangeun Jeon
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Chang-Seop Lee
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju 54986, Republic of Korea,Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
| | - Hee Min Yoo
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Republic of Korea,Corresponding authors H.M. Yoo Phone/Fax: +82-42-868-5362 E-mail:
| | - Seil Kim
- Microbiological Analysis Team, Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea,Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea,Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Republic of Korea,S. Kim Phone: +82-42-868-5619 Fax: +82-42-868-5801 E-mail:
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82
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Jafary F, Jafari S, Ganjalikhany MR. In silico investigation of critical binding pattern in SARS-CoV-2 spike protein with angiotensin-converting enzyme 2. Sci Rep 2021; 11:6927. [PMID: 33767306 PMCID: PMC7994905 DOI: 10.1038/s41598-021-86380-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/15/2021] [Indexed: 12/11/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a newly-discovered coronavirus and responsible for the spread of coronavirus disease 2019 (COVID-19). SARS-CoV-2 infected millions of people in the world and immediately became a pandemic in March 2020. SARS-CoV-2 belongs to the beta-coronavirus genus of the large family of Coronaviridae. It is now known that its surface spike glycoprotein binds to the angiotensin-converting enzyme-2 (ACE2), which is expressed on the lung epithelial cells, mediates the fusion of the cellular and viral membranes, and facilitates the entry of viral genome to the host cell. Therefore, blocking the virus-cell interaction could be a potential target for the prevention of viral infection. The binding of SARS-CoV-2 to ACE2 is a protein-protein interaction, and so, analyzing the structure of the spike glycoprotein of SARS-CoV-2 and its underlying mechanism to bind the host cell receptor would be useful for the management and treatment of COVID-19. In this study, we performed comparative in silico studies to deeply understand the structural and functional details of the interaction between the spike glycoprotein of SARS-CoV-2 and its cognate cellular receptor ACE2. According to our results, the affinity of the ACE2 receptor for SARS-CoV-2 was higher than SARS-CoV. According to the free energy decomposition of the spike glycoprotein-ACE2 complex, we found critical points in three areas which are responsible for the increased binding affinity of SARS-CoV-2 compared with SARS-CoV. These mutations occurred at the receptor-binding domain of the spike glycoprotein that play an essential role in the increasing the affinity of coronavirus to ACE2. For instance, mutations Pro462Ala and Leu472Phe resulted in the altered binding energy from - 2 kcal mol-1 in SARS-COV to - 6 kcal mol-1 in SARS-COV-2. The results demonstrated that some mutations in the receptor-binding motif could be considered as a hot-point for designing potential drugs to inhibit the interaction between the spike glycoprotein and ACE2.
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Affiliation(s)
- Farzaneh Jafary
- Core Research Facilities (CRF), Isfahan University of Medical Science, Isfahan, Iran
| | - Sepideh Jafari
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mohamad Reza Ganjalikhany
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
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83
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Iheanacho CO, Odili VU, Eze UIH. Risk of SARS-CoV-2 infection and COVID-19 prognosis with the use of renin-angiotensin-aldosterone system (RAAS) inhibitors: a systematic review. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021; 7:73. [PMID: 33778087 PMCID: PMC7988641 DOI: 10.1186/s43094-021-00224-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/09/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Angiotensin-converting-enzyme-2, being the receptor for SARS-CoV-2, is increased in the use of RAAS inhibitors. Therefore, concerns have been raised over risks of SARS-CoV-2 infection and poor prognosis of COVID-19 in persons with prior exposure to these drugs. This study aimed to systematically review available evidence for associations between exposure to RAAS inhibitors with susceptibility to SARS-CoV-2 infection and clinical outcomes in infected persons. It hopes to address the question on the effects of RAAS inhibitors on the risk of COVID-19 and its prognosis. MAIN BODY Search was conducted in the databases of PubMed, Scopus, Cochrane, Embase and MedRxiv.org from December 2019 to May 31, 2020, using relevant keywords. Additional articles were identified through hand-searching of reference lists. Studies that reported associations between positive tests to COVID-19 and use of RAAS inhibitors, and treatment outcomes of COVID-19 patients who had exposure to RAAS inhibitors were considered eligible. The Newcastle-Ottawa scale was used to assess risk of bias in individual studies. The review was conducted in line with Preferred Regulatory Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines 2009. From the 952 studies screened and 2 studies from reference hand-searching, 18 were reviewed. Four studies evaluated the risks for SARS-CoV-2 infection among RAAS inhibitors users, and 16 (including 2 of the 4 studies) evaluated the clinical outcomes associated with previous exposure to RAAS inhibitors. CONCLUSION Evidence does not suggest higher risks for SARS-CoV-2 infection or poor disease prognosis in the use of RAAS inhibitors. This suggests the continued use of RAAS inhibitors by patients with existing needs, which supports the position statements of American Heart Association and European societies for Cardiology. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s43094-021-00224-4.
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Affiliation(s)
- Chinonyerem O. Iheanacho
- Department of Clinical Pharmacy and Public Health, Faculty of Pharmacy, University of Calabar, Calabar, Nigeria
| | - Valentine U. Odili
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmacy, niversity of Benin, Benin City, Nigeria
| | - Uchenna I. H. Eze
- Department of Clinical Pharmacy and Biopharmacy, Faculty of Pharmacy, Olabisi Onabanjo University, Sagamu, Nigeria
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84
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Kaseb AO, Mohamed YI, Malek AE, Raad II, Altameemi L, Li D, Kaseb OA, Kaseb SA, Selim A, Ma Q. The Impact of Angiotensin-Converting Enzyme 2 (ACE2) Expression on the Incidence and Severity of COVID-19 Infection. Pathogens 2021; 10:379. [PMID: 33809851 PMCID: PMC8004186 DOI: 10.3390/pathogens10030379] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 01/08/2023] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) pandemic has led to an unprecedented threat to the international community and raised major concerns in terms of public health safety. Although our current understanding of the complexity of COVID-19 pathogenesis remains limited, the infection is largely mediated by the interaction of viral spike protein and angiotensin-converting enzyme 2 (ACE2). The functional importance of ACE2 in different demographic and comorbid conditions may explain the significant variation in incidence and mortality of COVID-19 in vulnerable groups, and highlights its candidacy as a potential therapeutic target. We provide evidence supporting the idea that differences in incidence and severity of COVID-19 infection may be related to ACE2. Emerging data based on the prevalence and severity of COVID-19 among those with established high levels of ACE2 expression strongly support our hypothesis. Considering the burden of COVID-19 infection in these vulnerable groups and the impact of the potential therapeutic and preventive measures that would result from adopting ACE2-driven anti-viral strategies, our hypothesis may expedite global efforts to control the current COVID-19 pandemic.
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Affiliation(s)
- Ahmed O. Kaseb
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.I.M.); (L.A.)
| | - Yehia I. Mohamed
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.I.M.); (L.A.)
| | - Alexandre E. Malek
- Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.E.M.); (I.I.R.)
| | - Issam I. Raad
- Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.E.M.); (I.I.R.)
| | - Lina Altameemi
- Departments of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.I.M.); (L.A.)
| | - Dan Li
- Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.L.); (Q.M.)
| | - Omar A. Kaseb
- Iman Academy, Webster, TX 77598, USA; (O.A.K.); (S.A.K.)
| | - Safa A. Kaseb
- Iman Academy, Webster, TX 77598, USA; (O.A.K.); (S.A.K.)
| | - Abdelhafez Selim
- Philadelphia College of Osteopathic Medicine (PCOM), Philadelphia, PA 19131, USA;
| | - Qing Ma
- Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (D.L.); (Q.M.)
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85
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Frutos R, Serra-Cobo J, Pinault L, Lopez Roig M, Devaux CA. Emergence of Bat-Related Betacoronaviruses: Hazard and Risks. Front Microbiol 2021; 12:591535. [PMID: 33790874 PMCID: PMC8005542 DOI: 10.3389/fmicb.2021.591535] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/15/2021] [Indexed: 01/08/2023] Open
Abstract
The current Coronavirus Disease 2019 (COVID-19) pandemic, with more than 111 million reported cases and 2,500,000 deaths worldwide (mortality rate currently estimated at 2.2%), is a stark reminder that coronaviruses (CoV)-induced diseases remain a major threat to humanity. COVID-19 is only the latest case of betacoronavirus (β-CoV) epidemics/pandemics. In the last 20 years, two deadly CoV epidemics, Severe Acute Respiratory Syndrome (SARS; fatality rate 9.6%) and Middle East Respiratory Syndrome (MERS; fatality rate 34.7%), plus the emergence of HCoV-HKU1 which causes the winter common cold (fatality rate 0.5%), were already a source of public health concern. Betacoronaviruses can also be a threat for livestock, as evidenced by the Swine Acute Diarrhea Syndrome (SADS) epizootic in pigs. These repeated outbreaks of β-CoV-induced diseases raise the question of the dynamic of propagation of this group of viruses in wildlife and human ecosystems. SARS-CoV, SARS-CoV-2, and HCoV-HKU1 emerged in Asia, strongly suggesting the existence of a regional hot spot for emergence. However, there might be other regional hot spots, as seen with MERS-CoV, which emerged in the Arabian Peninsula. β-CoVs responsible for human respiratory infections are closely related to bat-borne viruses. Bats are present worldwide and their level of infection with CoVs is very high on all continents. However, there is as yet no evidence of direct bat-to-human coronavirus infection. Transmission of β-CoV to humans is considered to occur accidentally through contact with susceptible intermediate animal species. This zoonotic emergence is a complex process involving not only bats, wildlife and natural ecosystems, but also many anthropogenic and societal aspects. Here, we try to understand why only few hot spots of β-CoV emergence have been identified despite worldwide bats and bat-borne β-CoV distribution. In this work, we analyze and compare the natural and anthropogenic environments associated with the emergence of β-CoV and outline conserved features likely to create favorable conditions for a new epidemic. We suggest monitoring South and East Africa as well as South America as these regions bring together many of the conditions that could make them future hot spots.
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Affiliation(s)
- Roger Frutos
- Centre de coopération Internationale en Recherche Agronomique pour le Développement, UMR 17, Intertryp, Montpellier, France.,Institut d'Électronique et des Systèmes, UMR 5214, Université de Montpellier-CNRS, Montpellier, France
| | - Jordi Serra-Cobo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Biodiversity Research Institute, Barcelona, Spain
| | - Lucile Pinault
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Marc Lopez Roig
- Department of Evolutionary Biology, Ecology and Environmental Sciences, University of Barcelona, Biodiversity Research Institute, Barcelona, Spain
| | - Christian A Devaux
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
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86
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Viswanathan V, Puvvula A, Jamthikar AD, Saba L, Johri AM, Kotsis V, Khanna NN, Dhanjil SK, Majhail M, Misra DP, Agarwal V, Kitas GD, Sharma AM, Kolluri R, Naidu S, Suri JS. Bidirectional link between diabetes mellitus and coronavirus disease 2019 leading to cardiovascular disease: A narrative review. World J Diabetes 2021; 12:215-237. [PMID: 33758644 PMCID: PMC7958478 DOI: 10.4239/wjd.v12.i3.215] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/20/2020] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a global pandemic where several comorbidities have been shown to have a significant effect on mortality. Patients with diabetes mellitus (DM) have a higher mortality rate than non-DM patients if they get COVID-19. Recent studies have indicated that patients with a history of diabetes can increase the risk of severe acute respiratory syndrome coronavirus 2 infection. Additionally, patients without any history of diabetes can acquire new-onset DM when infected with COVID-19. Thus, there is a need to explore the bidirectional link between these two conditions, confirming the vicious loop between "DM/COVID-19". This narrative review presents (1) the bidirectional association between the DM and COVID-19, (2) the manifestations of the DM/COVID-19 loop leading to cardiovascular disease, (3) an understanding of primary and secondary factors that influence mortality due to the DM/COVID-19 loop, (4) the role of vitamin-D in DM patients during COVID-19, and finally, (5) the monitoring tools for tracking atherosclerosis burden in DM patients during COVID-19 and "COVID-triggered DM" patients. We conclude that the bidirectional nature of DM/COVID-19 causes acceleration towards cardiovascular events. Due to this alarming condition, early monitoring of atherosclerotic burden is required in "Diabetes patients during COVID-19" or "new-onset Diabetes triggered by COVID-19 in Non-Diabetes patients".
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Affiliation(s)
- Vijay Viswanathan
- M Viswanathan Hospital for Diabetes, M Viswanathan Diabetes Research Centre, Chennai 600013, India
| | - Anudeep Puvvula
- Annu’s Hospitals for Skin and Diabetes, Nellore 524101, Andhra Pradesh, India
| | - Ankush D Jamthikar
- Department of Electronics and Communications, Visvesvaraya National Institute of Technology, Nagpur 440010, Maharashtra, India
| | - Luca Saba
- Department of Radiology, University of Cagliari, Monserrato 09045, Cagliari, Italy
| | - Amer M Johri
- Department of Medicine, Division of Cardiology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Vasilios Kotsis
- 3rd Department of Internal Medicine, Hypertension Center, Papageorgiou Hospital, Aristotle University of Thessaloniki, Thessaloniki 541-24, Greece
| | - Narendra N Khanna
- Department of Cardiology, Indraprastha APOLLO Hospitals, New Delhi 110020, India
| | - Surinder K Dhanjil
- Stroke Diagnosis and Monitoring Division, AtheroPoint™ LLC, CA 95661, United States
| | - Misha Majhail
- Stroke Diagnosis and Monitoring Division, AtheroPoint™, Roseville, CA 95661, United States
| | - Durga Prasanna Misra
- Department of Clinical Immunology and Rheumatology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, Uttar Pradesh, India
| | - Vikas Agarwal
- Departments of Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, Uttar Pradesh, India
| | - George D Kitas
- Academic Affairs, Dudley Group NHS Foundation Trust, Dudley DY1 2HQ, United Kingdom
- Arthritis Research UK Epidemiology Unit, Manchester University, Manchester M13 9PL, United Kingdom
| | - Aditya M Sharma
- Division of Cardiovascular Medicine, University of Virginia, Charlottesville, VA 22908, United States
| | - Raghu Kolluri
- OhioHealth Heart and Vascular, Ohio, OH 43082, United States
| | - Subbaram Naidu
- Electrical Engineering Department, University of Minnesota, Duluth, MN 55812, United States
| | - Jasjit S Suri
- Stroke Diagnosis and Monitoring Division, AtheroPoint™, Roseville, CA 95661, United States
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87
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Deng Y, Angelova A. Coronavirus-Induced Host Cubic Membranes and Lipid-Related Antiviral Therapies: A Focus on Bioactive Plasmalogens. Front Cell Dev Biol 2021; 9:630242. [PMID: 33791293 PMCID: PMC8006408 DOI: 10.3389/fcell.2021.630242] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses have lipid envelopes required for their activity. The fact that coronavirus infection provokes the formation of cubic membranes (CM) (denoted also as convoluted membranes) in host cells has not been rationalized in the development of antiviral therapies yet. In this context, the role of bioactive plasmalogens (vinyl ether glycerophospholipids) is not completely understood. These lipid species display a propensity for non-lamellar phase formation, facilitating membrane fusion, and modulate the activity of membrane-bound proteins such as enzymes and receptors. At the organism level, plasmalogen deficiency is associated with cardiometabolic disorders including obesity and type 2 diabetes in humans. A straight link is perceived with the susceptibility of such patients to SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) infection, the severity of illness, and the related difficulty in treatment. Based on correlations between the coronavirus-induced modifications of lipid metabolism in host cells, plasmalogen deficiency in the lung surfactant of COVID-19 patients, and the alterations of lipid membrane structural organization and composition including the induction of CM, we emphasize the key role of plasmalogens in the coronavirus (SARS-CoV-2, SARS-CoV, or MERS-CoV) entry and replication in host cells. Considering that plasmalogen-enriched lung surfactant formulations may improve the respiratory process in severe infected individuals, plasmalogens can be suggested as an anti-viral prophylactic, a lipid biomarker in SARS-CoV and SARS-CoV-2 infections, and a potential anti-viral therapeutic component of lung surfactant development for COVID-19 patients.
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Affiliation(s)
- Yuru Deng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Angelina Angelova
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay UMR 8612, Châtenay-Malabry, France
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88
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Vieira C, Nery L, Martins L, Jabour L, Dias R, Simões E Silva AC. Downregulation of Membrane-bound Angiotensin Converting Enzyme 2 (ACE2) Receptor has a Pivotal Role in COVID-19 Immunopathology. Curr Drug Targets 2021; 22:254-281. [PMID: 33081670 DOI: 10.2174/1389450121666201020154033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/06/2020] [Accepted: 09/22/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The Coronavirus Disease 2019 (COVID-19) is becoming the major health issue in recent human history with thousands of deaths and millions of cases worldwide. Newer research and old experience with other coronaviruses highlighted a probable underlying mechanism of disturbance of the renin-angiotensin system (RAS) that is associated with the intrinsic effects of SARS-CoV-2 infection. OBJECTIVE In this review, we aimed to describe the intimate connections between the RAS components, the immune system and COVID-19 pathophysiology. METHODS This non-systematic review article summarizes recent evidence on the relationship between COVID-19 and the RAS. RESULTS Several studies have indicated that the downregulation of membrane-bound ACE2 may exert a key role for the impairment of immune functions and for COVID-19 patients' outcomes. The downregulation may occur by distinct mechanisms, particularly: (1) the shedding process induced by the SARS-CoV-2 fusion pathway, which reduces the amount of membrane-bound ACE2, stimulating more shedding by the high levels of Angiotensin II; (2) the endocytosis of ACE2 receptor with the virus itself and (3) by the interferon inhibition caused by SARS-CoV-2 effects on the immune system, which leads to a reduction of ACE2 receptor expression. CONCLUSION Recent research provides evidence of a reduction of the components of the alternative RAS axis, including ACE2 and Angiotensin-(1-7). In contrast, increased levels of Angiotensin II can activate the AT1 receptor in several organs. Consequently, increased inflammation, thrombosis and angiogenesis occur in patients infected with SARS-COV-2. Attention should be paid to the interactions of the RAS and COVID-19, mainly in the context of novel vaccines and proposed medications.
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Affiliation(s)
- Cristina Vieira
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Lucas Nery
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ludimila Martins
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luiz Jabour
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Raphael Dias
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Ana Cristina Simões E Silva
- Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
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89
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Govind Kumar V, Ogden DS, Isu U, Polasa A, Losey J, Moradi M. Differential Dynamic Behavior of Prefusion Spike Proteins of SARS Coronaviruses 1 and 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33398271 DOI: 10.1101/2020.12.25.424008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The coronavirus spike protein, which binds to the same human receptor in both SARS-CoV-1 and 2, has been implied to be a potential source of their differential transmissibility. However, the mechanistic details of spike protein binding to its human receptor remain elusive at the molecular level. Here, we have used an extensive set of unbiased and biased microsecond-level all-atom molecular dynamics (MD) simulations of SARS-CoV-1 and 2 spike proteins to determine the differential dynamic behavior of prefusion spike protein structure in the two viruses. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. Our results also suggest that not only the receptor binding domain (RBD) but also other domains such as the N-terminal domain (NTD) could play a role in the differential binding behavior of SARS-CoV-1 and 2 spike proteins.
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90
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Jakhmola S, Indari O, Kashyap D, Varshney N, Das A, Manivannan E, Jha HC. Mutational analysis of structural proteins of SARS-CoV-2. Heliyon 2021; 7:e06572. [PMID: 33778179 PMCID: PMC7980187 DOI: 10.1016/j.heliyon.2021.e06572] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/16/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 transmissibility is higher than that of other human coronaviruses; therefore, it poses a threat to the populated communities. We investigated mutations among envelope (E), membrane (M), and spike (S) proteins from different isolates of SARS-CoV-2 and plausible signaling influenced by mutated virus in a host. We procured updated protein sequences from the NCBI virus database. Mutations were analyzed in the retrieved sequences of the viral proteins through multiple sequence alignment. Additionally, the data was subjected to ScanPROSITE to analyse if the mutations generated a relevant sequence for host signaling. Unique mutations in E, M, and S proteins resulted in modification sites like PKC phosphorylation and N-myristoylation sites. Based on structural analysis, our study revealed that the D614G mutation in the S protein diminished the interaction with T859 and K854 of adjacent chains. Moreover, the S protein of SARS-CoV-2 consists of an Arg-Gly-Asp (RGD) tripeptide sequence, which could potentially interact with various members of integrin family receptors. RGD sequence in S protein might aid in the initial virus attachment. We speculated crucial host pathways which the mutated isolates of SARS-CoV-2 may alter like PKC, Src, and integrin mediated signaling pathways. PKC signaling is known to influence the caveosome/raft pathway which is critical for virus entry. Additionally, the myristoylated proteins might activate NF-κB, a master molecule of inflammation. Thus the mutations may contribute to the disease pathogenesis and distinct lung pathophysiological changes. Further the frequently occurring mutations in the protein can be studied for possible therapeutic interventions.
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Affiliation(s)
- Shweta Jakhmola
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Omkar Indari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Ayan Das
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | | | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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91
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Verma J, Subbarao N. A comparative study of human betacoronavirus spike proteins: structure, function and therapeutics. Arch Virol 2021; 166:697-714. [PMID: 33483791 PMCID: PMC7821988 DOI: 10.1007/s00705-021-04961-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/20/2020] [Indexed: 01/24/2023]
Abstract
Coronaviruses are the paradigm of emerging 21st century zoonotic viruses, triggering numerous outbreaks and a severe global health crisis. The current COVID-19 pandemic caused by SARS-CoV-2 has affected more than 51 million people across the globe as of 12 November 2020. The crown-like spikes on the surface of the virion are the unique structural feature of viruses in the family Coronaviridae. The spike (S) protein adopts distinct conformations while mediating entry of the virus into the host. This multifunctional protein mediates the entry process by recognizing its receptor on the host cell, followed by the fusion of the viral membrane with the host cell membrane. This review article focuses on the structural and functional comparison of S proteins of the human betacoronaviruses, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we review the current state of knowledge about receptor recognition, the membrane fusion mechanism, structural epitopes, and glycosylation sites of the S proteins of these viruses. We further discuss various vaccines and other therapeutics such as monoclonal antibodies, peptides, and small molecules based on the S protein of these three viruses.
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Affiliation(s)
- Jyoti Verma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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92
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Simmonds P, Williams S, Harvala H. Understanding the outcomes of COVID-19 - does the current model of an acute respiratory infection really fit? J Gen Virol 2021; 102:001545. [PMID: 33331810 PMCID: PMC8222868 DOI: 10.1099/jgv.0.001545] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
Although coronavirus disease 2019 (COVID-19) is regarded as an acute, resolving infection followed by the development of protective immunity, recent systematic literature review documents evidence for often highly prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory and faecal samples, periodic recurrence of PCR positivity in a substantial proportion of individuals and increasingly documented instances of reinfection associated with a lack of protective immunity. This pattern of infection is quite distinct from the acute/resolving nature of other human pathogenic respiratory viruses, such as influenza A virus and respiratory syncytial virus. Prolonged shedding of SARS-CoV-2 furthermore occurs irrespective of disease severity or development of virus-neutralizing antibodies. SARS-CoV-2 possesses an intensely structured RNA genome, an attribute shared with other human and veterinary coronaviruses and with other mammalian RNA viruses such as hepatitis C virus. These are capable of long-term persistence, possibly through poorly understood RNA structure-mediated effects on innate and adaptive host immune responses. The assumption that resolution of COVID-19 and the appearance of anti-SARS-CoV-2 IgG antibodies represents virus clearance and protection from reinfection, implicit for example in the susceptible-infected-recovered (SIR) model used for epidemic prediction, should be rigorously re-evaluated.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Williams
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- National Microbiology Services, NHS Blood and Transplant, London, UK
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93
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Farouk AE, Baig MH, Khan MI, Park T, Alotaibi SS, Dong JJ. Screening of inhibitors against SARS-CoV-2 spike protein and their capability to block the viral entry mechanism: A viroinformatics study. Saudi J Biol Sci 2021; 28:3262-3269. [PMID: 33654454 PMCID: PMC7908882 DOI: 10.1016/j.sjbs.2021.02.066] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 01/12/2023] Open
Abstract
SARS-CoV-2, previously named 2019 novel coronavirus (2019-nCoV), has been associated with the global pandemic of acute respiratory distress syndrome. First reported in December 2019 in the Wuhan province of China, this new RNA virus has several folds higher transmission among humans than its other family member (SARS-CoV and MERS-CoV). The SARS-CoV-2 spike receptor-binding domain (RBD) is the region mediating the binding of the virus to host cells via Angiotensin-converting enzyme 2 (ACE2), a critical step of viral. Here in this study, we have utilized in silico approach for the virtual screening of antiviral library extracted from the Asinex database against the Receptor binding domain (RBD) of the S1 subunit of the SARS-CoV-2 spike glycoprotein. Further, the molecules were ranked based on their binding affinity against RBD, and the top 15 molecules were selected. The affinity of these selected molecules to interrupt the ACE2-Spike interaction was also studied. It was found that the chosen molecules were demonstrating excellent binding affinity against spike protein, and these molecules were also very effectively interrupting the ACE2-RBD interaction. Furthermore, molecular dynamics (MD) simulation studies were utilized to investigate the top 3 selected molecules' stability in the ACE2-RBD complexes. To the best of our knowledge, this is the first study where molecules' inhibitory potential against the Receptor binding domain (RBD) of the S1 subunit of the SARS-CoV-2 spike glycoprotein and their inhibitory potential against the ACE2-Spike has been studied. We believe that these compounds can be further tested as a potential therapeutic option against COVID-19.
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Affiliation(s)
- Abd-ElAziem Farouk
- Department of Biotechnology, College of Science, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Mohammad Hassan Baig
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mohd Imran Khan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Taehwan Park
- University-Industry Foundation, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saqer S Alotaibi
- Department of Biotechnology, College of Science, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Jae-June Dong
- Department of Family Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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94
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Zhang HL, Li YM, Sun J, Zhang YY, Wang TY, Sun MX, Wang MH, Yang YL, Hu XL, Tang YD, Zhao J, Cai X. Evaluating angiotensin-converting enzyme 2-mediated SARS-CoV-2 entry across species. J Biol Chem 2021; 296:100435. [PMID: 33610551 PMCID: PMC7892319 DOI: 10.1016/j.jbc.2021.100435] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 01/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic represents a global threat, and the interaction between the virus and angiotensin-converting enzyme 2 (ACE2), the primary entry receptor for SARS-CoV-2, is a key determinant of the range of hosts that can be infected by the virus. However, the mechanisms underpinning ACE2-mediated viral entry across species remains unclear. Using infection assay, we evaluated SARS-CoV-2 entry mediated by ACE2 of 11 different animal species. We discovered that ACE2 of Rhinolophus sinicus (Chinese rufous horseshoe bat), Felis catus (domestic cat), Canis lupus familiaris (dog), Sus scrofa (wild pig), Capra hircus (goat), and Manis javanica (Malayan pangolin) facilitated SARS-CoV-2 entry into nonsusceptible cells. Moreover, ACE2 of the pangolin also mediated SARS-CoV-2 entry, adding credence to the hypothesis that SARS-CoV-2 may have originated from pangolins. However, the ACE2 proteins of Rhinolophus ferrumequinum (greater horseshoe bat), Gallus gallus (red junglefowl), Notechis scutatus (mainland tiger snake), or Mus musculus (house mouse) did not facilitate SARS-CoV-2 entry. In addition, a natural isoform of the ACE2 protein of Macaca mulatta (rhesus monkey) with the Y217N mutation was resistant to SARS-CoV-2 infection, highlighting the possible impact of this ACE2 mutation on SARS-CoV-2 studies in rhesus monkeys. We further demonstrated that the Y217 residue of ACE2 is a critical determinant for the ability of ACE2 to mediate SARS-CoV-2 entry. Overall, these results clarify that SARS-CoV-2 can use the ACE2 receptors of multiple animal species and show that tracking the natural reservoirs and intermediate hosts of SARS-CoV-2 is complex.
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Affiliation(s)
- Hong-Liang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yu-Ming Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yu-Yuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ming-Xia Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Meng-Hang Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yue-Lin Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiao-Liang Hu
- School of Life Sciences and Food Engineering, Yibin University, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin, China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.
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95
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Wells HL, Letko M, Lasso G, Ssebide B, Nziza J, Byarugaba DK, Navarrete-Macias I, Liang E, Cranfield M, Han BA, Tingley MW, Diuk-Wasser M, Goldstein T, Johnson CK, Mazet JAK, Chandran K, Munster VJ, Gilardi K, Anthony SJ. The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus. Virus Evol 2021; 7:veab007. [PMID: 33754082 PMCID: PMC7928622 DOI: 10.1093/ve/veab007] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1) and SARS-CoV-2 are not phylogenetically closely related; however, both use the angiotensin-converting enzyme 2 (ACE2) receptor in humans for cell entry. This is not a universal sarbecovirus trait; for example, many known sarbecoviruses related to SARS-CoV-1 have two deletions in the receptor binding domain of the spike protein that render them incapable of using human ACE2. Here, we report three sequences of a novel sarbecovirus from Rwanda and Uganda that are phylogenetically intermediate to SARS-CoV-1 and SARS-CoV-2 and demonstrate via in vitro studies that they are also unable to utilize human ACE2. Furthermore, we show that the observed pattern of ACE2 usage among sarbecoviruses is best explained by recombination not of SARS-CoV-2, but of SARS-CoV-1 and its relatives. We show that the lineage that includes SARS-CoV-2 is most likely the ancestral ACE2-using lineage, and that recombination with at least one virus from this group conferred ACE2 usage to the lineage including SARS-CoV-1 at some time in the past. We argue that alternative scenarios such as convergent evolution are much less parsimonious; we show that biogeography and patterns of host tropism support the plausibility of a recombination scenario, and we propose a competitive release hypothesis to explain how this recombination event could have occurred and why it is evolutionarily advantageous. The findings provide important insights into the natural history of ACE2 usage for both SARS-CoV-1 and SARS-CoV-2 and a greater understanding of the evolutionary mechanisms that shape zoonotic potential of coronaviruses. This study also underscores the need for increased surveillance for sarbecoviruses in southwestern China, where most ACE2-using viruses have been found to date, as well as other regions such as Africa, where these viruses have only recently been discovered.
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Affiliation(s)
- H L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - M Letko
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 S. 4th St, Hamilton, MT 59840, USA.,Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - G Lasso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - B Ssebide
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J Nziza
- Gorilla Doctors, c/o MGVP, Inc., 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - D K Byarugaba
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,Makerere University, College of Veterinary Medicine, Living Stone Road, Kampala, Uganda
| | - I Navarrete-Macias
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - E Liang
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, 722 W 168th St, New York, NY 10032, USA
| | - M Cranfield
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA.,Department of Microbiology and Immunology, University of North Carolina School of Medicine, 125 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - B A Han
- Cary Institute of Ecosystem Studies, 2801 Sharon Turnpike, Millbrook, NY 12545, USA
| | - M W Tingley
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 612 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - M Diuk-Wasser
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 1200 Amsterdam Ave, New York, NY 10027, USA
| | - T Goldstein
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - C K Johnson
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - J A K Mazet
- One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - K Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10462, USA
| | - V J Munster
- Paul G. Allen School for Global Animal Health, Washington State University, 1155 College Ave, Pullman, WA 99164, USA
| | - K Gilardi
- Makerere University Walter Reed Project, Plot 42, Nakasero Road, Kampala, Uganda.,One Health Institute and Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California Davis, 1089 Veterinary Medicine Drive, Davis, CA 95616, USA
| | - S J Anthony
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
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96
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Kumar Verma A, Kumar V, Singh S, Goswami BC, Camps I, Sekar A, Yoon S, Lee KW. Repurposing potential of Ayurvedic medicinal plants derived active principles against SARS-CoV-2 associated target proteins revealed by molecular docking, molecular dynamics and MM-PBSA studies. Biomed Pharmacother 2021; 137:111356. [PMID: 33561649 PMCID: PMC7857054 DOI: 10.1016/j.biopha.2021.111356] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/26/2021] [Accepted: 01/31/2021] [Indexed: 12/11/2022] Open
Abstract
All the plants and their secondary metabolites used in the present study were obtained from Ayurveda, with historical roots in the Indian subcontinent. The selected secondary metabolites have been experimentally validated and reported as potent antiviral agents against genetically-close human viruses. The plants have also been used as a folk medicine to treat cold, cough, asthma, bronchitis, and severe acute respiratory syndrome in India and across the globe since time immemorial. The present study aimed to assess the repurposing possibility of potent antiviral compounds with SARS-CoV-2 target proteins and also with host-specific receptor and activator protease that facilitates the viral entry into the host body. Molecular docking (MDc) was performed to study molecular affinities of antiviral compounds with aforesaid target proteins. The top-scoring conformations identified through docking analysis were further validated by 100 ns molecular dynamic (MD) simulation run. The stability of the conformation was studied in detail by investigating the binding free energy using MM-PBSA method. Finally, the binding affinities of all the compounds were also compared with a reference ligand, remdesivir, against the target protein RdRp. Additionally, pharmacophore features, 3D structure alignment of potent compounds and Bayesian machine learning model were also used to support the MDc and MD simulation. Overall, the study emphasized that curcumin possesses a strong binding ability with host-specific receptors, furin and ACE2. In contrast, gingerol has shown strong interactions with spike protein, and RdRp and quercetin with main protease (Mpro) of SARS-CoV-2. In fact, all these target proteins play an essential role in mediating viral replication, and therefore, compounds targeting aforesaid target proteins are expected to block the viral replication and transcription. Overall, gingerol, curcumin and quercetin own multitarget binding ability that can be used alone or in combination to enhance therapeutic efficacy against COVID-19. The obtained results encourage further in vitro and in vivo investigations and also support the traditional use of antiviral plants preventively.
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Affiliation(s)
- Akalesh Kumar Verma
- Department of Zoology, Cell and Biochemical Technology Laboratory, Cotton University, Guwahati 781001, Assam, India.
| | - Vikas Kumar
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Sweta Singh
- District Malaria Office, Amingaon, Guwahati, Assam 786031, India
| | | | - Ihosvany Camps
- Laboratório de Modelagem Computacional, Instituto de Ciências Exatas, Universidade Federal de Alfenas - UNIFAL-MG, Alfenas, Minas Gerais 37133-840, Brazil
| | - Aishwarya Sekar
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, Tamil Nadu 600086, India
| | - Sanghwa Yoon
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Life Science, Department of Bio & Medical Big Data (BK4 Program), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Republic of Korea.
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97
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Bonam SR, Kotla NG, Bohara RA, Rochev Y, Webster TJ, Bayry J. Potential immuno-nanomedicine strategies to fight COVID-19 like pulmonary infections. NANO TODAY 2021; 36:101051. [PMID: 33519949 PMCID: PMC7834523 DOI: 10.1016/j.nantod.2020.101051] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/15/2020] [Accepted: 11/30/2020] [Indexed: 05/08/2023]
Abstract
COVID-19, coronavirus disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic. At the time of writing this (October 14, 2020), more than 38.4 million people have become affected, and 1.0 million people have died across the world. The death rate is undoubtedly correlated with the cytokine storm and other pathological pulmonary characteristics, as a result of which the lungs cannot provide sufficient oxygen to the body's vital organs. While diversified drugs have been tested as a first line therapy, the complexity of fatal cases has not been reduced so far, and the world is looking for a treatment to combat the virus. However, to date, and despite such promise, we have received very limited information about the potential of nanomedicine to fight against COVID-19 or as an adjunct therapy in the treatment regimen. Over the past two decades, various therapeutic strategies, including direct-acting antiviral drugs, immunomodulators, a few non-specific drugs (simple to complex), have been explored to treat Acute Respiratory Distress Syndrome (ARDS), Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), influenza, and sometimes the common flu, thus, correlating and developing specific drugs centric to COVID-19 is possible. This review article focuses on the pulmonary pathology caused by SARS-CoV-2 and other viral pathogens, highlighting possible nanomedicine therapeutic strategies that should be further tested immediately.
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Affiliation(s)
- Srinivasa Reddy Bonam
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe-Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, Université de Paris, Paris F-75006, France
| | - Niranjan G Kotla
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Ireland
| | - Raghvendra A Bohara
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Ireland
- Centre for Interdisciplinary Research, D. Y. Patil Education Society (Institution Deemed to be University), Kolhapur (MS), India
| | - Yury Rochev
- CÚRAM, SFI Research Centre for Medical Devices, National University of Ireland Galway, Ireland
- Sechenov First Moscow State Medical University, Institute for Regenerative Medicine, Moscow 119992, Russia
| | - Thomas J Webster
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Jagadeesh Bayry
- Institut National de la Santé et de la Recherche Médicale; Centre de Recherche des Cordeliers, Equipe-Immunopathologie et Immunointervention Thérapeutique, Sorbonne Université, Université de Paris, Paris F-75006, France
- Indian Institute of Technology Palakkad, Kozhippara, Palakkad 678557, India
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98
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Datta S, Hett EC, Vora KA, Hazuda DJ, Oslund RC, Fadeyi OO, Emili A. The chemical biology of coronavirus host-cell interactions. RSC Chem Biol 2021; 2:30-46. [PMID: 34458775 PMCID: PMC8340996 DOI: 10.1039/d0cb00197j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/06/2020] [Indexed: 12/25/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current coronavirus disease 2019 (COVID-19) pandemic that has led to a global economic disruption and collapse. With several ongoing efforts to develop vaccines and treatments for COVID-19, understanding the molecular interaction between the coronavirus, host cells, and the immune system is critical for effective therapeutic interventions. Greater insight into these mechanisms will require the contribution and combination of multiple scientific disciplines including the techniques and strategies that have been successfully deployed by chemical biology to tease apart complex biological pathways. We highlight in this review well-established strategies and methods to study coronavirus-host biophysical interactions and discuss the impact chemical biology will have on understanding these interactions at the molecular level.
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Affiliation(s)
- Suprama Datta
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine Boston MA USA
| | - Erik C Hett
- Exploratory Science Center, Merck & Co., Inc. Cambridge Massachusetts USA
| | - Kalpit A Vora
- Infectious Diseases and Vaccine Research, Merck & Co., Inc. West Point Pennsylvania USA
| | - Daria J Hazuda
- Exploratory Science Center, Merck & Co., Inc. Cambridge Massachusetts USA
- Infectious Diseases and Vaccine Research, Merck & Co., Inc. West Point Pennsylvania USA
| | - Rob C Oslund
- Exploratory Science Center, Merck & Co., Inc. Cambridge Massachusetts USA
| | | | - Andrew Emili
- Center for Network Systems Biology, Department of Biochemistry, Boston University School of Medicine Boston MA USA
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99
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Mishra SK, Tripathi T. One year update on the COVID-19 pandemic: Where are we now? Acta Trop 2021; 214:105778. [PMID: 33253656 PMCID: PMC7695590 DOI: 10.1016/j.actatropica.2020.105778] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
We are living through an unprecedented crisis with the rapid spread of the new coronavirus disease (COVID-19) worldwide within a short time. The timely availability of thousands of SARS-CoV-2 genomes has enabled the scientific community to study the origin, structures, and pathogenesis of the virus. The pandemic has spurred research publication and resulted in an unprecedented number of therapeutic proposals. Because the development of new drugs is time consuming, several strategies, including drug repurposing and repositioning, are being tested to treat patients with COVID-19. Researchers have developed several potential vaccine candidates that have shown promise in phase II and III trials. As of 12 November 2020, 164 candidate vaccines are in preclinical evaluation, and 48 vaccines are in clinical evaluation, of which four have cleared phase III trials (Pfizer/BioNTech's BNT162b2, Moderna's mRNA-1273, University of Oxford & AstraZeneca's AZD1222, and Gamaleya's Sputnik V vaccine). Despite the acquisition of a vast body of scientific information, treatment depends only on the clinical management of the disease through supportive care. At the pandemic's 1-year mark, we summarize current information on SARS-CoV-2 origin and biology, and advances in the development of therapeutics. The updated information presented here provides a comprehensive report on the scientific progress made in the past year in understanding of SARS-CoV-2 biology and therapeutics.
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Affiliation(s)
- Sanjay Kumar Mishra
- Department of Botany, Ewing Christian College, Prayagraj- 211003, Uttar Pradesh, India
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, Meghalaya, India.
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100
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Chan KK, Tan TJC, Narayanan KK, Procko E. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. SCIENCE ADVANCES 2021; 7:eabf1738. [PMID: 33597251 PMCID: PMC7888922 DOI: 10.1126/sciadv.abf1738] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/31/2020] [Indexed: 05/04/2023]
Abstract
The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, because of close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find that an engineered decoy receptor, sACE22v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain followed by in vitro selection, with wild-type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild-type receptor. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign, IL 61821, USA
| | - Timothy J C Tan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Krishna K Narayanan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61801, USA.
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