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Kumawat P, Agarwal LK, Sharma K. An Overview of SARS-CoV-2 Potential Targets, Inhibitors, and Computational Insights to Enrich the Promising Treatment Strategies. Curr Microbiol 2024; 81:169. [PMID: 38733424 DOI: 10.1007/s00284-024-03671-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 03/18/2024] [Indexed: 05/13/2024]
Abstract
The rapid spread of the SARS-CoV-2 virus has emphasized the urgent need for effective therapies to combat COVID-19. Investigating the potential targets, inhibitors, and in silico approaches pertinent to COVID-19 are of utmost need to develop novel therapeutic agents and reprofiling of existing FDA-approved drugs. This article reviews the viral enzymes and their counter receptors involved in the entry of SARS-CoV-2 into host cells, replication of genomic RNA, and controlling the host cell physiology. In addition, the study provides an overview of the computational techniques such as docking simulations, molecular dynamics, QSAR modeling, and homology modeling that have been used to find the FDA-approved drugs and other inhibitors against SARS-CoV-2. Furthermore, a comprehensive overview of virus-based and host-based druggable targets from a structural point of view, together with the reported therapeutic compounds against SARS-CoV-2 have also been presented. The current study offers future perspectives for research in the field of network pharmacology investigating the large unexplored molecular libraries. Overall, the present in-depth review aims to expedite the process of identifying and repurposing drugs for researchers involved in the field of COVID-19 drug discovery.
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Affiliation(s)
- Pooja Kumawat
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
| | - Lokesh Kumar Agarwal
- Department of Chemistry, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
| | - Kuldeep Sharma
- Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India
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2
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Mushebenge AGA, Ugbaja SC, Mbatha NA, B. Khan R, Kumalo HM. Assessing the Potential Contribution of In Silico Studies in Discovering Drug Candidates That Interact with Various SARS-CoV-2 Receptors. Int J Mol Sci 2023; 24:15518. [PMID: 37958503 PMCID: PMC10647470 DOI: 10.3390/ijms242115518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The COVID-19 pandemic has spurred intense research efforts to identify effective treatments for SARS-CoV-2. In silico studies have emerged as a powerful tool in the drug discovery process, particularly in the search for drug candidates that interact with various SARS-CoV-2 receptors. These studies involve the use of computer simulations and computational algorithms to predict the potential interaction of drug candidates with target receptors. The primary receptors targeted by drug candidates include the RNA polymerase, main protease, spike protein, ACE2 receptor, and transmembrane protease serine 2 (TMPRSS2). In silico studies have identified several promising drug candidates, including Remdesivir, Favipiravir, Ribavirin, Ivermectin, Lopinavir/Ritonavir, and Camostat Mesylate, among others. The use of in silico studies offers several advantages, including the ability to screen a large number of drug candidates in a relatively short amount of time, thereby reducing the time and cost involved in traditional drug discovery methods. Additionally, in silico studies allow for the prediction of the binding affinity of the drug candidates to target receptors, providing insight into their potential efficacy. This study is aimed at assessing the useful contributions of the application of computational instruments in the discovery of receptors targeted in SARS-CoV-2. It further highlights some identified advantages and limitations of these studies, thereby revealing some complementary experimental validation to ensure the efficacy and safety of identified drug candidates.
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Affiliation(s)
- Aganze Gloire-Aimé Mushebenge
- Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa;
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Faculty of Pharmaceutical Sciences, University of Lubumbashi, Lubumbashi 1825, Democratic Republic of the Congo
| | - Samuel Chima Ugbaja
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Africa Health Research Institute, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nonkululeko Avril Mbatha
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
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Maldonato BJ, Vergara AG, Yadav J, Glass SM, Paragas EM, Li D, Lazarus P, McClay JL, Ning B, Daly AK, Russell LE. Epigenetics in drug disposition & drug therapy: symposium report of the 24 th North American meeting of the International Society for the Study of Xenobiotics (ISSX). Drug Metab Rev 2022; 54:318-330. [PMID: 35876105 PMCID: PMC9970013 DOI: 10.1080/03602532.2022.2101662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
The 24th North American International Society for the Study of Xenobiotics (ISSX) meeting, held virtually from September 13 to 17, 2021, embraced the theme of "Broadening Our Horizons." This reinforces a key mission of ISSX: striving to share innovative science related to drug discovery and development. Session speakers and the ISSX New Investigators Group, which supports the scientific and professional development of student and early career ISSX members, elected to highlight the scientific content presented during the captivating session titled, "Epigenetics in Drug Disposition & Drug Therapy." The impact genetic variation has on drug response is well established; however, this session underscored the importance of investigating the role of epigenetics in drug disposition and drug discovery. Session speakers, Drs. Ning, McClay, and Lazarus, detailed mechanisms by which epigenetic players including long non-coding RNA (lncRNAs), microRNA (miRNAs), DNA methylation, and histone acetylation can alter the expression of genes involved in pharmacokinetics, pharmacodynamics, and toxicity. Dr. Ning detailed current knowledge about miRNAs and lncRNAs and the mechanisms by which they can affect the expression of drug metabolizing enzymes (DMEs) and nuclear receptors. Dr. Lazarus discussed the potential role of miRNAs on UDP-glucuronosyltransferase (UGT) expression and activity. Dr. McClay provided evidence that aging alters methylation and acetylation of DMEs in the liver, affecting gene expression and activity. These topics, compiled by the symposium organizers, presenters, and the ISSX New Investigators Group, are herein discussed, along with exciting future perspectives for epigenetics in drug disposition and drug discovery research.
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Affiliation(s)
- Benjamin J Maldonato
- Department of Nonclinical Development and Clinical Pharmacology, Revolution Medicines, Inc, Redwood City, CA, United States
| | - Ana G Vergara
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Jaydeep Yadav
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Sarah M Glass
- Janssen Research & Development, San Diego, CA, United States
| | | | - Dongying Li
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, United States
| | - Joseph L McClay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Baitang Ning
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laura E Russell
- Drug Metabolism and Pharmacokinetics, AbbVie Inc, North Chicago, Illinois, United States
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Li J, Jia H, Tian M, Wu N, Yang X, Qi J, Ren W, Li F, Bian H. SARS-CoV-2 and Emerging Variants: Unmasking Structure, Function, Infection, and Immune Escape Mechanisms. Front Cell Infect Microbiol 2022; 12:869832. [PMID: 35646741 PMCID: PMC9134119 DOI: 10.3389/fcimb.2022.869832] [Citation(s) in RCA: 2] [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: 02/05/2022] [Accepted: 04/06/2022] [Indexed: 12/24/2022] Open
Abstract
As of April 1, 2022, over 468 million COVID-19 cases and over 6 million deaths have been confirmed globally. Unlike the common coronavirus, SARS-CoV-2 has highly contagious and attracted a high level of concern worldwide. Through the analysis of SARS-CoV-2 structural, non-structural, and accessory proteins, we can gain a deeper understanding of structure-function relationships, viral infection mechanisms, and viable strategies for antiviral therapy. Angiotensin-converting enzyme 2 (ACE2) is the first widely acknowledged SARS-CoV-2 receptor, but researches have shown that there are additional co-receptors that can facilitate the entry of SARS-CoV-2 to infect humans. We have performed an in-depth review of published papers, searching for co-receptors or other auxiliary membrane proteins that enhance viral infection, and analyzing pertinent pathogenic mechanisms. The genome, and especially the spike gene, undergoes mutations at an abnormally high frequency during virus replication and/or when it is transmitted from one individual to another. We summarized the main mutant strains currently circulating global, and elaborated the structural feature for increased infectivity and immune evasion of variants. Meanwhile, the principal purpose of the review is to update information on the COVID-19 outbreak. Many countries have novel findings on the early stage of the epidemic, and accruing evidence has rewritten the timeline of the outbreak, triggering new thinking about the origin and spread of COVID-19. It is anticipated that this can provide further insights for future research and global epidemic prevention and control.
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Affiliation(s)
| | | | | | | | | | | | | | - Feifei Li
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Hongjun Bian
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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Gu M, Pan H, Yuan Y, Zhou X, Chen L, Wang X, Fang F, Hu L, Xie Y, Shen C. Sera Metabolomics Characterization of Patients at Different Stages in Wuhan Identifies Critical Biomarkers of COVID-19. Front Cell Infect Microbiol 2022; 12:882661. [PMID: 35586248 PMCID: PMC9108257 DOI: 10.3389/fcimb.2022.882661] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/28/2022] [Indexed: 12/15/2022] Open
Abstract
We have witnessed the 2-year-long global rampage of COVID-19 caused by the wide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, knowledge about biomarkers of the entire COVID-19 process is limited. Identification of the systemic features of COVID-19 will lead to critical biomarkers and therapeutic targets for early intervention and clinical disease course prediction. Here, we performed a comprehensive analysis of clinical measurements and serum metabolomics in 199 patients with different stages of COVID-19. In particular, our study is the first serum metabolomic analysis of critical rehabilitation patients and critical death patients. We found many differential metabolites in the comparison of metabolomic results between ordinary, severe, and critical patients and uninfected patients. Through the metabolomic results of COVID-19 patients in various stages, and critical rehabilitation patients and critical death patients, we identified a series of differential metabolites as biomarkers, a separate queue and precise distinction, and predicted COVID-19 verification. These differentially expressed metabolites, included 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphate, propylparaben, 20-hydroxyeicosatetraenoic acid, triethanolamine, chavicol, disialosyl galactosyl globoside, 1-arachidonoylglycerophosphoinositol, and alpha-methylstyrene, all of which have been identified for the first time as biomarkers in COVID-19 progression. These biomarkers are involved in many pathological and physiological pathways of COVID-19, for example, immune responses, platelet degranulation, and metabolism which might result in pathogenesis. Our results showed valuable information about metabolites obviously altered in COVID-19 patients with different stages, which could shed light on the pathogenesis as well as serve as potential therapeutic agents of COVID-19.
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Affiliation(s)
- Meijia Gu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Huaqin Pan
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University; Clinical Research Center of Hubei Critical Care Medicine, Wuhan, China
| | - Yuncong Yuan
- College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
| | - Xuemin Zhou
- Shanghai BIOTREE Biological Technology Co., Ltd, Shanghai, China
| | - Luojia Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xingran Wang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Fang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Liu Hu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yaxuan Xie
- School of Health Sciences, Wuhan University, Wuhan, China
| | - Chao Shen
- College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
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Dumache R, Enache A, Macasoi I, Dehelean CA, Dumitrascu V, Mihailescu A, Popescu R, Vlad D, Vlad CS, Muresan C. SARS-CoV-2: An Overview of the Genetic Profile and Vaccine Effectiveness of the Five Variants of Concern. Pathogens 2022; 11:pathogens11050516. [PMID: 35631037 PMCID: PMC9144800 DOI: 10.3390/pathogens11050516] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
With the onset of the COVID-19 pandemic, enormous efforts have been made to understand the genus SARS-CoV-2. Due to the high rate of global transmission, mutations in the viral genome were inevitable. A full understanding of the viral genome and its possible changes represents one of the crucial aspects of pandemic management. Structural protein S plays an important role in the pathogenicity of SARS-CoV-2, mutations occurring at this level leading to viral forms with increased affinity for ACE2 receptors, higher transmissibility and infectivity, resistance to neutralizing antibodies and immune escape, increasing the risk of infection and disease severity. Thus, five variants of concern are currently being discussed, Alpha, Beta, Gamma, Delta and Omicron. In the present review, a comprehensive summary of the following critical aspects regarding SARS-CoV-2 has been made: (i) the genomic characteristics of SARS-CoV-2; (ii) the pathological mechanism of transmission, penetration into the cell and action on specific receptors; (iii) mutations in the SARS-CoV-2 genome; and (iv) possible implications of mutations in diagnosis, treatment, and vaccination.
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Affiliation(s)
- Raluca Dumache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Alexandra Enache
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
| | - Ioana Macasoi
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Cristina Adriana Dehelean
- Departament of Toxicology and Drug Industry, Faculty of Pharmacy, “Victor Babeş” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square No. 2, 300041 Timisoara, Romania
- Correspondence: (I.M.); (C.A.D.)
| | - Victor Dumitrascu
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Alexandra Mihailescu
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
- Genetics, Genomic Medicine Research Center, Department of Microscopic Morphology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Roxana Popescu
- Department of Microscopic Morphology, Discipline of Molecular and Cell Biology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Daliborca Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Cristian Sebastian Vlad
- Department of Pharmacology and Biochemistry, Discipline of Pharmacology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (V.D.); (D.V.); (C.S.V.)
| | - Camelia Muresan
- Ethics and Human Identification Research Center, Department of Neurosciences, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (R.D.); (A.E.); (A.M.); (C.M.)
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Vázquez-Mendoza LH, Mendoza-Figueroa HL, García-Vázquez JB, Correa-Basurto J, García-Machorro J. In Silico Drug Repositioning to Target the SARS-CoV-2 Main Protease as Covalent Inhibitors Employing a Combined Structure-Based Virtual Screening Strategy of Pharmacophore Models and Covalent Docking. Int J Mol Sci 2022; 23:ijms23073987. [PMID: 35409348 PMCID: PMC8999907 DOI: 10.3390/ijms23073987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
The epidemic caused by the SARS-CoV-2 coronavirus, which has spread rapidly throughout the world, requires urgent and effective treatments considering that the appearance of viral variants limits the efficacy of vaccines. The main protease of SARS-CoV-2 (Mpro) is a highly conserved cysteine proteinase, fundamental for the replication of the coronavirus and with a specific cleavage mechanism that positions it as an attractive therapeutic target for the proposal of irreversible inhibitors. A structure-based strategy combining 3D pharmacophoric modeling, virtual screening, and covalent docking was employed to identify the interactions required for molecular recognition, as well as the spatial orientation of the electrophilic warhead, of various drugs, to achieve a covalent interaction with Cys145 of Mpro. The virtual screening on the structure-based pharmacophoric map of the SARS-CoV-2 Mpro in complex with an inhibitor N3 (reference compound) provided high efficiency by identifying 53 drugs (FDA and DrugBank databases) with probabilities of covalent binding, including N3 (Michael acceptor) and others with a variety of electrophilic warheads. Adding the energy contributions of affinity for non-covalent and covalent docking, 16 promising drugs were obtained. Our findings suggest that the FDA-approved drugs Vaborbactam, Cimetidine, Ixazomib, Scopolamine, and Bicalutamide, as well as the other investigational peptide-like drugs (DB04234, DB03456, DB07224, DB7252, and CMX-2043) are potential covalent inhibitors of SARS-CoV-2 Mpro.
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Affiliation(s)
- Luis Heriberto Vázquez-Mendoza
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
| | - Humberto L. Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
- Correspondence: (H.L.M.-F.); (J.B.G.-V.)
| | - Juan Benjamín García-Vázquez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
- Cátedras CONACyT-Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico
- Correspondence: (H.L.M.-F.); (J.B.G.-V.)
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Posgrado en Farmacología de la Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico; (L.H.V.-M.); (J.C.-B.)
| | - Jazmín García-Machorro
- Laboratorio de Medicina de la Conservación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Salvador Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de Mexico 11340, Mexico;
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Functional nucleic acids as modular components against SARS-CoV-2: From diagnosis to therapeutics. Biosens Bioelectron 2022; 201:113944. [PMID: 35026546 PMCID: PMC8718887 DOI: 10.1016/j.bios.2021.113944] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/28/2021] [Accepted: 12/28/2021] [Indexed: 01/05/2023]
Abstract
Coronavirus Disease 2019 (COVID-19), which poses an extremely serious global impact on human public healthcare, represents a high transmission and disease-causing viral infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is expanding at a rapid pace. Therefore, it is urgent for researchers to establish effective platforms for the assay and treatment of SARS-CoV-2. Functional nucleic acids (FNAs), comprising aptamers and nucleases, are of primary concern within the biological and medical communities owing of the distinctive properties of their target recognition and catalysis. This review will concentrate on the essential aspects of insights regarding FNAs and their technological expertise for the diagnostic and therapeutic utilization against COVID-19. We first offer a historical perspective of the COVID-19 pandemics, its clinical characteristics and potential biomarkers. Then, we briefly discuss the current diagnostic and therapeutic methodology towards COVID-19, highlighting the superiorities and existing shortcomings. After that, we introduce the key features of FNAs, and summarize recent progress of in vitro selection of FNAs for SARS-CoV-2 specific proteins and RNAs, followed by highlighting the general concept of translating FNAs into functional probes for diagnostic and therapeutic purposes. Then, we critically review the emerging FNAs-based diagnostic and therapeutic strategies that are fast, precise, efficient, and highly specific to fight COVID-19. Finally, we identify remaining challenges and offer future outlook of this emerging field.
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Identification of Kukoamine A, Zeaxanthin, and Clexane as New Furin Inhibitors. Int J Mol Sci 2022; 23:ijms23052796. [PMID: 35269938 PMCID: PMC8911046 DOI: 10.3390/ijms23052796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
The endogenous protease furin is a key protein in many different diseases, such as cancer and infections. For this reason, a wide range of studies has focused on targeting furin from a therapeutic point of view. Our main objective consisted of identifying new compounds that could enlarge the furin inhibitor arsenal; secondarily, we assayed their adjuvant effect in combination with a known furin inhibitor, CMK, which avoids the SARS-CoV-2 S protein cleavage by means of that inhibition. Virtual screening was carried out to identify potential furin inhibitors. The inhibition of physiological and purified recombinant furin by screening selected compounds, Clexane, and these drugs in combination with CMK was assayed in fluorogenic tests by using a specific furin substrate. The effects of the selected inhibitors from virtual screening on cell viability (293T HEK cell line) were assayed by means of flow cytometry. Through virtual screening, Zeaxanthin and Kukoamine A were selected as the main potential furin inhibitors. In fluorogenic assays, these two compounds and Clexane inhibited both physiological and recombinant furin in a dose-dependent way. In addition, these compounds increased physiological furin inhibition by CMK, showing an adjuvant effect. In conclusion, we identified Kukoamine A, Zeaxanthin, and Clexane as new furin inhibitors. In addition, these drugs were able to increase furin inhibition by CMK, so they could also increase its efficiency when avoiding S protein proteolysis, which is essential for SARS-CoV-2 cell infection.
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Thakur S, Sasi S, Pillai SG, Nag A, Shukla D, Singhal R, Phalke S, Velu GSK. SARS-CoV-2 Mutations and Their Impact on Diagnostics, Therapeutics and Vaccines. Front Med (Lausanne) 2022; 9:815389. [PMID: 35273977 PMCID: PMC8902153 DOI: 10.3389/fmed.2022.815389] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/04/2022] [Indexed: 12/11/2022] Open
Abstract
With the high rate of COVID-19 infections worldwide, the emergence of SARS-CoV-2 variants was inevitable. Several mutations have been identified in the SARS-CoV-2 genome, with the spike protein as one of the mutational hot spots. Specific amino acid substitutions such as D614G and N501Y were found to alter the transmissibility and virulence of the virus. The WHO has classified the variants identified with fitness-enhancing mutations as variants of concern (VOC), variants of interest (VOI) or variants under monitoring (VUM). The VOCs pose an imminent threat as they exhibit higher transmissibility, disease severity and ability to evade vaccine-induced and natural immunity. Here we review the mutational landscape on the SARS-CoV-2 structural and non-structural proteins and their impact on diagnostics, therapeutics and vaccines. We also look at the effectiveness of approved vaccines, antibody therapy and convalescent plasma on the currently prevalent VOCs, which are B.1.17, B.1.351, P.1, B.1.617.2 and B.1.1.529. We further discuss the possible factors influencing mutation rates and future directions.
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Affiliation(s)
- Suresh Thakur
- Trivitron Healthcare Pvt., Ltd., Visakhapatnam, India
| | - Shalitha Sasi
- Blue Horizon International Therapeutic Sciences, Hackensack, NJ, United States
| | | | | | - Dhananjay Shukla
- Department of Biotechnology, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, India
| | - Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Disease, New Delhi, India
| | - Sameer Phalke
- Trivitron Healthcare Pvt., Ltd., Visakhapatnam, India
| | - G. S. K. Velu
- Trivitron Healthcare Pvt., Ltd., Visakhapatnam, India
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11
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Wu J, Chen Z, Han X, Chen Q, Wang Y, Feng T. SARS-CoV-2 RNA-dependent RNA polymerase as a target for high-throughput drug screening. Future Virol 2022:10.2217/fvl-2021-0335. [PMID: 36794167 PMCID: PMC9910510 DOI: 10.2217/fvl-2021-0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023]
Abstract
The ongoing COVID-19 pandemic caused by the SARS-CoV-2 has necessitated rapid development of drug screening tools. RNA-dependent RNA polymerase (RdRp) is a promising target due to its essential functions in replication and transcription of viral genome. To date, through minimal RNA synthesizing machinery established from cryo-electron microscopy structural data, there has been development of high-throughput screening assays for directly screening inhibitors that target the SARS-CoV-2 RdRp. Here, we analyze and present verified techniques that could be used to discover potential anti-RdRp agents or repurposing of approved drugs to target the SARS-CoV-2 RdRp. In addition, we highlight the characteristics and application value of cell-free or cell-based assays in drug discovery.
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Affiliation(s)
- Jiahui Wu
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Zhiqiang Chen
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China,2Department of Nuclear Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province, China
| | - Xue Han
- 3Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, 59 Haier Road, Qingdao, 266000, Shandong Province, China
| | - Qiaoqiao Chen
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Yintao Wang
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Tingting Feng
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China,Author for correspondence: Tel.: +86 512 6588 2429;
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12
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Khanali J, Azangou-Khyavy M, Asaadi Y, Jamalkhah M, Kiani J. Nucleic Acid-Based Treatments Against COVID-19: Potential Efficacy of Aptamers and siRNAs. Front Microbiol 2021; 12:758948. [PMID: 34858370 PMCID: PMC8630580 DOI: 10.3389/fmicb.2021.758948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/19/2021] [Indexed: 01/10/2023] Open
Abstract
Despite significant efforts, there are currently no approved treatments for COVID-19. However, biotechnological approaches appear to be promising in the treatment of the disease. Accordingly, nucleic acid-based treatments including aptamers and siRNAs are candidates that might be effective in COVID-19 treatment. Aptamers can hamper entry and replication stages of the SARS-CoV-2 infection, while siRNAs can cleave the viral genomic and subgenomic RNAs to inhibit the viral life cycle and reduce viral loads. As a conjugated molecule, aptamer–siRNA chimeras have proven to be dual-functioning antiviral therapy, acting both as virus-neutralizing and replication-interfering agents as well as being a siRNA targeted delivery approach. Previous successful applications of these compounds against various stages of the pathogenesis of diseases and viral infections, besides their advantages over other alternatives, might provide sufficient rationale for the application of these nucleic acid-based drugs against the SARS-CoV-2. However, none of them are devoid of limitations. Here, the literature was reviewed to assess the plausibility of using aptamers, siRNAs, and aptamer–siRNA chimeras against the SARS-CoV-2 based on their previously established effectiveness, and discussing challenges lie in applying these molecules.
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Affiliation(s)
- Javad Khanali
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Monire Jamalkhah
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jafar Kiani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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13
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Sheik Amamuddy O, Afriyie Boateng R, Barozi V, Wavinya Nyamai D, Tastan Bishop Ö. Novel dynamic residue network analysis approaches to study allosteric modulation: SARS-CoV-2 M pro and its evolutionary mutations as a case study. Comput Struct Biotechnol J 2021; 19:6431-6455. [PMID: 34849191 PMCID: PMC8613987 DOI: 10.1016/j.csbj.2021.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/09/2021] [Accepted: 11/13/2021] [Indexed: 01/15/2023] Open
Abstract
The rational search for allosteric modulators and the allosteric mechanisms of these modulators in the presence of mutations is a relatively unexplored field. Here, we established novel in silico approaches and applied them to SARS-CoV-2 main protease (Mpro) as a case study. First, we identified six potential allosteric modulators. Then, we focused on understanding the allosteric effects of these modulators on each of its protomers. We introduced a new combinatorial approach and dynamic residue network (DRN) analysis algorithms to examine patterns of change and conservation of critical nodes, according to five independent criteria of network centrality. We observed highly conserved network hubs for each averaged DRN metric on the basis of their existence in both protomers in the absence and presence of all ligands (persistent hubs). We also detected ligand specific signal changes. Using eigencentrality (EC) persistent hubs and ligand introduced hubs we identified a residue communication path connecting the allosteric binding site to the catalytic site. Finally, we examined the effects of the mutations on the behavior of the protein in the presence of selected potential allosteric modulators and investigated the ligand stability. One crucial outcome was to show that EC centrality hubs form an allosteric communication path between the allosteric ligand binding site to the active site going through the interface residues of domains I and II; and this path was either weakened or lost in the presence of some of the mutations. Overall, the results revealed crucial aspects that need to be considered in rational computational drug discovery.
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Affiliation(s)
| | | | - Victor Barozi
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Dorothy Wavinya Nyamai
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
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14
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Ghosh M, Basak S, Dutta S. Underlying selection for the diversity of spike protein sequences of SARS-CoV-2. IUBMB Life 2021; 74:213-220. [PMID: 34780121 PMCID: PMC8652778 DOI: 10.1002/iub.2577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023]
Abstract
The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present article, we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS-CoV-2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.
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Affiliation(s)
- Manisha Ghosh
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Surajit Basak
- Division of Bioinformatics, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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15
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Corrêa RP, Castro HC, Quaresma BMCS, Stephens PRS, Araujo-Jorge TC, Ferreira RR. Perceptions and Feelings of Brazilian Health Care Professionals Regarding the Effects of COVID-19: Cross-sectional Web-Based Survey. JMIR Form Res 2021; 5:e28088. [PMID: 34519656 PMCID: PMC8544742 DOI: 10.2196/28088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/19/2021] [Accepted: 08/01/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The importance of health professionals has been recognized in COVID-19 pandemic-affected countries, especially in those such as Brazil, which is one of the top 3 countries that have been affected in the world. However, the workers' perception of the stress and the changes that the pandemic has caused in their lives vary according to the conditions offered by these affected countries, including salaries, individual protection equipment, and psychological support. OBJECTIVE The purpose of this study was to identify the perceptions of Brazilian health workers regarding the COVID-19 pandemic impact on their lives, including possible self-contamination and mental health. METHODS This cross-sectional web-based survey was conducted in Brazil by applying a 32-item questionnaire, including multiple-choice questions by using the Google Forms electronic assessment. This study was designed to capture spontaneous perceptions from health professionals. All questions were mandatory and divided into 2 blocks with different proposals: personal profile and COVID-19 pandemic impact. RESULTS We interviewed Brazilian health professionals from all 5 Brazilian regions (N=1376). Our study revealed that 1 in 5 (23%) complained about inadequate personal protective equipment, including face shields (234/1376, 17.0%), masks (206/1376, 14.9%), and laboratory coats (138/1376, 10.0%), whereas 1 in 4 health professionals did not have enough information to protect themselves from the coronavirus disease. These professionals had anxiety due to COVID-19 (604/1376, 43.9%), difficulties in sleep (593/1376, 43.1%), and concentrating on work (453/1376, 32.9%). Almost one-third experienced traumatic situations at work (385/1376, 28.0%), which may have led to negative feelings of fear of COVID-19 and sadness. Despite this situation, there was hope and empathy among their positive feelings. The survey also showed that 1 in 5 acquired COVID-19 with the most classic and minor symptoms, including headache (274/315, 87.0%), body pain (231/315, 73.3%), tiredness (228/315, 72.4%), and loss of taste and smell (208/315, 66.0%). Some of their negative feelings were higher than those of noninfected professionals (fear of COVID-19, 243/315, 77.1% vs 509/1061, 48.0%; impotence, 142/315, 45.1% vs 297/1061, 28.0%; and fault, 38/315, 12.1% vs 567/1061, 53.4%, respectively). Another worrying outcome was that 61.3% (193/315) reported acquiring an infection while working at a health facility and as expected, most of the respondents felt affected (344/1376, 25.0%) or very affected (619/1376, 45.0%) by the COVID-19. CONCLUSIONS In Brazil, the health professionals were exposed to a stressful situation and to the risk of self-contamination-conditions that can spell future psychological problems for these workers. Our survey findings showed that the psychological support for this group should be included in the future health planning of Brazil and of other hugely affected countries to assure a good mental health condition for the medical teams in the near future.
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Affiliation(s)
- Roberta Pires Corrêa
- Program in Education in Biosciences and Health, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Helena Carla Castro
- Program in Education in Biosciences and Health, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Sciences, Technology and Inclusion, Federal Fluminense University, Niterói, Brazil
| | | | - Paulo Roberto Soares Stephens
- Program in Education in Biosciences and Health, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Laboratory of Innovations in Therapies, Education and Bioproducts, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Tania Cremonini Araujo-Jorge
- Program in Education in Biosciences and Health, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Laboratory of Innovations in Therapies, Education and Bioproducts, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Roberto Rodrigues Ferreira
- Program in Education in Biosciences and Health, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Laboratory of Innovations in Therapies, Education and Bioproducts, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
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16
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Taha HR, Keewan N, Slati F, Al-Sawalha NA. Remdesivir: A Closer Look at Its Effect in COVID-19 Pandemic. Pharmacology 2021; 106:462-468. [PMID: 34515227 PMCID: PMC8450841 DOI: 10.1159/000518440] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/08/2021] [Indexed: 12/22/2022]
Abstract
Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiology of COVID-19 pandemic, resulted in significant harm to the affected countries in every aspect of life. The virus infected over 139 million patients and resulted in over 2.9 million deaths until April 16, 2021. New variants of this virus were identified that spread rapidly worldwide. Summary Remdesivir, a prodrug of adenosine nucleotide analog, is an antiviral with a broad spectrum of activity that was tested on SARS and Middle East respiratory syndrome infections. In vitro studies conducted on SARS-CoV-2 revealed that remdesivir inhibited viral replication with high selectivity index in cell cultures. In vivo studies showed that remdesivir reduced viral load in bronchoalveolar lavage fluid and attenuated pulmonary infiltrates in infected animals. Further, remdesivir showed promising results in terms of clinical improvement, shortening the recovery time, mortality rate, and the duration of oxygen need, despite that some clinical trials did not reveal significant effect on remdesivir use. Several studies showed positive results of remdesivir against the new variants. Key Messages Remdesivir showed a promising beneficial effect against new variants of SARS-CoV-2, but more clinical evidence is needed to confirm this effect.
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Affiliation(s)
- Huda R Taha
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Nour Keewan
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Farah Slati
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Nour A Al-Sawalha
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan.,Faculty of Pharmacy, Jadara University, Irbid, Jordan
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17
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Anifandis G, Taylor TH, Messini CI, Chatzimeletiou K, Daponte A, Ioannou D, Tempest HG. The Impact of SARS-CoV-2 on Sperm Cryostorage, Theoretical or Real Risk? ACTA ACUST UNITED AC 2021; 57:medicina57090946. [PMID: 34577870 PMCID: PMC8467274 DOI: 10.3390/medicina57090946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 12/24/2022]
Abstract
Cryopreservation of human gametes and embryos as well as human reproductive tissues has been characterized as an essential process and aspect of assisted reproductive technology (ART). Notably, sperm cryopreservation is a fundamental aspect of cryopreservation in oncological patients or patients undergoing gonadotoxic treatment. Given that there is a risk of contamination or cross-contamination, either theoretical or real, during the procedures of cryopreservation and cryostorage, both the European Society for Human Reproduction and Embryology (ESHRE) and the American Society for Reproductive Medicine (ASRM) have provided updated guidelines for preventing or reducing the contamination risk of sexually transmitted viruses. Given the ongoing and worldwide COVID-19 pandemic, there is considerable interest in what measures should be taken to mitigate SARS-CoV-2 contamination during cryopreservation and cryostorage of semen samples. The SARS-CoV-2 virus is the virus that causes COVID-19, and whose transmission and infection is mainly aerosol-mediated. Several ART professional societies, including ESHRE and ASRM have proposed measures to mitigate the spread of the SARS-CoV-2 virus. Whether the proposed safety directives are enough to mitigate the possible SARS-CoV-2-contamination of sperm samples during cryopreservation or whether the policies should be re-evaluated will be discussed in this review. Additionally, insights regarding the possible impact of COVID-19 vaccination on the safety of sperm cryopreservation will be discussed.
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Affiliation(s)
- George Anifandis
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, 41200 Larisa, Greece; (C.I.M.); (A.D.)
- Correspondence: ; Tel.: +30-6975865861
| | - Tyl H Taylor
- Reproductive Endocrinology Associates of Charlotte, Charlotte, NC 28207, USA;
| | - Christina I Messini
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, 41200 Larisa, Greece; (C.I.M.); (A.D.)
| | - Katerina Chatzimeletiou
- 1st Department of Obstetrics and Gynecology, Unit for Human Reproduction, School of Health Sciences, Faculty of Medicine, Aristotelian University of Thessaloniki, 56403 Thessaloniki, Greece;
| | - Alexandros Daponte
- Department of Obstetrics and Gynecology, School of Health Sciences, Faculty of Medicine, University of Thessaly, 41200 Larisa, Greece; (C.I.M.); (A.D.)
| | - Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA; (D.I.); (H.G.T.)
| | - Helen G Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA; (D.I.); (H.G.T.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- College of Medicine, Roseman University of Health Sciences, Las Vegas, NV 89135, USA
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18
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Lou Y, Zhao W, Wei H, Chu M, Chao R, Yao H, Su J, Li Y, Li X, Cao Y, Feng Y, Wang P, Xia Y, Shang Y, Li F, Ge P, Zhang X, Gao W, Song G, Du B, Liang T, Qiu Y, Liu M. Cross-neutralization of RBD mutant strains of SARS-CoV-2 by convalescent patient derived antibodies. Biotechnol J 2021; 16:e2100207. [PMID: 34379353 PMCID: PMC8420279 DOI: 10.1002/biot.202100207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND The emergence of COVID-19 pandemic resulted in an urgent need for the development of therapeutic interventions. Of which, neutralizing antibodies play a crucial role in the prevention and resolution of viral infection. METHODS We generated antibody libraries from 18 different COVID-19 recovered patients and screened neutralizing antibodies to SARS-CoV-2 and its mutants. After 3 rounds of panning, 456 positive phage clones were obtained with high affinity to RBD (receptor binding domain). Clones were then reconstituted into whole human IgG for epitope binning assay and all 19 IgG were classified into 6 different epitope groups or Bins. RESULTS Although all antibodies were found to bind RBD, the antibodies in Bin2 had superior inhibitory ability of the interaction between spike protein and angiotensin converting enzyme 2 receptor (ACE2). Most importantly, the antibodies from Bin2 showed stronger binding affinity or ability to mutant RBDs (N501Y, W463R, R408I, N354D, V367F and N354D/D364Y) derived from different SARS-CoV-2 strains as well, suggesting the great potential of these antibodies in preventing infection of SARS-CoV-2 and its mutations. Furthermore, such neutralizing antibodies strongly restricted the binding of RBD to hACE2 overexpressed 293T cells. Consistently, these antibodies effectively neutralized wildtype and more transmissible mutant pseudovirus entry into hACE2 overexpressed 293T cells. In Vero-E6 cells, one of these antibodies can even block the entry of live SARS-CoV-2 into cells at 12.5 nM. DISCUSSION These results indicate that the neutralizing human antibodies from the patient-derived antibody libraries have the potential to fight SARS-CoV-2 and its mutants in this global pandemic. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yan Lou
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Wenxiang Zhao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.,SymRay Biopharma Inc., Shanghai, 200241, China
| | - Haitao Wei
- SymRay Biopharma Inc., Shanghai, 200241, China
| | - Min Chu
- SymRay Biopharma Inc., Shanghai, 200241, China
| | - Ruihua Chao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.,SymRay Biopharma Inc., Shanghai, 200241, China
| | - Hangping Yao
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Junwei Su
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yanan Li
- SymRay Biopharma Inc., Shanghai, 200241, China
| | - Xiulan Li
- SymRay Biopharma Inc., Shanghai, 200241, China
| | - Yu Cao
- SymRay Biopharma Inc., Shanghai, 200241, China
| | - Yanyan Feng
- SymRay Biopharma Inc., Shanghai, 200241, China
| | - Ping Wang
- SymRay Biopharma Inc., Shanghai, 200241, China
| | | | | | - Fengping Li
- SymRay Biopharma Inc., Shanghai, 200241, China
| | - Pingju Ge
- Acrobiosystems Inc., Beijing, 100176, China
| | | | | | - Gaojie Song
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Bing Du
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Tingbo Liang
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yunqing Qiu
- State Key Laboratory for diagnosis and treatment of infectious diseases, Key Laboratory for Drug Evaluation and Clinical Research of Zhejiang Province, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
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19
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Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides. mBio 2021; 12:e0142321. [PMID: 34154407 PMCID: PMC8262916 DOI: 10.1128/mbio.01423-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The catalytic subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) Nsp12 has a unique nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain that transfers nucleoside monophosphates to the Nsp9 protein and the nascent RNA. The NiRAN and RdRp modules form a dynamic interface distant from their catalytic sites, and both activities are essential for viral replication. We report that codon-optimized (for the pause-free translation in bacterial cells) Nsp12 exists in an inactive state in which NiRAN-RdRp interactions are broken, whereas translation by slow ribosomes and incubation with accessory Nsp7/8 subunits or nucleoside triphosphates (NTPs) partially rescue RdRp activity. Our data show that adenosine and remdesivir triphosphates promote the synthesis of A-less RNAs, as does ppGpp, while amino acid substitutions at the NiRAN-RdRp interface augment activation, suggesting that ligand binding to the NiRAN catalytic site modulates RdRp activity. The existence of allosterically linked nucleotidyl transferase sites that utilize the same substrates has important implications for understanding the mechanism of SARS-CoV-2 replication and the design of its inhibitors.
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20
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Rybicka M, Miłosz E, Bielawski KP. Superiority of MALDI-TOF Mass Spectrometry over Real-Time PCR for SARS-CoV-2 RNA Detection. Viruses 2021; 13:v13050730. [PMID: 33922195 PMCID: PMC8145549 DOI: 10.3390/v13050730] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.
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Affiliation(s)
- Magda Rybicka
- Department of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland;
- Correspondence: ; Tel.: +48-058-523-6435
| | - Ewa Miłosz
- Laboratory of Molecular Biology, Medical University of Gdansk, Marii Skłodowskiej-Curie 3A, 80-210 Gdansk, Poland;
| | - Krzysztof Piotr Bielawski
- Department of Molecular Diagnostics, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland;
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21
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Ning B, Yu AM. RNA therapeutics: From biochemical pharmacology to technology development and clinical applications. Biochem Pharmacol 2021; 189:114567. [PMID: 33865832 DOI: 10.1016/j.bcp.2021.114567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Baitang Ning
- National Center for Toxicological Research, US Food and Drug Administration (NCTR), 3900 NCTR Road, HFT100, Jefferson, AR 72079, United States.
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, 2700 Stockton Blvd, Suite 2130, Sacramento, CA 95817, United States.
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Miao M, Clercq ED, Li G. Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Biomedicines 2021; 9:biomedicines9040412. [PMID: 33920487 PMCID: PMC8069977 DOI: 10.3390/biomedicines9040412] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/26/2021] [Accepted: 04/07/2021] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic of coronavirus disease in 2019 (COVID-19). Genome surveillance is a key method to track the spread of SARS-CoV-2 variants. Genetic diversity and evolution of SARS-CoV-2 were analyzed based on 260,673 whole-genome sequences, which were sampled from 62 countries between 24 December 2019 and 12 January 2021. We found that amino acid (AA) substitutions were observed in all SARS-CoV-2 proteins, and the top six proteins with the highest substitution rates were ORF10, nucleocapsid, ORF3a, spike glycoprotein, RNA-dependent RNA polymerase, and ORF8. Among 25,629 amino acid substitutions at 8484 polymorphic sites across the coding region of the SARS-CoV-2 genome, the D614G (93.88%) variant in spike and the P323L (93.74%) variant in RNA-dependent RNA polymerase were the dominant variants on six continents. As of January 2021, the genomic sequences of SARS-CoV-2 could be divided into at least 12 different clades. Distributions of SARS-CoV-2 clades were featured with temporal and geographical dynamics on six continents. Overall, this large-scale analysis provides a detailed mapping of SARS-CoV-2 variants in different geographic areas at different time points, highlighting the importance of evaluating highly prevalent variants in the development of SARS-CoV-2 antiviral drugs and vaccines.
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Affiliation(s)
- Miao Miao
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China;
| | - Erik De Clercq
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium;
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, China;
- Correspondence: ; Tel.: +86-731-84805414
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