201
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Kung YA, Lee KM, Chiang HJ, Huang SY, Wu CJ, Shih SR. Molecular Virology of SARS-CoV-2 and Related Coronaviruses. Microbiol Mol Biol Rev 2022; 86:e0002621. [PMID: 35343760 PMCID: PMC9199417 DOI: 10.1128/mmbr.00026-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.
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Affiliation(s)
- Yu-An Kung
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Huan-Jung Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Sheng-Yu Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Jung Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
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202
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Rabie AM. Efficacious Preclinical Repurposing of the Nucleoside Analogue Didanosine against COVID-19 Polymerase and Exonuclease. ACS OMEGA 2022; 7:21385-21396. [PMID: 35785294 PMCID: PMC9244909 DOI: 10.1021/acsomega.1c07095] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/16/2022] [Indexed: 01/18/2023]
Abstract
![]()
Analogues and derivatives
of natural nucleosides/nucleotides are
considered among the most successful bioactive species of drug-like
compounds in modern medicinal chemistry, as they are well recognized
for their diverse and efficient pharmacological activities in humans,
especially as antivirals and antitumors. Coronavirus disease 2019
(COVID-19) is still almost incurable, with its infectious viral microbe,
the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),
continuing to wreak devastation around the world. This global crisis
pushed all involved scientists, including drug discoverers and clinical
researchers, to try to find an effective and broad-spectrum anti-COVID-19
drug. Didanosine (2′,3′-dideoxyinosine, DDI) is a synthetic
inosine/adenosine/guanosine analogue and highly active antiretroviral
therapeutic agent used for the treatment of human immunodeficiency
virus infection and acquired immunodeficiency syndrome (HIV/AIDS).
This potent reverse-transcriptase inhibitor is characterized by proven
strong pharmacological effects against the viral genome, which may
successfully take part in the effective treatment of SARS-CoV-2/COVID-19.
Additionally, targeting the pivotal SARS-CoV-2 replication enzyme,
RNA-dependent RNA polymerase (RdRp), is a very successful tactic to
combat COVID-19 irrespective of the SARS-CoV-2 variant type because
RdRps are broadly conserved among all SARS-CoV-2 strains. Herein,
the current study proved for the first time, using the in
vitro antiviral evaluation, that DDI is capable of potently
inhibiting the replication of the novel virulent progenies of SARS-CoV-2
with quite tiny in vitro anti-SARS-CoV-2 and anti-RdRp
EC50 values of around 3.1 and 0.19 μM, respectively,
surpassing remdesivir together with its active metabolite (GS-441524).
Thereafter, the in silico computational interpretation
of the biological results supported that DDI strongly targets the
key pocket of the SARS-CoV-2 RdRp main catalytic active site. The
ideal pharmacophoric characteristics of the ligand DDI make it a typical
inhibiting agent of SARS-CoV-2 multiplication processes (including
high-fidelity proofreading), with its elastic structure open for many
kinds of derivatization. In brief, the present results further uphold
and propose the repurposing potentials of DDI against the different
types of COVID-19 and convincingly motivate us to quickly launch its
extensive preclinical/clinical pharmacological evaluations, hoping
to combine it in the COVID-19 therapeutic protocols soon.
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Affiliation(s)
- Amgad M. Rabie
- Dr. Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura 35511, Egypt
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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203
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Jones AN, Mourão A, Czarna A, Matsuda A, Fino R, Pyrc K, Sattler M, Popowicz GM. Characterization of SARS-CoV-2 replication complex elongation and proofreading activity. Sci Rep 2022; 12:9593. [PMID: 35688849 PMCID: PMC9185715 DOI: 10.1038/s41598-022-13380-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/14/2022] [Indexed: 01/18/2023] Open
Abstract
The replication complex (RC) of SARS-CoV-2 was recently shown to be one of the fastest RNA-dependent RNA polymerases of any known coronavirus. With this rapid elongation, the RC is more prone to incorporate mismatches during elongation, resulting in a highly variable genomic sequence. Such mutations render the design of viral protein targets difficult, as drugs optimized for a given viral protein sequence can quickly become inefficient as the genomic sequence evolves. Here, we use biochemical experiments to characterize features of RNA template recognition and elongation fidelity of the SARS-CoV-2 RdRp, and the role of the exonuclease, nsp14. Our study highlights the 2'OH group of the RNA ribose as a critical component for RdRp template recognition and elongation. We show that RdRp fidelity is reduced in the presence of the 3' deoxy-terminator nucleotide 3'dATP, which promotes the incorporation of mismatched nucleotides (leading to U:C, U:G, U:U, C:U, and A:C base pairs). We find that the nsp10-nsp14 heterodimer is unable to degrade RNA products lacking free 2'OH or 3'OH ribose groups. Our results suggest the potential use of 3' deoxy-terminator nucleotides in RNA-derived oligonucleotide inhibitors as antivirals against SARS-CoV-2.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Roberto Fino
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
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204
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Characterization of Aurintricarboxylic Acid (ATA) Interactions with Plasma Transporter Protein and SARS-CoV-2 Viral Targets: Correlation of Functional Activity and Binding Energetics. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060872. [PMID: 35743905 PMCID: PMC9227171 DOI: 10.3390/life12060872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
In an effort to identify functional-energetic correlations leading to the development of efficient anti-SARS-CoV-2 therapeutic agents, we have designed synthetic analogs of aurintricarboxylic acid (ATA), a heterogeneous polymeric mixture of structurally related linear homologs known to exhibit a host of biological properties, including antiviral activity. These derivatives are evaluated for their ability to interact with a plasma transporter protein (human serum albumin), eukaryotic (yeast) ribosomes, and a SARS-CoV-2 target, the RNA-dependent RNA polymerase (RdRp). The resultant data are critical for characterizing drug distribution, bioavailability, and effective inhibition of host and viral targets. Promising lead compounds are selected on the basis of their binding energetics which have been characterized and correlated with functional activities as assessed by inhibition of RNA replication and protein synthesis. Our results reveal that the activity of heterogeneous ATA is mimicked by linear compounds of defined molecular weight, with a dichlorohexamer salicylic-acid derivative exhibiting the highest potency. These findings are instrumental for optimizing the design of structurally defined ATA analogs that fulfill the requirements of an antiviral drug with respect to bioavailability, homogeneity, and potency, thereby expanding the arsenal of therapeutic regimens that are currently available to address the urgent need for effective SARS-CoV-2 treatment strategies.
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205
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Martínez-González B, Soria ME, Vázquez-Sirvent L, Ferrer-Orta C, Lobo-Vega R, Mínguez P, de la Fuente L, Llorens C, Soriano B, Ramos-Ruíz R, Cortón M, López-Rodríguez R, García-Crespo C, Somovilla P, Durán-Pastor A, Gallego I, de Ávila AI, Delgado S, Morán F, López-Galíndez C, Gómez J, Enjuanes L, Salar-Vidal L, Esteban-Muñoz M, Esteban J, Fernández-Roblas R, Gadea I, Ayuso C, Ruíz-Hornillos J, Verdaguer N, Domingo E, Perales C. SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations. Pathogens 2022; 11:662. [PMID: 35745516 PMCID: PMC9227345 DOI: 10.3390/pathogens11060662] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 12/23/2022] Open
Abstract
Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.
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Affiliation(s)
- Brenda Martínez-González
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - María Eugenia Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Lucía Vázquez-Sirvent
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, 08028 Barcelona, Spain; (C.F.-O.); (N.V.)
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, Universidad de Valencia, 46980 Valencia, Spain; (C.L.); (B.S.)
| | - Beatriz Soriano
- Biotechvana, “Scientific Park”, Universidad de Valencia, 46980 Valencia, Spain; (C.L.); (B.S.)
| | - Ricardo Ramos-Ruíz
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rosario López-Rodríguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Pilar Somovilla
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - Antoni Durán-Pastor
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Soledad Delgado
- Departamento de Sistemas Informáticos, Escuela Técnica Superior de Ingeniería de Sistemas Informáticos (ETSISI), Universidad Politécnica de Madrid, 28031 Madrid, Spain;
| | - Federico Morán
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, 28005 Madrid, Spain;
| | - Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, Spain;
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, 18016 Granada, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Mario Esteban-Muñoz
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Ricardo Fernández-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (P.M.); (L.d.l.F.); (M.C.); (R.L.-R.); (C.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Javier Ruíz-Hornillos
- Allergy Unit, Hospital Infanta Elena, Valdemoro, 28342 Madrid, Spain;
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, 28223 Madrid, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, 08028 Barcelona, Spain; (C.F.-O.); (N.V.)
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (C.G.-C.); (P.S.); (A.D.-P.); (I.G.); (A.I.d.Á.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
| | - Celia Perales
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos 2, 28040 Madrid, Spain; (B.M.-G.); (M.E.S.); (L.V.-S.); (R.L.-V.); (L.S.-V.); (M.E.-M.); (J.E.); (R.F.-R.); (I.G.)
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain;
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206
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Sarma H, Jamir E, Sastry GN. Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV. J Mol Struct 2022; 1257:132602. [PMID: 35153334 PMCID: PMC8824464 DOI: 10.1016/j.molstruc.2022.132602] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/09/2023]
Abstract
In this study we explored the molecular mechanism of RdRp (Non-Structural Protein, NSP12) interaction with its co-factors NSP7 and NSP8 which is the main toolbox for RNA replication and transcription of SARS-CoV-2 and SARS-CoV. The replication complex is a heterotetramer consists of one NSP12, one NSP7 and two NSP8. Extensive molecular dynamics (MD) simulations were applied on both the heterotetramer complexes to generate the conformations and were used to estimate the MMPBSA binding free energy (BFE) and per-residue energy decomposition of NSP12-NSP8 and NSP12-NSP7 and NSP7-NSP8 complexes. The BFE of SARS-CoV-2 heterotetramer complex with its corresponding partner protein was significantly higher as compared to SARS-CoV. Interface hotspot residues were predicted using different methods implemented in KFC (Knowledge-based FADA and Contracts), HotRegion and Robetta web servers. Per-residue energy decomposition analysis showed that the predicted interface hotspot residues contribute more energy towards the formation of complexes and most of the predicted hotspot residues are clustered together. However, there is a slight difference in the residue-wise energy contribution in the interface NSPs on heterotetramer viral replication complex of both coronaviruses. While the overall replication complex of SARS-CoV-2 was found to be slightly flexible as compared to SARS-CoV. This difference in terms of structural flexibility/stability and energetic characteristics of interface residues including hotspots at PPI interface in the viral replication complexes may be the reason of higher rate of RNA replication of SARS-CoV-2 as compared to SARS-CoV. Overall, the interaction profile at PPI interface such as, interface area, hotspot residues, nature of bonds and energies between NSPs, may provide valuable insights in designing of small molecules or peptide/peptidomimetic ligands which can fit into the PPI interface to disrupt the interaction.
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Affiliation(s)
- Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India
| | - Esther Jamir
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - G Narahari Sastry
- Advanced Computation and Data Sciences Division, CSIR - North East Institute of Science and Technology, Jorhat, Assam, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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207
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Kooshkaki O, Asghari A, Mahdavi R, Azarkar G, Parsamanesh N. Potential of MicroRNAs As Biomarkers and Therapeutic Targets in Respiratory Viruses: A Literature Review. DNA Cell Biol 2022; 41:544-563. [PMID: 35699380 DOI: 10.1089/dna.2021.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression through recognition of cognate sequences and interference of transcriptional, translational, or epigenetic processes. Hundreds of miRNA genes have been found in diverse viruses, and many of these are phylogenetically conserved. Respiratory viruses are the most frequent causative agents of disease in humans, with a significant impact on morbidity and mortality worldwide. Recently, the role of miRNAs in respiratory viral gene regulation, as well as host gene regulation during disease progression, has become a field of interest. This review highlighted the importance of various miRNAs and their potential role in fighting with respiratory viruses as therapeutic molecules with a focus on COVID-19.
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Affiliation(s)
- Omid Kooshkaki
- Department of Hematology, Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Arghavan Asghari
- Department of Hematology, Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran.,Department of Hematology, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Reza Mahdavi
- Department of Hematology, Kerman University of Medical Sciences, Kerman, Iran
| | - Ghodsiyeh Azarkar
- Department of Hematology, Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Negin Parsamanesh
- Department of Hematology, Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Science, Zanjan, Iran
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208
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in 2020 and has led to an unprecedented global pandemic. Understanding the virology behind SARS-CoV-2 infection has provided key insights into our efforts to develop antiviral agents and control the COVID-19 pandemic. In this review, the authors focus on the genomic features of SARS-CoV-2, its intrahost and interhost evolution, viral dynamics in respiratory tract, and systemic dissemination.
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Affiliation(s)
- Yijia Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA,Corresponding author. 65 Landsdowne Street, Room 421 Cambridge, MA 02139
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209
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Khater I, Nassar A. Seeking antiviral drugs to inhibit SARS-CoV-2 RNA dependent RNA polymerase: A molecular docking analysis. PLoS One 2022; 17:e0268909. [PMID: 35639751 PMCID: PMC9154104 DOI: 10.1371/journal.pone.0268909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/10/2022] [Indexed: 11/26/2022] Open
Abstract
COVID-19 outbreak associated with the severe acute respiratory syndrome coronavirus (SARS-CoV-2) raised health concerns across the globe and has been considered highly transmissible between people. In attempts for finding therapeutic treatment for the new disease, this work has focused on examining the polymerase inhibitors against the SARS-CoV-2 nsp12 and co-factors nsp8 and nsp7. Several polymerase inhibitors were examined against PDB ID: 6M71 using computational analysis evaluating the ligand's binding affinity to replicating groove to the active site. The findings of this analysis showed Cytarabine of -5.65 Kcal/mol with the highest binding probability (70%) to replicating groove of 6M71. The complex stability was then examined over 19 ns molecular dynamics simulation suggesting that Cytarabine might be possible potent inhibitor for the SARS-CoV-2 RNA Dependent RNA Polymerase.
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Affiliation(s)
- Ibrahim Khater
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Aaya Nassar
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
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210
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Liang J, Shi J, Chen S, Duan G, Yang F, Cheng Z, Li X, Ruan J, Mi D, Gao S. How the Replication and Transcription Complex Functions in Jumping Transcription of SARS-CoV-2. Front Genet 2022; 13:904513. [PMID: 35706445 PMCID: PMC9191571 DOI: 10.3389/fgene.2022.904513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/13/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although unprecedented efforts are underway to develop therapeutic strategies against this disease, scientists have acquired only a little knowledge regarding the structures and functions of the CoV replication and transcription complex (RTC). Ascertaining all the RTC components and the arrangement of them is an indispensably step for the eventual determination of its global structure, leading to completely understanding all of its functions at the molecular level. Results: The main results include: 1) hairpins containing the canonical and non-canonical NSP15 cleavage motifs are canonical and non-canonical transcription regulatory sequence (TRS) hairpins; 2) TRS hairpins can be used to identify recombination regions in CoV genomes; 3) RNA methylation participates in the determination of the local RNA structures in CoVs by affecting the formation of base pairing; and 4) The eventual determination of the CoV RTC global structure needs to consider METTL3 in the experimental design. Conclusions: In the present study, we proposed the theoretical arrangement of NSP12-15 and METTL3 in the global RTC structure and constructed a model to answer how the RTC functions in the jumping transcription of CoVs. As the most important finding, TRS hairpins were reported for the first time to interpret NSP15 cleavage, RNA methylation of CoVs and their association at the molecular level. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, providing a crucial basis for future studies.
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Affiliation(s)
| | - Jinsong Shi
- National Clinical Research Center of Kidney Disease, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Shunmei Chen
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Biomedical Engineering Research Center, Kunming Medical University, Kunming, China
| | - Guangyou Duan
- School of Life Sciences, Qilu Normal University, Jinan, China
| | - Fan Yang
- National Clinical Research Center of Kidney Disease, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhi Cheng
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xin Li
- College of Life Sciences, Nankai University, Tianjin, China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin, China
| | - Dong Mi
- Department of Clinical Laboratory, Affiliated Maternity Hospital, Nankai University, Tianjin, China
- *Correspondence: Dong Mi, ; Shan Gao,
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, China
- *Correspondence: Dong Mi, ; Shan Gao,
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211
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Bignon E, Marazzi M, Grandemange S, Monari A. Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer. Chem Sci 2022; 13:6098-6105. [PMID: 35685814 PMCID: PMC9132136 DOI: 10.1039/d2sc00108j] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/29/2022] [Indexed: 12/21/2022] Open
Abstract
The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms. Among the complex pathways induced by the viral infection, autophagy is particularly crucial and is strongly influenced by the action of the non-structural protein 6 (Nsp6) interacting with the endoplasmic reticulum membrane. Importantly, differently from other non-structural proteins, Nsp6 is mutated in the recently emerged Omicron variant, suggesting a possible different role of autophagy. In this contribution we explore, for the first time, the structural properties of Nsp6 thanks to long-timescale molecular dynamics simulations and machine learning analysis, identifying the interaction patterns with the lipid membrane. We also show how the mutation brought by the Omicron variant may indeed modify some of the specific interactions, and more particularly help anchor the viral protein to the lipid bilayer interface. The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms.![]()
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Affiliation(s)
| | - Marco Marazzi
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering and Chemical Research Institute "Andres M. del Rio" (IQAR), Universidad de Alcalá 28805 Alcalá de Hénares Spain
| | | | - Antonio Monari
- Université Paris Cité and CNRS, ITODYS F-75006 Paris France
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212
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Obermeyer F, Jankowiak M, Barkas N, Schaffner SF, Pyle JD, Yurkovetskiy L, Bosso M, Park DJ, Babadi M, MacInnis BL, Luban J, Sabeti PC, Lemieux JE. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness. Science 2022; 376:1327-1332. [PMID: 35608456 PMCID: PMC9161372 DOI: 10.1126/science.abm1208] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Repeated emergence of SARS-CoV-2 variants with increased fitness underscores the value of rapid detection and characterization of new lineages. We have developed PyR0, a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR0 to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR0 forecasts growth of new lineages from their mutational profile, ranks the fitness of lineages as new sequences become available, and prioritizes mutations of biological and public health concern for functional characterization.
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213
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Aranda J, Wieczór M, Terrazas M, Brun-Heath I, Orozco M. Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2. CHEM CATALYSIS 2022; 2:1084-1099. [PMID: 35465139 PMCID: PMC9016896 DOI: 10.1016/j.checat.2022.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 01/21/2023]
Abstract
We combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while being poorly recognized by human RNA polymerase II (RNA Pol II). A comparison of incorporation rates between natural and antiviral nucleotides shows that remdesivir is incorporated more slowly into the nascent RNA compared with ATP, leading to an RNA duplex that is structurally very similar to an unmodified one, arguing against the hypothesis that remdesivir is a competitive inhibitor of ATP. We characterize the entire mechanism of reaction, finding that viral RdRp is highly processive and displays a higher catalytic rate of incorporation than human RNA Pol II. Overall, our study provides the first detailed explanation of the replication mechanism of RdRp.
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Affiliation(s)
- Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Milosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament de Bioquímica i Biomedicine, Universitat de Barcelona, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
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214
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Li Y, Zhang D, Gao X, Wang X, Zhang L. 2'- and 3'-Ribose Modifications of Nucleotide Analogues Establish the Structural Basis to Inhibit the Viral Replication of SARS-CoV-2. J Phys Chem Lett 2022; 13:4111-4118. [PMID: 35503748 PMCID: PMC9088111 DOI: 10.1021/acs.jpclett.2c00087] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/27/2022] [Indexed: 05/12/2023]
Abstract
Inhibition of RNA-dependent RNA polymerase (RdRp) by nucleotide analogues with ribose modification provides a promising antiviral strategy for the treatment of SARS-CoV-2. Previous works have shown that remdesivir carrying 1'-substitution can act as a "delayed chain terminator", while nucleotide analogues with 2'-methyl group substitution could immediately terminate the chain extension. However, how the inhibition can be established by the 3'-ribose modification as well as other 2'-ribose modifications is not fully understood. Herein, we have evaluated the potential of several adenosine analogues with 2'- and/or 3'-modifications as obligate chain terminators by comprehensive structural analysis based on extensive molecular dynamics simulations. Our results suggest that 2'-modification couples with the protein environment to affect the structural stability, while 3'-hydrogen substitution inherently exerts "immediate termination" without compromising the structural stability in the active site. Our study provides an alternative promising modification scheme to orientate the further optimization of obligate terminators for SARS-CoV-2 RdRp.
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Affiliation(s)
- Yongfang Li
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
| | - Dong Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
| | - Xin Gao
- Computational
Bioscience Research Center (CBRC), Computer, Electrical and Mathematical
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Xiaowei Wang
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon 999077, Hong Kong
| | - Lu Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
- Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry, 361005, Xiamen, Fujian, China
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215
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Zhang J, Yuan S, Peng Q, Ding Z, Hao W, Peng G, Xiao S, Fang L. Porcine Epidemic Diarrhea Virus nsp7 Inhibits Interferon-Induced JAK-STAT Signaling through Sequestering the Interaction between KPNA1 and STAT1. J Virol 2022; 96:e0040022. [PMID: 35442061 PMCID: PMC9093119 DOI: 10.1128/jvi.00400-22] [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: 03/05/2022] [Accepted: 04/01/2022] [Indexed: 11/20/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic enteric coronavirus that causes high mortality in piglets. Interferon (IFN) responses are the primary defense mechanism against viral infection; however, viruses always evolve elaborate strategies to antagonize the antiviral action of IFN. Previous study showed that PEDV nonstructural protein 7 (nsp7), a component of the viral replicase polyprotein, can antagonize ploy(I:C)-induced type I IFN production. Here, we found that PEDV nsp7 also antagonized IFN-α-induced JAK-STAT signaling and the production of IFN-stimulated genes. PEDV nsp7 did not affect the protein and phosphorylation levels of JAK1, Tyk2, STAT1, and STAT2 or the formation of the interferon-stimulated gene factor 3 (ISGF3) complex. However, PEDV nsp7 prevented the nuclear translocation of STAT1 and STAT2. Mechanistically, PEDV nsp7 interacted with the DNA binding domain of STAT1/STAT2, which sequestered the interaction between karyopherin α1 (KPNA1) and STAT1, thereby blocking the nuclear transport of ISGF3. Collectively, these data reveal a new mechanism developed by PEDV to inhibit type I IFN signaling pathway. IMPORTANCE In recent years, an emerging porcine epidemic diarrhea virus (PEDV) variant has gained attention because of serious outbreaks of piglet diarrhea in China and the United States. Coronavirus nonstructural protein 7 (nsp7) has been proposed to act with nsp8 as part of an RNA primase to generate RNA primers for viral RNA synthesis. However, accumulating evidence indicates that coronavirus nsp7 can also antagonize type I IFN production. Our present study extends previous findings and demonstrates that PEDV nsp7 also antagonizes IFN-α-induced IFN signaling by competing with KPNA1 for binding to STAT1, thereby enriching the immune regulation function of coronavirus nsp7.
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Affiliation(s)
- Jiansong Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shuangling Yuan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Qi Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhen Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Department of Preventive Veterinary Medicine, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Wenqi Hao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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216
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Antiviral Drug Discovery for the Treatment of COVID-19 Infections. Viruses 2022; 14:v14050961. [PMID: 35632703 PMCID: PMC9143071 DOI: 10.3390/v14050961] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a recently emerged human coronavirus. COVID-19 vaccines have proven to be successful in protecting the vaccinated from infection, reducing the severity of disease, and deterring the transmission of infection. However, COVID-19 vaccination faces many challenges, such as the decline in vaccine-induced immunity over time, and the decrease in potency against some SARS-CoV-2 variants including the recently emerged Omicron variant, resulting in breakthrough infections. The challenges that COVID-19 vaccination is facing highlight the importance of the discovery of antivirals to serve as another means to tackle the pandemic. To date, neutralizing antibodies that block viral entry by targeting the viral spike protein make up the largest class of antivirals that has received US FDA emergency use authorization (EUA) for COVID-19 treatment. In addition to the spike protein, other key targets for the discovery of direct-acting antivirals include viral enzymes that are essential for SARS-CoV-2 replication, such as RNA-dependent RNA polymerase and proteases, as judged by US FDA approval for remdesivir, and EUA for Paxlovid (nirmatrelvir + ritonavir) for treating COVID-19 infections. This review presents an overview of the current status and future direction of antiviral drug discovery for treating SARS-CoV-2 infections, covering important antiviral targets such as the viral spike protein, non-structural protein (nsp) 3 papain-like protease, nsp5 main protease, and the nsp12/nsp7/nsp8 RNA-dependent RNA polymerase complex.
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217
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Deval J, Gurard-Levin ZA. Opportunities and Challenges in Targeting the Proofreading Activity of SARS-CoV-2 Polymerase Complex. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092918. [PMID: 35566268 PMCID: PMC9103157 DOI: 10.3390/molecules27092918] [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] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 01/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic. While the development of vaccines and the emergence of antiviral therapeutics is promising, alternative strategies to combat COVID-19 (and potential future pandemics) remain an unmet need. Coronaviruses feature a unique mechanism that may present opportunities for therapeutic intervention: the RNA polymerase complex of coronaviruses is distinct in its ability to proofread and remove mismatched nucleotides during genome replication and transcription. The proofreading activity has been linked to the exonuclease (ExoN) activity of non-structural protein 14 (NSP14). Here, we review the role of NSP14, and other NSPs, in SARS-CoV-2 replication and describe the assays that have been developed to assess the ExoN function. We also review the nucleoside analogs and non-nucleoside inhibitors known to interfere with the proofreading activity of NSP14. Although not yet validated, the potential use of non-nucleoside proofreading inhibitors in combination with chain-terminating nucleosides may be a promising avenue for the development of anti-CoV agents.
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Affiliation(s)
- Jerome Deval
- Aligos Therapeutics, Inc., San Francisco, CA 94080, USA
- Correspondence:
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218
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Fayad N, Habib WA, El-Shesheny R, Kandeil A, Mourad Y, Mokhbat J, Kayali G, Goldstein J, Abdallah J. Lebanese SARS-CoV-2 genomics: 24 months of the pandemic. Virus Res 2022; 317:198824. [PMID: 35605880 PMCID: PMC9121641 DOI: 10.1016/j.virusres.2022.198824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/16/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic continues to pose a global health concern, despite the ongoing vaccination campaigns, due to the emergence and rapid spread of new variants of the causative agent SARS-CoV-2. These variants are identified and tracked via the marker mutations they carry, and the classification system put in place following tremendous sequencing efforts. In this study, the genomes of 1,230 Lebanese SARS-CoV-2 strains collected throughout 2 years of the outbreak in Lebanon were analyzed, 115 of which sequenced within this project. Strains were classified into seven GISAID clades, the major one being GRY, and 36 Pango lineages, with three variants of concern identified: alpha, delta and omicron. A time course distribution of GISAID clades allowed the visualization of change throughout the two years of the Lebanese outbreak, in conjunction with major events and measures in the country. Subsequent phylogenetic analysis showed the clustering of strains belonging to the same clades. In addition, a mutational survey showed the presence of mutations in the structural, non-structural and accessory proteins. Twenty five (25) mutations were labeled as major, i.e. present in more than 30% of the strains, such as the common Spike_D614G and NSP3_T183I. Whereas 635 were labeled as uncommon, i.e. found in very few of the analyzed strains as well as GISAID records, such as NSP2_I349V. Distribution of these mutations differed between 2020, and the first and the second half of 2021. In summary, this study highlights key genomic aspects of the Lebanese SARS-CoV-2 strains collected in 2020, the first year of the outbreak in Lebanon, versus those collected in 2021, the second year of COVID-19 in Lebanon.
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Affiliation(s)
- Nancy Fayad
- Multi-Omics Laboratory, School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos 1401, Lebanon
| | - Walid Abi Habib
- Multi-Omics Laboratory, School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos 1401, Lebanon
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States of America
| | | | - Jacques Mokhbat
- School of Medicine, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | | | - Jimi Goldstein
- Human Link, Dubai, United Arab Emirates; School of Engineering and Technology, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, UK.
| | - Jad Abdallah
- Multi-Omics Laboratory, School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos 1401, Lebanon.
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219
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Grellet E, L'Hôte I, Goulet A, Imbert I. Replication of the coronavirus genome: A paradox among positive-strand RNA viruses. J Biol Chem 2022; 298:101923. [PMID: 35413290 PMCID: PMC8994683 DOI: 10.1016/j.jbc.2022.101923] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 01/18/2023] Open
Abstract
Coronavirus (CoV) genomes consist of positive-sense single-stranded RNA and are among the largest viral RNAs known to date (∼30 kb). As a result, CoVs deploy sophisticated mechanisms to replicate these extraordinarily large genomes as well as to transcribe subgenomic messenger RNAs. Since 2003, with the emergence of three highly pathogenic CoVs (SARS-CoV, MERS-CoV, and SARS-CoV-2), significant progress has been made in the molecular characterization of the viral proteins and key mechanisms involved in CoV RNA genome replication. For example, to allow for the maintenance and integrity of their large RNA genomes, CoVs have acquired RNA proofreading 3'-5' exoribonuclease activity (in nonstructural protein nsp14). In order to replicate the large genome, the viral-RNA-dependent RNA polymerase (RdRp; in nsp12) is supplemented by a processivity factor (made of the viral complex nsp7/nsp8), making it the fastest known RdRp. Lastly, a viral structural protein, the nucleocapsid (N) protein, which is primarily involved in genome encapsidation, is required for efficient viral replication and transcription. Therefore, CoVs are a paradox among positive-strand RNA viruses in the sense that they use both a processivity factor and have proofreading activity reminiscent of DNA organisms in addition to structural proteins that mediate efficient RNA synthesis, commonly used by negative-strand RNA viruses. In this review, we present a historical perspective of these unsuspected discoveries and detail the current knowledge on the core replicative machinery deployed by CoVs.
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Affiliation(s)
- Emeline Grellet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - India L'Hôte
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Adeline Goulet
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France
| | - Isabelle Imbert
- Aix Marseille Université, Centre National de la Recherche Scientifique, AMU CNRS UMR 7255, LISM, Marseille, France.
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220
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Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alfaro Alvarado LH, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie‐Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, Ortiz‐Alvarez de la Campa M, Paredes I, Wheeler B, Rupert A, Sam A, See K, Soto Zapata S, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. Proteins 2022; 90:1054-1080. [PMID: 34580920 PMCID: PMC8661935 DOI: 10.1002/prot.26250] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 01/18/2023]
Abstract
Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
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Affiliation(s)
- Joseph H. Lubin
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Christine Zardecki
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Elliott M. Dolan
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Zhuofan Shen
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Shuchismita Dutta
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - John D. Westbrook
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Brian P. Hudson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - David S. Goodsell
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- The Scripps Research InstituteLa JollaCaliforniaUSA
| | - Jonathan K. Williams
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Maria Voigt
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Vidur Sarma
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Lingjun Xie
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Thejasvi Venkatachalam
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Steven Arnold
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | - Aaliyah Khan
- University of Maryland Baltimore CountyBaltimoreMarylandUSA
| | | | | | | | | | | | | | - Helen Zheng
- Watchung Hills Regional High SchoolWarrenNew JerseyUSA
| | | | | | - Mark Dresel
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | | | | | - Evan Lenkeit
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | - Andrew Sam
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Katherine See
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Paul A. Craig
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Jennifer Jiang
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | - Yana Bromberg
- Department of Biochemistry and MicrobiologyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Jay Tischfield
- Department of GeneticsRutgers, The State University of New Jersey, and Human Genetics Institute of New JerseyPiscatawayNew JerseyUSA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Eddy Arnold
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jean Baum
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jesse Sandberg
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Grace Brannigan
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
- Department of PhysicsRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Stephen K. Burley
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
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221
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Jiang AZ, Nian F, Chen H, McBean EA. Passive Samplers, an Important Tool for Continuous Monitoring of the COVID-19 Pandemic. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:32326-32334. [PMID: 35137317 PMCID: PMC9072756 DOI: 10.1007/s11356-022-19073-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
The global pandemic caused by COVID-19 has resulted in major costs around the world, costs with dimensions in every aspect, from peoples' daily living to the global economy. As the pandemic progresses, the virus evolves, and more vaccines become available, and the 'battle against the virus' continues. As part of the battle, Wastewater-Based Epidemiology (WBE) technologies are being widely deployed in essential roles for SARS-CoV-2 detection and monitoring. While focusing on demonstrating the advantages of passive samplers as a tool in WBE, this review provides a holistic view of the current WBE applications in monitoring SARS-CoV-2 with the integration of the most up-to-date data. A novel scenario example based on a recent Nanjing (China) outbreak in July 2021 is used to illustrate the potential benefits of using passive samplers to monitor COVID-19 and to facilitate effective control of future major outbreaks. The presented contents and how the application of passive samplers indicates that this technology can be beneficial at different levels, varying from building to community to regional. Countries and regions that have the pandemic well under control or have low positive case occurrences have the potential to significantly benefit from deploying passive samplers as a measure to identify and suppress outbreaks.
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Affiliation(s)
- Albert Z. Jiang
- School of Engineering, University of Guelph, 50 Stone Rd. E, Guelph, N1G 2W1 Canada
| | - Fulin Nian
- Department of Digestive, Shanghai Pudong Hospital, Fudan University Affiliated Pudong Medical Center, 2800 Gongwei Road, Shanghai, 201399 China
| | - Han Chen
- College of Environmental Science and Engineering/Sino-Canada Joint R&D Centre for Water and Environmental Safety, Nankai University, Tianjin, 300071 China
| | - Edward A. McBean
- School of Engineering, University of Guelph, 50 Stone Rd. E, Guelph, N1G 2W1 Canada
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222
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Martínez-González B, Soria ME, Vázquez-Sirvent L, Ferrer-Orta C, Lobo-Vega R, Mínguez P, de la Fuente L, Llorens C, Soriano B, Ramos R, Cortón M, López-Rodríguez R, García-Crespo C, Gallego I, de Ávila AI, Gómez J, Enjuanes L, Salar-Vidal L, Esteban J, Fernandez-Roblas R, Gadea I, Ayuso C, Ruíz-Hornillos J, Verdaguer N, Domingo E, Perales C. SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes. Microbiol Spectr 2022; 10:e0022122. [PMID: 35348367 PMCID: PMC9045161 DOI: 10.1128/spectrum.00221-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCE The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.
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Affiliation(s)
- Brenda Martínez-González
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María Eugenia Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Lucía Vázquez-Sirvent
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, Universidad de Valencia, Valencia, Spain
| | - Beatriz Soriano
- Biotechvana, “Scientific Park”, Universidad de Valencia, Valencia, Spain
| | - Ricardo Ramos
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, Madrid, Spain
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario López-Rodríguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ricardo Fernandez-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Ruíz-Hornillos
- Allergy Unit, Hospital Infanta Elena, Valdemoro, Madrid, Spain
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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223
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Bai X, Sun H, Wu S, Li Y, Wang L, Hong B. Identifying Small-Molecule Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase by Establishing a Fluorometric Assay. Front Immunol 2022; 13:844749. [PMID: 35464436 PMCID: PMC9021610 DOI: 10.3389/fimmu.2022.844749] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/11/2022] [Indexed: 01/18/2023] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), a member of the coronavirus family, appeared in 2019 and has caused the largest global public health and economic emergency in recent history, affecting almost all sectors of society. SARS-CoV-2 is a single-stranded positive-sense RNA virus that relies on RNA-dependent RNA polymerase (RdRp) activity in viral transcription and replication. Due to its high sequence and structural conservation in coronavirus and new SARS-CoV-2 variants, RdRp has been recognized as the key therapeutic target to design novel antiviral strategies. Nucleotide analogs (NAs), such as remdesivir, is the most promising class of RdRp inhibitors to be used in the treatment of COVID-19. However, the presence of exonucleases in SARS-CoV-2 caused a great challenge to NAs; the excision of incorporated NAs will lead to viral resistance to this group of inhibitors. Here, we expressed active RdRp protein in both a eukaryotic expression system of baculovirus-infected insect cells and a prokaryotic expression system of Escherichia coli cells. Nsp7 and nsp8 of the functional RdRp holoenzyme were generated in E. coli. An in vitro RdRp activity assay has been established with a reconstituted nsp12/nsp7/nsp8 complex and biotin-labeled self-priming RNAs, and the activity of the RdRp complex was determined by detecting binding and extension of RNAs. Moreover, to meet the needs of high-throughput drug screening, we developed a fluorometric approach based on dsRNA quantification to assess the catalytic activity of the RdRp complex, which is also suitable for testing in 96-well plates. We demonstrated that the active triphosphate form of remdesivir (RTP) and several reported non-nucleotide analog viral polymerase inhibitors blocked the RdRp in the in vitro RdRp activity assay and high-throughput screening model. This high-throughput screening model has been applied to a custom synthetic chemical and natural product library of thousands of compounds for screening SARS-CoV-2 RdRp inhibitors. Our efficient RdRp inhibitor discovery system provides a powerful platform for the screening, validation, and evaluation of novel antiviral molecules targeting SARS-CoV-2 RdRp, particularly for non-nucleotide antivirals drugs (NNAs).
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Affiliation(s)
- Xiaoming Bai
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences (CAMS) Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hongmin Sun
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences (CAMS) Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shuo Wu
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences (CAMS) Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuhuan Li
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences (CAMS) Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lifei Wang
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences (CAMS) Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Hong
- National Health Commission of the People's Republic of China (NHC) Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Chinese Academy of Medical Sciences (CAMS) Key Laboratory of Synthetic Biology for Drug Innovation, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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224
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Zhou H, Ni WJ, Huang W, Wang Z, Cai M, Sun YC. Advances in Pathogenesis, Progression, Potential Targets and Targeted Therapeutic Strategies in SARS-CoV-2-Induced COVID-19. Front Immunol 2022; 13:834942. [PMID: 35450063 PMCID: PMC9016159 DOI: 10.3389/fimmu.2022.834942] [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: 12/14/2021] [Accepted: 03/07/2022] [Indexed: 01/18/2023] Open
Abstract
As the new year of 2020 approaches, an acute respiratory disease quietly caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as coronavirus disease 2019 (COVID-19) was reported in Wuhan, China. Subsequently, COVID-19 broke out on a global scale and formed a global public health emergency. To date, the destruction that has lasted for more than two years has not stopped and has caused the virus to continuously evolve new mutant strains. SARS-CoV-2 infection has been shown to cause multiple complications and lead to severe disability and death, which has dealt a heavy blow to global development, not only in the medical field but also in social security, economic development, global cooperation and communication. To date, studies on the epidemiology, pathogenic mechanism and pathological characteristics of SARS-CoV-2-induced COVID-19, as well as target confirmation, drug screening, and clinical intervention have achieved remarkable effects. With the continuous efforts of the WHO, governments of various countries, and scientific research and medical personnel, the public’s awareness of COVID-19 is gradually deepening, a variety of prevention methods and detection methods have been implemented, and multiple vaccines and drugs have been developed and urgently marketed. However, these do not appear to have completely stopped the pandemic and ravages of this virus. Meanwhile, research on SARS-CoV-2-induced COVID-19 has also seen some twists and controversies, such as potential drugs and the role of vaccines. In view of the fact that research on SARS-CoV-2 and COVID-19 has been extensive and in depth, this review will systematically update the current understanding of the epidemiology, transmission mechanism, pathological features, potential targets, promising drugs and ongoing clinical trials, which will provide important references and new directions for SARS-CoV-2 and COVID-19 research.
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Affiliation(s)
- Hong Zhou
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wei Huang
- The Third People's Hospital of Hefei, The Third Clinical College of Anhui Medical University, Hefei, China
| | - Zhen Wang
- Anhui Provincial Children's Hospital, Children's Hospital of Fudan University-Anhui Campus, Hefei, China
| | - Ming Cai
- Department of Pharmacy, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Yan-Cai Sun
- Department of Pharmacy, Anhui Provincial Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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225
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Low ZY, Yip AJW, Lal SK. Repositioning anticancer drugs as novel COVID-19 antivirals: targeting structural and functional similarities between viral proteins and cancer. Expert Rev Mol Med 2022; 24:1-23. [PMID: 35450545 PMCID: PMC9114731 DOI: 10.1017/erm.2022.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/13/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
The current COVID-19 pandemic contributed by the SARS-CoV-2 has put in place an urgent need for new and promising antiviral therapeutics. The viral RNA-dependent RNA polymerase (RdRp) enzyme plays a vital role in viral replication for all RNA viruses, including SARS-CoV-2, thereby making it a prime and promising candidate for novel antiviral targeting. Interestingly, the human telomerase reverse transcriptase (hTERT), a common catalytic subunit of the telomerase enzyme in many cancers, has also been identified with structural and functional similarities to the viral RdRp. Therefore, it becomes essential to evaluate and consider anticancer drugs that target hTERT towards antiviral RdRp activity, and vice versa. For instance, Floxuridine, an hTERT inhibitor, and VX-222, a hepatitis C virus RdRp inhibitor, are now gaining recognition as a potential antiviral against SARS-CoV-2 and anti-hTERT for cancer, simultaneously. While limited studies on hTERT inhibitors for use as viral RdRp, and anti-RdRp inhibitors as hTERT inhibitors are available, in this review, we aim at bringing to light this close structural and functional relationship between both these enzymes. We punctuate this idea with specific examples on how potential anticancer inhibitors can effectively be brought to use as inhibitors against the SARS-CoV-2 virus, a relatively new pathogen, compared to the very well-studied field of cancer research.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor DE, Malaysia
| | - Ashley Jia Wen Yip
- School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor DE, Malaysia
| | - Sunil Kumar Lal
- School of Science, Monash University Malaysia, 47500 Bandar Sunway, Selangor DE, Malaysia
- Tropical Medicine and Biology Platform, Monash University Malaysia, 47500 Bandar Sunway, Selangor DE, Malaysia
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226
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Yuan H, Liu L, Zhou J, Zhang T, Daily JW, Park S. Bioactive Components of Houttuynia cordata Thunb and Their Potential Mechanisms Against COVID-19 Using Network Pharmacology and Molecular Docking Approaches. J Med Food 2022; 25:355-366. [PMID: 35438554 DOI: 10.1089/jmf.2021.k.0144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We investigated the molecular mechanism by which Houttuynia cordata Thunb (HCT) may intervene in coronavirus disease 2019 (COVID-19) and COVID-19-induced cytokine storms using network pharmacology and molecular docking approaches. Using the Traditional Chinese medicine Systems Pharmacology Database and Analysis Platform (TCMSP), a "component-target-pathway" topology map of HCT for COVID-19 treatment was constructed using Cytoscape. Core target genes were analyzed using the STRING database, and the signal pathway map and biological mechanism of COVID-19 therapy were obtained using cluster profilers. Active components of HCT were docked with severe respiratory syndrome coronavirus 2 (SARS-CoV-2) 3C-like protease (3CLpro) and RNA-dependent RNA polymerase (RdRp) using AutoDockTools. Data visualization and statistical analysis were conducted using the R program. A molecular dynamic simulation was carried out with the Groningen Machine for Chemical Simulation program. HCT had six active anti-COVID-19 ingredients and 45 molecular targets. Their crucial target proteins for COVID-19 treatment were the RELA (nuclear factor kappa B [NF-κB] p65 subunit), interleukin 6, and mitogen-activated protein kinase 1. In functional enrichment analysis, the potential molecular targets of active components of HCT for COVID-19 treatment belonged to 18 signaling pathways (adjusted P = 2.12E-11). Gene ontology obtained by Kyoto Encyclopedia of Genes and Genome enrichment screening showed that the primary mechanism of COVID-19 treatment was upregulation of protein kinase C followed by downregulations of T cell differentiation and proliferation and NF-κB signaling. Molecular docking showed that the active components of HCT (quercetin and kaempferol) had similar binding affinities for SARS-CoV-2 3CLpro and SARS-CoV-2 RdRp, primary COVID-19 target proteins as did clinically used drugs. These results were confirmed with molecular dynamics simulation. In conclusion, multiple components of HCT, especially quercetin and kaempferol, have the potential to treat COVID-19 infection and COVID-19-induced cytokine storm by targeting multiple proteins.
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Affiliation(s)
- Heng Yuan
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea
| | - Liping Liu
- College of Biological & Environmental Sciences, Zhejiang Wanli University, Ningbo, China
| | - Junyu Zhou
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea
| | - Ting Zhang
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea
| | - James W Daily
- Daily Manufacturing, Inc., Rockwell, North Carolina, USA
| | - Sunmin Park
- Department of Bio-Convergence System, Hoseo University, Asan, South Korea.,Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, Asan, South Korea
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227
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Naseem-Khan S, Berger MB, Leddin EM, Maghsoud Y, Cisneros GA. Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase. J Chem Inf Model 2022; 62:2456-2465. [PMID: 35435671 DOI: 10.1021/acs.jcim.2c00201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Remdesivir was the first antiviral drug that received emergency use authorization from the United States Food and Drug Administration and is now formally approved to treat COVID-19. Remdesivir is a nucleotide analogue that targets the RNA-dependent RNA polymerase (RdRp) of coronaviruses, including SARS-CoV-2. The solution of multiple RdRp structures has been one of the main axes of research in the race against the SARS-CoV-2 virus. Several hypotheses of the mechanism of inhibition of RdRp by remdesivir have been proposed, although open questions remain. This work uses molecular dynamics simulations to explore the impact of remdesivir and two analogues as incoming nucleotides and of up to four incorporations of remdesivir along the primer strand on RdRp. The simulation results suggest that the overall structure and the dynamical behavior of RdRp are destabilized by remdesivir and the two analogues in the incoming position. The incorporation of remdesivir along the primer strand impacts specific non-bonded interactions between the nascent RNA and the polymerase subunit, as well as the overall dynamical networks on RdRp. The strongest impact on the structure and dynamics are observed after three incorporations, when remdesivir is located at position -A3, in agreement with previously reported experimental and computational results. Our results provide atomic-level details of the role played by remdesivir on the disruption of RNA synthesis by RdRp and the main drivers of these disruptions.
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Affiliation(s)
- Sehr Naseem-Khan
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Madison B Berger
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Emmett M Leddin
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Yazdan Maghsoud
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
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228
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Repurposing of Four Drugs as Anti-SARS-CoV-2 Agents and Their Interactions with Protein Targets. Sci Pharm 2022. [DOI: 10.3390/scipharm90020024] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although there are existing vaccines against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), new COVID-19 cases are increasing due to low immunization coverage and the emergence of new variants. For this reason, new drugs to treat and prevent severe COVID-19 are needed. Here, we provide four different FDA-approved drugs against SARS-CoV-2 proteins involved in the entry and replication process, aiming to identify potential drugs to treat COVID-19. We use the main protease (Mpro), the spike glycoprotein (S protein), and RNA-dependent RNA polymerase (RdRp) as protein targets for anti- SARS-CoV-2 drugs. In our constructed database, we selected different drugs against each target (Mpro, S protein, and RdRp) based on their common interactions with relevant residues involved in viral entry at the host cell and replication. Furthermore, their stability inside the binding pocket, as well as their predicted binding-free energy, allow us to provide new insight into the possible drug repurposing of viomycin (interacting with Mpro) due to its interactions with key residues, such as Asn 143, Glu 166, and Gln 189 at the same time as hesperidin (interacting with the S protein) is interacting with residues Tyr 449, Ser 494, and Thr 500, keeping inside the predicted binding pocket, as well as interacting with residues in different variants of concern. Finally, we also suggest nystatin and elvitegravir (interacting with RdRp) as possible drugs due to their stability within the predicted pocket along the simulation and their interaction with key residues, such as Asp 760, Asp 761, and Asp 618. Altogether our results provide new knowledge about the possible mechanism of the inhibition of viomycin, hesperidin, elvitegravir, and nystatin to inhibit the viral life cycle of SARS-CoV-2 and some of its variants of concern (VOC). Additionally, some iodide-based contrast agents were also found to bind the S protein strongly, i.e., iohexol (−58.99 Kcal/mol), iotrolan (−76.19 Kcal/mol), and ioxilan (−62.37 Kcal/mol). Despite the information we report here as the possible strong interaction between these contrast agents and the SARS-CoV-2′s S protein, Mpro, and RdRp, we believe that further investigation, including chemical modifications in their structures, are needed for COVID-19 treatment.
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229
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Calleja DJ, Kuchel N, Lu BGC, Birkinshaw RW, Klemm T, Doerflinger M, Cooney JP, Mackiewicz L, Au AE, Yap YQ, Blackmore TR, Katneni K, Crighton E, Newman J, Jarman KE, Call MJ, Lechtenberg BC, Czabotar PE, Pellegrini M, Charman SA, Lowes KN, Mitchell JP, Nachbur U, Lessene G, Komander D. Insights Into Drug Repurposing, as Well as Specificity and Compound Properties of Piperidine-Based SARS-CoV-2 PLpro Inhibitors. Front Chem 2022; 10:861209. [PMID: 35494659 PMCID: PMC9039177 DOI: 10.3389/fchem.2022.861209] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic continues unabated, emphasizing the need for additional antiviral treatment options to prevent hospitalization and death of patients infected with SARS-CoV-2. The papain-like protease (PLpro) domain is part of the SARS-CoV-2 non-structural protein (nsp)-3, and represents an essential protease and validated drug target for preventing viral replication. PLpro moonlights as a deubiquitinating (DUB) and deISGylating enzyme, enabling adaptation of a DUB high throughput (HTS) screen to identify PLpro inhibitors. Drug repurposing has been a major focus through the COVID-19 pandemic as it may provide a fast and efficient route for identifying clinic-ready, safe-in-human antivirals. We here report our effort to identify PLpro inhibitors by screening the ReFRAME library of 11,804 compounds, showing that none inhibit PLpro with any reasonable activity or specificity to justify further progression towards the clinic. We also report our latest efforts to improve piperidine-scaffold inhibitors, 5c and 3k, originally developed for SARS-CoV PLpro. We report molecular details of binding and selectivity, as well as in vitro absorption, distribution, metabolism and excretion (ADME) studies of this scaffold. A co-crystal structure of SARS-CoV-2 PLpro bound to inhibitor 3k guides medicinal chemistry efforts to improve binding and ADME characteristics. We arrive at compounds with improved and favorable solubility and stability characteristics that are tested for inhibiting viral replication. Whilst still requiring significant improvement, our optimized small molecule inhibitors of PLpro display decent antiviral activity in an in vitro SARS-CoV-2 infection model, justifying further optimization.
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Affiliation(s)
- Dale J. Calleja
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Nathan Kuchel
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Bernadine G. C. Lu
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Richard W. Birkinshaw
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Theresa Klemm
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Marcel Doerflinger
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - James P. Cooney
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Liana Mackiewicz
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda E. Au
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Yu Q. Yap
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Timothy R Blackmore
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Kasiram Katneni
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Elly Crighton
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, VIC, Australia
| | - Kate E. Jarman
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Melissa J. Call
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Bernhard C. Lechtenberg
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Peter E. Czabotar
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Marc Pellegrini
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Kym N. Lowes
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Jeffrey P. Mitchell
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Ueli Nachbur
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Guillaume Lessene
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
- Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - David Komander
- Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia
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230
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231
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Esposito S, D’Abrosca G, Antolak A, Pedone PV, Isernia C, Malgieri G. Host and Viral Zinc-Finger Proteins in COVID-19. Int J Mol Sci 2022; 23:ijms23073711. [PMID: 35409070 PMCID: PMC8998646 DOI: 10.3390/ijms23073711] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023] Open
Abstract
An unprecedented effort to tackle the ongoing COVID-19 pandemic has characterized the activity of the global scientific community over the last two years. Hundreds of published studies have focused on the comprehension of the immune response to the virus and on the definition of the functional role of SARS-CoV-2 proteins. Proteins containing zinc fingers, both belonging to SARS-CoV-2 or to the host, play critical roles in COVID-19 participating in antiviral defenses and regulation of viral life cycle. Differentially expressed zinc finger proteins and their distinct activities could thus be important in determining the severity of the disease and represent important targets for drug development. Therefore, we here review the mechanisms of action of host and viral zinc finger proteins in COVID-19 as a contribution to the comprehension of the disease and also highlight strategies for therapeutic developments.
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232
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Jung C, Kmiec D, Koepke L, Zech F, Jacob T, Sparrer KMJ, Kirchhoff F. Omicron: What Makes the Latest SARS-CoV-2 Variant of Concern So Concerning? J Virol 2022; 96:e0207721. [PMID: 35225672 PMCID: PMC8941872 DOI: 10.1128/jvi.02077-21] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
Emerging strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, that show increased transmission fitness and/or immune evasion are classified as "variants of concern" (VOCs). Recently, a SARS-CoV-2 variant first identified in November 2021 in South Africa has been recognized as a fifth VOC, termed "Omicron." What makes this VOC so alarming is the high number of changes, especially in the viral Spike protein, and accumulating evidence for increased transmission efficiency and escape from neutralizing antibodies. In an amazingly short time, the Omicron VOC has outcompeted the previously dominating Delta VOC. However, it seems that the Omicron VOC is overall less pathogenic than other SARS-CoV-2 VOCs. Here, we provide an overview of the mutations in the Omicron genome and the resulting changes in viral proteins compared to other SARS-CoV-2 strains and discuss their potential functional consequences.
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Affiliation(s)
- Christoph Jung
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | - Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, Ulm, Germany
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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233
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
- *Correspondence: Carina Almeida,
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234
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Maiti AK. Identification of G-quadruplex DNA sequences in SARS-CoV2. Immunogenetics 2022; 74:455-463. [PMID: 35303126 PMCID: PMC8931451 DOI: 10.1007/s00251-022-01257-6] [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: 01/17/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
G-quadruplex structure or Putative Quadruplex Sequences (PQSs) are abundant in human, microbial, DNA, or RNA viral genomes. These sequences in RNA viral genome play critical roles in integration into human genome as LTR (Long Terminal Repeat), genome replication, chromatin rearrangements, gene regulation, antigen variation (Av), and virulence. Here, we investigated whether the genome of SARS-CoV2, an RNA virus, contained such potential G-quadruplex structures. Using bioinformatic tools, we searched for such sequences and found thirty-seven (forward strand (twenty-five) + reverse strand (Twelve)) QGRSs (Quadruplex forming G-Rich Sequences)/PQSs in SARS-CoV2 genome. These sequences are dispersed mainly in the upstream of SARS-CoV2 genes. We discuss whether existing PQS/QGRS ligands could inhibit the SARS-CoV2 replication and gene transcription as has been observed in other RNA viruses. Further experimental validation would determine the role of these G-quadruplex sequences in SARS-CoV2 genome function to survive in the host cells and identify therapeutic agents to destabilize these PQSs/QGRSs.
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Affiliation(s)
- Amit K Maiti
- Mydnavar, Department of Genetics and Genomics, 2645 Somerset Boulevard, Troy, MI, 48084, USA.
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235
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Zaffagni M, Harris JM, Patop IL, Pamudurti NR, Nguyen S, Kadener S. SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome. eLife 2022; 11:71945. [PMID: 35293857 PMCID: PMC9054133 DOI: 10.7554/elife.71945] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 03/10/2022] [Indexed: 11/15/2022] Open
Abstract
Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in the presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy. Viruses are parasites, relying on the cells they infect to make more of themselves. In doing so they change how an infected cell turns its genes on and off, forcing it to build new virus particles and turning off the immune surveillance that would allow the body to intervene. This is how SARS-CoV-2, the virus that causes COVID, survives with a genome that carries instructions to make just 29 proteins. One of these proteins, known as Nsp14, is involved in both virus reproduction and immune escape. Previous work has shown that it interacts with IMPDH2, the cellular enzyme that controls the production of the building blocks of the genetic code. The impact of this interaction is not clear. To find out more, Zaffagni et al. introduced 26 of the SARS-CoV-2 proteins into human cells one at a time. Nsp14 had the most dramatic effect, dialing around 4,000 genes up or down and changing how the cell interprets over 1,000 genes. Despite being just one protein, it mimicked the genetic changes seen during real SARS-CoV-2 infection. Blocking IMPDH2 partially reversed the effects, which suggests that the interaction of Nsp14 with the enzyme might be responsible for the effects of SARS-CoV-2 on the genes of the cell. Understanding how viral proteins affect cells can explain what happens during infection. This could lead to the discovery of new treatments designed to counteract the effects of the virus. Further work could investigate whether interfering with Nsp14 helps cells to overcome infection.
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Affiliation(s)
- Michela Zaffagni
- Department of Biology, Brandeis University, Waltham, United States
| | - Jenna M Harris
- Department of Biology, Brandeis University, Waltham, United States
| | - Ines L Patop
- Department of Biology, Brandeis University, Waltham, United States
| | | | - Sinead Nguyen
- Department of Biology, Brandeis University, Waltham, United States
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236
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Gonzalez Lomeli F, Elmaraghy N, Castro A, Osuna Guerrero CV, Newcomb LL. Conserved Targets to Prevent Emerging Coronaviruses. Viruses 2022; 14:v14030563. [PMID: 35336969 PMCID: PMC8949862 DOI: 10.3390/v14030563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
Novel coronaviruses emerged as zoonotic outbreaks in humans in 2003 (SARS), 2012 (MERS), and notably in 2019 (SARS2), which resulted in the COVID-19 pandemic, causing worldwide health and economic disaster. Vaccines provide the best protection against disease but cannot be developed and engineered quickly enough to prevent emerging viruses, zoonotic outbreaks, and pandemics. Antivirals are the best first line of therapeutic defense against novel emerging viruses. Coronaviruses are plus sense, single stranded, RNA genome viruses that undergo frequent genetic mutation and recombination, allowing for the emergence of novel coronavirus strains and variants. The molecular life cycle of the coronavirus family offers many conserved activities to be exploited as targets for antivirals. Here, we review the molecular life cycle of coronaviruses and consider antiviral therapies, approved and under development, that target the conserved activities of coronaviruses. To identify additional targets to inhibit emerging coronaviruses, we carried out in silico sequence and structure analysis of coronavirus proteins isolated from bat and human hosts. We highlight conserved and accessible viral protein domains and residues as possible targets for the development of viral inhibitors. Devising multiple antiviral therapies that target conserved viral features to be used in combination is the best first line of therapeutic defense to prevent emerging viruses from developing into outbreaks and pandemics.
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237
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Moll T, Odon V, Harvey C, Collins MO, Peden A, Franklin J, Graves E, Marshall JN, Souza CDS, Zhang S, Azzouz M, Gordon D, Krogan N, Ferraiuolo L, Snyder MP, Shaw PJ, Rehwinkel J, Cooper-Knock J. Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.06.483172. [PMID: 35291294 PMCID: PMC8923113 DOI: 10.1101/2022.03.06.483172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
New therapeutic targets are a valuable resource in the struggle to reduce the morbidity and mortality associated with the COVID-19 pandemic, caused by the SARS-CoV-2 virus. Genome-wide association studies (GWAS) have identified risk loci, but some loci are associated with co-morbidities and are not specific to host-virus interactions. Here, we identify and experimentally validate a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. EXOSC2 was one of 332 host proteins examined, all of which interact directly with SARS-CoV-2 proteins; EXOSC2 interacts with Nsp8 which forms part of the viral RNA polymerase. Lung-specific eQTLs were identified from GTEx (v7) for each of the 332 host proteins. Aggregating COVID-19 GWAS statistics for gene-specific eQTLs revealed an association between increased expression of EXOSC2 and higher risk of clinical COVID-19 which survived stringent multiple testing correction. EXOSC2 is a component of the RNA exosome and indeed, LC-MS/MS analysis of protein pulldowns demonstrated an interaction between the SARS-CoV-2 RNA polymerase and the majority of human RNA exosome components. CRISPR/Cas9 introduction of nonsense mutations within EXOSC2 in Calu-3 cells reduced EXOSC2 protein expression, impeded SARS-CoV-2 replication and upregulated oligoadenylate synthase ( OAS) genes, which have been linked to a successful immune response against SARS-CoV-2. Reduced EXOSC2 expression did not reduce cellular viability. OAS gene expression changes occurred independent of infection and in the absence of significant upregulation of other interferon-stimulated genes (ISGs). Targeted depletion or functional inhibition of EXOSC2 may be a safe and effective strategy to protect at-risk individuals against clinical COVID-19.
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Affiliation(s)
- Tobias Moll
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Valerie Odon
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Calum Harvey
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew Peden
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - John Franklin
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Emily Graves
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Jack N.G. Marshall
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Sai Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - David Gordon
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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238
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Friedrich M, Pfeifer G, Binder S, Aigner A, Vollmer Barbosa P, Makert GR, Fertey J, Ulbert S, Bodem J, König EM, Geiger N, Schambach A, Schilling E, Buschmann T, Hauschildt S, Koehl U, Sewald K. Selection and Validation of siRNAs Preventing Uptake and Replication of SARS-CoV-2. Front Bioeng Biotechnol 2022; 10:801870. [PMID: 35309990 PMCID: PMC8925020 DOI: 10.3389/fbioe.2022.801870] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022] Open
Abstract
In 2019, the novel highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak rapidly led to a global pandemic with more than 346 million confirmed cases worldwide, resulting in 5.5 million associated deaths (January 2022). Entry of all SARS-CoV-2 variants is mediated by the cellular angisin-converting enzyme 2 (ACE2). The virus abundantly replicates in the epithelia of the upper respiratory tract. Beyond vaccines for immunization, there is an imminent need for novel treatment options in COVID-19 patients. So far, only a few drugs have found their way into the clinics, often with modest success. Specific gene silencing based on small interfering RNA (siRNA) has emerged as a promising strategy for therapeutic intervention, preventing/limiting SARS-CoV-2 entry into host cells or interfering with viral replication. Here, we pursued both strategies. We designed and screened nine siRNAs (siA1-9) targeting the viral entry receptor ACE2. SiA1, (siRNA against exon1 of ACE2 mRNA) was most efficient, with up to 90% knockdown of the ACE2 mRNA and protein for at least six days. In vitro, siA1 application was found to protect Vero E6 and Huh-7 cells from infection with SARS-CoV-2 with an up to ∼92% reduction of the viral burden indicating that the treatment targets both the endosomal and the viral entry at the cytoplasmic membrane. Since the RNA-encoded genome makes SARS-CoV-2 vulnerable to RNA interference (RNAi), we designed and analysed eight siRNAs (siV1-8) directly targeting the Orf1a/b region of the SARS-CoV-2 RNA genome, encoding for non-structural proteins (nsp). As a significant hallmark of this study, we identified siV1 (siRNA against leader protein of SARS-CoV-2), which targets the nsp1-encoding sequence (a.k.a. ‘host shutoff factor’) as particularly efficient. SiV1 inhibited SARS-CoV-2 replication in Vero E6 or Huh-7 cells by more than 99% or 97%, respectively. It neither led to toxic effects nor induced type I or III interferon production. Of note, sequence analyses revealed the target sequence of siV1 to be highly conserved in SARS-CoV-2 variants. Thus, our results identify the direct targeting of the viral RNA genome (ORF1a/b) by siRNAs as highly efficient and introduce siV1 as a particularly promising drug candidate for therapeutic intervention.
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Affiliation(s)
- Maik Friedrich
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- *Correspondence: Maik Friedrich,
| | - Gabriele Pfeifer
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Stefanie Binder
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Achim Aigner
- Rudolf Boehm Institute for Pharmacology and Toxicology, Clinical Pharmacology, Leipzig University, Faculty of Medicine, Leipzig, Germany
| | | | - Gustavo R. Makert
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Jasmin Fertey
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Sebastian Ulbert
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Jochen Bodem
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Eva-Maria König
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Nina Geiger
- Institute of Virology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Erik Schilling
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | - Tilo Buschmann
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
| | | | - Ulrike Koehl
- Institute of Clinical Immunology, Faculty of Leipzig University of Leipzig, Max-Bürger-Forschungszentrum (MBFZ), Leipzig, Germany
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
- REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
- Institute for Cellular Therapeutics, Hannover Medical School, Hannover, Germany
| | - Katherina Sewald
- Fraunhofer Institute of Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) of the German Center for Lung Research (DZL), Hannover, Germany
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239
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Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proc Natl Acad Sci U S A 2022; 119:2106379119. [PMID: 35165203 PMCID: PMC8892293 DOI: 10.1073/pnas.2106379119] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in nonstructural protein 14 (nsp14), which excises nucleotides including antiviral drugs misincorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here, we determined a 1.6-Å resolution crystal structure of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) ExoN in complex with its essential cofactor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. We also show that the ExoN activity can rescue a stalled RNA primer poisoned with sofosbuvir and allow RdRp to continue its extension in the presence of the chain-terminating drug, biochemically recapitulating proofreading in SARS-CoV-2 replication. Molecular dynamics simulations further show remarkable flexibility of multidomain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA binding to support its exonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN-nsp10 complex serves as a platform for future development of anticoronaviral drugs or strategies to attenuate the viral virulence.
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240
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Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex. Nat Struct Mol Biol 2022; 29:250-260. [PMID: 35260847 DOI: 10.1038/s41594-022-00734-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 nonstructural proteins coordinate genome replication and gene expression. Structural analyses revealed the basis for coupling of the essential nsp13 helicase with the RNA-dependent RNA polymerase (RdRp) where the holo-RdRp and RNA substrate (the replication-transcription complex or RTC) associated with two copies of nsp13 (nsp132-RTC). One copy of nsp13 interacts with the template-RNA in an opposing polarity to the RdRp and is envisaged to drive the RdRp backward on the RNA template (backtracking), prompting questions as to how the RdRp can efficiently synthesize RNA in the presence of nsp13. Here we use cryogenic-electron microscopy and molecular dynamics simulations to analyze the nsp132-RTC, revealing four distinct conformational states of the helicases. The results indicate a mechanism for the nsp132-RTC to turn backtracking on and off, using an allosteric mechanism to switch between RNA synthesis or backtracking in response to stimuli at the RdRp active site.
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241
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Alam ASMRU, Islam OK, Hasan MS, Islam MR, Mahmud S, Al‐Emran HM, Jahid IK, Crandall KA, Hossain MA. Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. J Med Virol 2022; 94:1035-1049. [PMID: 34676891 PMCID: PMC8661685 DOI: 10.1002/jmv.27416] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co-occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5'-UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane-domain interaction of cysteine(C81)-histidine(H57). The GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS-CoV-2.
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Affiliation(s)
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Shazid Hasan
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Mir Raihanul Islam
- Division of Poverty, Health, and NutritionInternational Food Policy Research InstituteBangladesh
| | - Shafi Mahmud
- Department Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Hassan M. Al‐Emran
- Department of Biomedical EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Iqbal Kabir Jahid
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Keith A. Crandall
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public HealthThe George Washington UniversityWashington DCUSA
| | - M. Anwar Hossain
- Office of the Vice ChancellorJashore University of Science and TechnologyJashoreBangladesh
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
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242
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Cannalire R, Cerchia C, Beccari AR, Di Leva FS, Summa V. Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities. J Med Chem 2022; 65:2716-2746. [PMID: 33186044 PMCID: PMC7688049 DOI: 10.1021/acs.jmedchem.0c01140] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 02/07/2023]
Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | | | - Francesco Saverio Di Leva
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department
of Pharmacy, University of Naples “Federico
II”, via D. Montesano 49, 80131 Napoli, Italy
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243
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Anjum F, Mohammad T, Asrani P, Shafie A, Singh S, Yadav DK, Uversky VN, Hassan MI. Identification of intrinsically disorder regions in non-structural proteins of SARS-CoV-2: New insights into drug and vaccine resistance. Mol Cell Biochem 2022; 477:1607-1619. [PMID: 35211823 PMCID: PMC8869350 DOI: 10.1007/s11010-022-04393-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
The outbreak of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in December 2019 and caused coronavirus disease 2019 (COVID-19), which causes pneumonia and severe acute respiratory distress syndrome. It is a highly infectious pathogen that promptly spread. Like other beta coronaviruses, SARS‐CoV‐2 encodes some non-structural proteins (NSPs), playing crucial roles in viral transcription and replication. NSPs likely have essential roles in viral pathogenesis by manipulating many cellular processes. We performed a sequence-based analysis of NSPs to get insights into their intrinsic disorders, and their functions in viral replication were annotated and discussed in detail. Here, we provide newer insights into the structurally disordered regions of SARS-CoV-2 NSPs. Our analysis reveals that the SARS-CoV-2 proteome has a chunk of the disordered region that might be responsible for increasing its virulence. In addition, mutations in these regions are presumably responsible for drug and vaccine resistance. These findings suggested that the structurally disordered regions of SARS-CoV-2 NSPs might be invulnerable in COVID-19.
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Affiliation(s)
- Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Purva Asrani
- Department of Microbiology, University of Delhi, New Delhi, 110021, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP, Pune University Campus, Pune, 411007, India
| | - Dharmendra Kumar Yadav
- College of Pharmacy, Gachon University of Medicine and Science, Hambakmoeiro, Yeonsu-gu, Incheon City, 21924, South Korea.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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244
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Cannalire R, Cerchia C, Beccari AR, Di Leva FS, Summa V. Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities. J Med Chem 2022. [PMID: 33186044 DOI: 10.1021/acs.jmedchem.0c01140/suppl_file/jm0c01140_si_001.pdf] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The newly emerged coronavirus, called SARS-CoV-2, is the causing pathogen of pandemic COVID-19. The identification of drugs to treat COVID-19 and other coronavirus diseases is an urgent global need, thus different strategies targeting either virus or host cell are still under investigation. Direct-acting agents, targeting protease and polymerase functionalities, represent a milestone in antiviral therapy. The 3C-like (or Main) protease (3CLpro) and the nsp12 RNA-dependent RNA-polymerase (RdRp) are the best characterized SARS-CoV-2 targets and show the highest degree of conservation across coronaviruses fostering the identification of broad-spectrum inhibitors. Coronaviruses also possess a papain-like protease, another essential enzyme, still poorly characterized and not equally conserved, limiting the identification of broad-spectrum agents. Herein, we provide an exhaustive comparative analysis of SARS-CoV-2 proteases and RdRp with respect to other coronavirus homologues. Moreover, we highlight the most promising inhibitors of these proteins reported so far, including the possible strategies for their further development.
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Affiliation(s)
- Rolando Cannalire
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Carmen Cerchia
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Andrea R Beccari
- Dompé Farmaceutici SpA, via Campo di Pile, 67100 L'Aquila, Italy
| | - Francesco Saverio Di Leva
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
| | - Vincenzo Summa
- Department of Pharmacy, University of Naples "Federico II", via D. Montesano 49, 80131 Napoli, Italy
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Xiang JS, Mueller JR, Luo EC, Yee BA, Schafer D, Schmok JC, Tan FE, Rothamel K, McVicar RN, Kwong EM, Jones KL, Her HL, Chen CY, Vu AQ, Jin W, Park SS, Le P, Brannan KW, Kofman ER, Li Y, Tankka AT, Dong KD, Song Y, Carlin AF, Van Nostrand EL, Leibel SL, Yeo GW. Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.21.481223. [PMID: 35233578 PMCID: PMC8887137 DOI: 10.1101/2022.02.21.481223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.
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Affiliation(s)
- Joy S. Xiang
- Institute of Molecular and Cellular Biology, A*STAR, Singapore
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jasmine R. Mueller
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jonathan C. Schmok
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Frederick E. Tan
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Katherine Rothamel
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rachael N. McVicar
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Elizabeth M. Kwong
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Krysten L. Jones
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chun-Yuan Chen
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Anthony Q. Vu
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Wenhao Jin
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Samuel S. Park
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Phuong Le
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kristopher W. Brannan
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric R. Kofman
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yanhua Li
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexandra T. Tankka
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kevin D. Dong
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yan Song
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Eric L. Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L. Leibel
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92037, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA
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246
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Baddock HT, Brolih S, Yosaatmadja Y, Ratnaweera M, Bielinski M, Swift L, Cruz-Migoni A, Fan H, Keown JR, Walker AP, Morris G, Grimes J, Fodor E, Schofield C, Gileadi O, McHugh P. Characterization of the SARS-CoV-2 ExoN (nsp14ExoN-nsp10) complex: implications for its role in viral genome stability and inhibitor identification. Nucleic Acids Res 2022; 50:1484-1500. [PMID: 35037045 PMCID: PMC8860572 DOI: 10.1093/nar/gkab1303] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 12/19/2022] Open
Abstract
The SARS-CoV-2 coronavirus is the causal agent of the current global pandemic. SARS-CoV-2 belongs to an order, Nidovirales, with very large RNA genomes. It is proposed that the fidelity of coronavirus (CoV) genome replication is aided by an RNA nuclease complex, comprising the non-structural proteins 14 and 10 (nsp14-nsp10), an attractive target for antiviral inhibition. Our results validate reports that the SARS-CoV-2 nsp14-nsp10 complex has RNase activity. Detailed functional characterization reveals nsp14-nsp10 is a versatile nuclease capable of digesting a wide variety of RNA structures, including those with a blocked 3'-terminus. Consistent with a role in maintaining viral genome integrity during replication, we find that nsp14-nsp10 activity is enhanced by the viral RNA-dependent RNA polymerase complex (RdRp) consisting of nsp12-nsp7-nsp8 (nsp12-7-8) and demonstrate that this stimulation is mediated by nsp8. We propose that the role of nsp14-nsp10 in maintaining replication fidelity goes beyond classical proofreading by purging the nascent replicating RNA strand of a range of potentially replication-terminating aberrations. Using our developed assays, we identify drug and drug-like molecules that inhibit nsp14-nsp10, including the known SARS-CoV-2 major protease (Mpro) inhibitor ebselen and the HIV integrase inhibitor raltegravir, revealing the potential for multifunctional inhibitors in COVID-19 treatment.
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Affiliation(s)
- Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sanja Brolih
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Yuliana Yosaatmadja
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Malitha Ratnaweera
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Marcin Bielinski
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Lonnie P Swift
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Abimael Cruz-Migoni
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jeremy R Keown
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Alexander P Walker
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Garrett M Morris
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford OX1 3LB, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot OX11 0DE, UK
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
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247
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Wang X, Sacramento CQ, Jockusch S, Chaves OA, Tao C, Fintelman-Rodrigues N, Chien M, Temerozo JR, Li X, Kumar S, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Bozza PT, Russo JJ, Souza TML, Ju J. Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease and demonstrates COVID-19 therapeutic potential in viral cell culture. Commun Biol 2022; 5:154. [PMID: 35194144 PMCID: PMC8863796 DOI: 10.1038/s42003-022-03101-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/02/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.
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Affiliation(s)
- Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Carolina Q Sacramento
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Otávio Augusto Chaves
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Natalia Fintelman-Rodrigues
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Dinshaw J Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Patrícia T Bozza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Thiago Moreno L Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil. .,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA. .,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA. .,Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA.
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248
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Abstract
Molnupiravir (Lagevrio®) is an orally-administered antiviral prodrug that inhibits replication of RNA viruses through viral error induction. It is being developed by Merck and Ridgeback Biotherapeutics for the prevention and treatment of Coronavirus disease 2019 (COVID-19). Molnupiravir received its first approval on 4 November 2021 in the UK for the treatment of mild to moderate COVID-19 in adults with a positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic test and who have at least one risk factor for developing severe illness. Molnupiravir is filed for approval and has emergency use authorization for the treatment of COVID-19 in several countries, including the USA, Japan and those in the EU. This article summarizes the milestones in the development of molnupiravir leading to this first approval for COVID-19.
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249
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Obermeyer F, Jankowiak M, Barkas N, Schaffner SF, Pyle JD, Yurkovetskiy L, Bosso M, Park DJ, Babadi M, MacInnis BL, Luban J, Sabeti PC, Lemieux JE. Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.09.07.21263228. [PMID: 35194619 PMCID: PMC8863165 DOI: 10.1101/2021.09.07.21263228] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Repeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR 0 , a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR 0 to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR 0 forecasts growth of new lineages from their mutational profile, identifies viral lineages of concern as they emerge, and prioritizes mutations of biological and public health concern for functional characterization. ONE SENTENCE SUMMARY A Bayesian hierarchical model of all SARS-CoV-2 viral genomes predicts lineage fitness and identifies associated mutations.
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Affiliation(s)
- Fritz Obermeyer
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Pyro Committee, Linux AI & Data Foundation; 548 Market St San Francisco, California 94104
| | - Martin Jankowiak
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Pyro Committee, Linux AI & Data Foundation; 548 Market St San Francisco, California 94104
| | - Nikolaos Barkas
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Stephen F. Schaffner
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA, USA
| | - Jesse D. Pyle
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Lonya Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School; Worcester, MA 01605, USA
| | - Matteo Bosso
- Program in Molecular Medicine, University of Massachusetts Medical School; Worcester, MA 01605, USA
| | - Daniel J. Park
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Mehrtash Babadi
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
| | - Bronwyn L. MacInnis
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
| | - Jeremy Luban
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Program in Molecular Medicine, University of Massachusetts Medical School; Worcester, MA 01605, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard; 400 Technology Square, Cambridge, MA 02139, USA
| | - Pardis C. Sabeti
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University; Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness; Boston, MA 02115, USA
- Howard Hughes Medical Institute; 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Jacob E. Lemieux
- Broad Institute of MIT and Harvard; 415 Main Street, Cambridge, MA 02142, USA
- Division of Infectious Diseases, Massachusetts General Hospital; Boston, MA, USA
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250
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Zaffagni M, Harris JM, Patop IL, Pamudurti NR, Nguyen S, Kadener S. SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.07.02.450964. [PMID: 35194610 PMCID: PMC8863146 DOI: 10.1101/2021.07.02.450964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1,000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.
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