1
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Oo A, Chen Z, Cao D, Cho YJ, Liang B, Schinazi RF, Kim B. Biochemical simulation of mutation synthesis and repair during SARS-CoV-2 RNA polymerization. Virology 2024; 600:110255. [PMID: 39366027 DOI: 10.1016/j.virol.2024.110255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 09/24/2024] [Accepted: 09/27/2024] [Indexed: 10/06/2024]
Abstract
We biochemically simulated the mutation synthesis process of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex (nsp7/nsp8/nsp12) involving two sequential mechanistic steps that occur during genomic replication: misinsertion (incorporation of incorrect nucleotides) and mismatch extension. Then, we also simulated mismatch repair process catalyzed by the viral nsp10/nsp14 ExoN complex. In these mechanistic simulations, while SARS-CoV-2 RdRp displays efficient mutation synthesis capability, the viral ExoN complex was able to effectively repair the mismatch primers generated during the mutation synthesis. Also, we observed that the delayed RNA synthesis induced by mutation synthesis process was rescued by the viral ExoN activity. Collectively, our biochemical simulations suggest that SARS-CoV-2 ExoN complex may contribute to both maintenance of proper viral genetic diversity levels and successful completion of the viral large RNA genome replication by removing mismatches generated by the viral RdRp.
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Affiliation(s)
- Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Zhenhang Chen
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, 30329, USA
| | - Dongdong Cao
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, 30329, USA
| | - Young-Jae Cho
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Bo Liang
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, 30329, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, GA, 30322, USA.
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2
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Glasner DR, Daugherty MD. Unchecked growth: Pushing the limits on RNA virus genome size in the absence of known proofreading. Proc Natl Acad Sci U S A 2024; 121:e2414223121. [PMID: 39186661 PMCID: PMC11388401 DOI: 10.1073/pnas.2414223121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024] Open
Affiliation(s)
- Dustin R Glasner
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Matthew D Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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3
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Holmes EC. The Emergence and Evolution of SARS-CoV-2. Annu Rev Virol 2024; 11:21-42. [PMID: 38631919 DOI: 10.1146/annurev-virology-093022-013037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The origin of SARS-CoV-2 has evoked heated debate and strong accusations, yet seemingly little resolution. I review the scientific evidence on the origin of SARS-CoV-2 and its subsequent spread through the human population. The available data clearly point to a natural zoonotic emergence within, or closely linked to, the Huanan Seafood Wholesale Market in Wuhan. There is no direct evidence linking the emergence of SARS-CoV-2 to laboratory work conducted at the Wuhan Institute of Virology. The subsequent global spread of SARS-CoV-2 was characterized by a gradual adaptation to humans, with dual increases in transmissibility and virulence until the emergence of the Omicron variant. Of note has been the frequent transmission of SARS-CoV-2 from humans to other animals, marking it as a strongly host generalist virus. Unless lessons from the origin of SARS-CoV-2 are learned, it is inevitable that more zoonotic events leading to more epidemics and pandemics will plague human populations.
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Affiliation(s)
- Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia;
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4
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Ferreira Sa Antunes T, Huguet-Tapia JC, Elena SF, Folimonova SY. Intra-Host Citrus Tristeza Virus Populations during Prolonged Infection Initiated by a Well-Defined Sequence Variant in Nicotiana benthamiana. Viruses 2024; 16:1385. [PMID: 39339861 PMCID: PMC11437405 DOI: 10.3390/v16091385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 08/24/2024] [Accepted: 08/27/2024] [Indexed: 09/30/2024] Open
Abstract
Due to the error-prone nature of viral RNA-dependent RNA polymerases, the replication of RNA viruses results in a diversity of viral genomes harboring point mutations, deletions, insertions, and genome rearrangements. Citrus tristeza virus (CTV), a causal agent of diseases of economically important citrus species, shows intrinsic genetic stability. While the virus appears to have some mechanism that limits the accumulation of single-nucleotide variants, the production of defective viral genomes (DVGs) during virus infection has been reported for certain variants of CTV. The intra-host diversity generated during plant infection with variant T36 (CTV-T36) remains unclear. To address this, we analyzed the RNA species accumulated in the initially infected and systemic leaves of Nicotiana benthamiana plants inoculated with an infectious cDNA clone of CTV-T36, which warranted that infection was initiated by a known, well-defined sequence variant of the virus. CTV-T36 limited the accumulation of single-nucleotide mutants during infection. With that, four types of DVGs-deletions, insertions, and copy- and snap-backs-were found in all the samples, with deletions and insertions being the most common types. Hot-spots across the genome for DVG recombination and short direct sequence repeats suggest that sequence complementarity could mediate DVG formation. In conclusion, our study illustrates the formation of diverse DVGs during CTV-T36 infection. To the best of our knowledge, this is the first study that has analyzed the genetic variability and recombination of a well-defined sequence variant of CTV in an herbaceous host.
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Affiliation(s)
| | - José C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (T.F.S.A.); (J.C.H.-T.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, 46980 Valencia, Spain;
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Svetlana Y. Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (T.F.S.A.); (J.C.H.-T.)
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5
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Chayka A, Danda M, Dostálková A, Spiwok V, Klimešová A, Kapisheva M, Zgarbová M, Weber J, Ruml T, Rumlová M, Janeba Z. Developing Allosteric Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase. ChemMedChem 2024:e202400367. [PMID: 39140451 DOI: 10.1002/cmdc.202400367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/15/2024]
Abstract
The use of Fpocket and virtual screening techniques enabled us to identify potential allosteric druggable pockets within the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Of the compounds screened, compound 1 was identified as a promising inhibitor, lowering a SARS-CoV-2 RdRp activity to 57 % in an enzymatic assay at 10 μM concentration. The structure of compound 1 was subsequently optimized in order to preserve or enhance inhibitory activity. This involved the substitution of problematic ester and aromatic nitro groups with more inert functionalities. The N,N'-diphenylurea scaffold with two NH groups was identified as essential for the compound's activity but also exhibited high toxicity in Calu-3 cells. To address this issue, a scaffold hopping approach was employed to replace the urea core with potentially less toxic urea isosteres. This approach yielded several structural analogues with notable activity, specifically 2,2'-bisimidazol (in compound 55 with residual activity RA=42 %) and (1H-imidazol-2-yl)urea (in compounds 59 and 60, with RA=50 and 28 %, respectively). Despite these advances, toxicity remained a major concern. These compounds represent a promising starting point for further structure-activity relationship studies of allosteric inhibitors of SARS-CoV-2 RdRp, with the goal of reducing their cytotoxicity and improving aqueous solubility.
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Affiliation(s)
- Artem Chayka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Matěj Danda
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Anna Klimešová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Marina Kapisheva
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Michala Zgarbová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
- Department of Genetics and Microbiology, Charles University, Faculty of Sciences, Viničná 5, 12844, Prague 2, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 16628, Prague 6, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000, Prague 6, Czech Republic
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6
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Zhu Y, Yurgelonis I, Noell S, Yang Q, Guan S, Li Z, Hao L, Rothan H, Rai DK, McMonagle P, Baniecki ML, Greasley SE, Plotnikova O, Lee J, Nicki JA, Ferre R, Byrnes LJ, Liu W, Craig TK, Steppan CM, Liberator P, Soares HD, Allerton CMN, Anderson AS, Cardin RD. In vitro selection and analysis of SARS-CoV-2 nirmatrelvir resistance mutations contributing to clinical virus resistance surveillance. SCIENCE ADVANCES 2024; 10:eadl4013. [PMID: 39047088 PMCID: PMC11268423 DOI: 10.1126/sciadv.adl4013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
To facilitate the detection and management of potential clinical antiviral resistance, in vitro selection of drug-resistant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) against the virus Mpro inhibitor nirmatrelvir (Paxlovid active component) was conducted. Six Mpro mutation patterns containing T304I alone or in combination with T21I, L50F, T135I, S144A, or A173V emerged, with A173V+T304I and T21I+S144A+T304I mutations showing >20-fold resistance each. Biochemical analyses indicated inhibition constant shifts aligned to antiviral results, with S144A and A173V each markedly reducing nirmatrelvir inhibition and Mpro activity. SARS-CoV-2 surveillance revealed that in vitro resistance-associated mutations from our studies and those reported in the literature were rarely detected in the Global Initiative on Sharing All Influenza Data database. In the Paxlovid Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients trial, E166V was the only emergent resistance mutation, observed in three Paxlovid-treated patients, none of whom experienced COVID-19-related hospitalization or death.
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Affiliation(s)
- Yuao Zhu
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Irina Yurgelonis
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Stephen Noell
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Qingyi Yang
- Pfizer Worldwide Research, Development & Medical, Cambridge MA 02139, USA
| | - Shunjie Guan
- Pfizer Worldwide Research, Development & Medical, Cambridge MA 02139, USA
| | - Zhenghui Li
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Li Hao
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Hussin Rothan
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Devendra K. Rai
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Patricia McMonagle
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Mary Lynn Baniecki
- Pfizer Worldwide Research, Development & Medical, Cambridge MA 02139, USA
| | | | - Olga Plotnikova
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Jonathan Lee
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Jennifer A. Nicki
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - RoseAnn Ferre
- Pfizer Worldwide Research, Development & Medical, La Jolla, CA 92121, USA
| | - Laura J. Byrnes
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Wei Liu
- Pfizer Worldwide Research, Development & Medical, La Jolla, CA 92121, USA
| | - Timothy K. Craig
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | - Paul Liberator
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
| | - Holly D. Soares
- Pfizer Worldwide Research, Development & Medical, Groton, CT 06340, USA
| | | | | | - Rhonda D. Cardin
- Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA
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7
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Petrone ME, Grove J, Mélade J, Mifsud JCO, Parry RH, Marzinelli EM, Holmes EC. A ~40-kb flavi-like virus does not encode a known error-correcting mechanism. Proc Natl Acad Sci U S A 2024; 121:e2403805121. [PMID: 39018195 PMCID: PMC11287256 DOI: 10.1073/pnas.2403805121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/13/2024] [Indexed: 07/19/2024] Open
Abstract
It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order Nidovirales (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb. The recent discovery of large-genome flavi-like viruses (Flaviviridae), which comprise genomes up to 27 kb in length yet seemingly do not encode exonuclease domains, has led to the proposal that a proofreading mechanism is required to facilitate the expansion of nonsegmented RNA virus genomes above 30 kb. Herein, we describe a ~40 kb flavi-like virus identified in a Haliclona sponge metatranscriptome that does not encode a known exonuclease. Structural analysis revealed that this virus may have instead captured cellular domains associated with nucleic acid metabolism that have not been previously found in RNA viruses. Phylogenetic inference placed this virus as a divergent pesti-like lineage, such that we have provisionally termed it "Maximus pesti-like virus." This virus represents an instance of a flavi-like virus achieving a genome size comparable to that of the Nidovirales and demonstrates that RNA viruses have evolved multiple solutions to overcome the error threshold.
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Affiliation(s)
- Mary E. Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
| | - Joe Grove
- MRC-University of Glasgow Centre for Virus Research, GlasgowG61 1QH, United Kingdom
| | - Julien Mélade
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Jonathon C. O. Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Rhys H. Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4067, Australia
| | - Ezequiel M. Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
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8
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Ueno S, Amarbayasgalan S, Sugiura Y, Takahashi T, Shimizu K, Nakagawa K, Kawabata-Iwakawa R, Kamitani W. Eight-amino-acid sequence at the N-terminus of SARS-CoV-2 nsp1 is involved in stabilizing viral genome replication. Virology 2024; 595:110068. [PMID: 38593595 DOI: 10.1016/j.virol.2024.110068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/11/2024]
Abstract
Coronavirus disease 19 is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) enveloped virus with a single-stranded positive-sense ribonucleic acid (RNA) genome. The CoV non-structural protein (nsp) 1 is a multifunctional protein that undergoes translation shutoff, messenger RNA (mRNA) cleavage, and RNA binding. The C-terminal region is involved in translational shutoff and RNA cleavage. The N-terminal region of SARS-CoV-2 nsp1 is highly conserved among isolated SARS-CoV-2 variants. However, the I-004 variant, isolated during the early SARS-CoV-2 pandemic, lost eight amino acids in the nsp1 region. In this study, we showed that the eight amino acids are important for viral replication in infected interferon-incompetent cells and that the recombinant virus that lost these amino acids had low pathogenicity in the lungs of hamster models. The loss of eight amino acids-induced mutations occurred in the 5' untranslated region (UTR), suggesting that nsp1 contributes to the stability of the viral genome during replication.
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Affiliation(s)
- Shiori Ueno
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | | | - Yoshiro Sugiura
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Tatsuki Takahashi
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Kenta Shimizu
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan
| | - Keisuke Nakagawa
- Laboratory of Veterinary Microbiology, Joint Department of Veterinary Medicine, Gifu University, Yanagido, Gifu, Japan
| | - Reika Kawabata-Iwakawa
- Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, Gunma University, Gunma, Japan
| | - Wataru Kamitani
- Department of Infectious Diseases and Host Defense, Graduate School of Medicine, Gunma University, Gunma, Japan.
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9
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Steiner S, Kratzel A, Barut GT, Lang RM, Aguiar Moreira E, Thomann L, Kelly JN, Thiel V. SARS-CoV-2 biology and host interactions. Nat Rev Microbiol 2024; 22:206-225. [PMID: 38225365 DOI: 10.1038/s41579-023-01003-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
The zoonotic emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease 2019 (COVID-19) pandemic have profoundly affected our society. The rapid spread and continuous evolution of new SARS-CoV-2 variants continue to threaten global public health. Recent scientific advances have dissected many of the molecular and cellular mechanisms involved in coronavirus infections, and large-scale screens have uncovered novel host-cell factors that are vitally important for the virus life cycle. In this Review, we provide an updated summary of the SARS-CoV-2 life cycle, gene function and virus-host interactions, including recent landmark findings on general aspects of coronavirus biology and newly discovered host factors necessary for virus replication.
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Affiliation(s)
- Silvio Steiner
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Annika Kratzel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - G Tuba Barut
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Reto M Lang
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Etori Aguiar Moreira
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Lisa Thomann
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- European Virus Bioinformatics Center, Jena, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern and Mittelhäusern, Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
- European Virus Bioinformatics Center, Jena, Germany.
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10
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Rabie AM, Eltayb WA. Potent Dual Polymerase/Exonuclease Inhibitory Activities of Antioxidant Aminothiadiazoles Against the COVID-19 Omicron Virus: A Promising In Silico/In Vitro Repositioning Research Study. Mol Biotechnol 2024; 66:592-611. [PMID: 36690820 PMCID: PMC9870775 DOI: 10.1007/s12033-022-00551-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/10/2022] [Indexed: 01/25/2023]
Abstract
Recently, natural and synthetic nitrogenous heterocyclic antivirals topped the scene as first choices for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying disease, the coronavirus disease 2019 (COVID-19). Meanwhile, the mysterious evolution of a new strain of SARS-CoV-2, the Omicron variant and its sublineages, caused a new defiance in the continual COVID-19 battle. Hitting the two principal coronaviral-2 multiplication enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) synchronously using the same ligand is a highly effective novel dual pathway to hinder SARS-CoV-2 reproduction and stop COVID-19 progression irrespective of the SARS-CoV-2 variant type since RdRps and ExoNs are widely conserved among all SARS-CoV-2 strains. Herein, the present computational/biological study screened our previous small libraries of nitrogenous heterocyclic compounds, searching for the most ideal drug candidates predictably able to efficiently act through this double approach. Theoretical filtration gave rise to three promising antioxidant nitrogenous heterocyclic compounds of the 1,3,4-thiadiazole type, which are CoViTris2022, Taroxaz-26, and ChloViD2022. Further experimental evaluation proved for the first time, utilizing the in vitro anti-RdRp/ExoN and anti-SARS-CoV-2 bioassays, that ChloViD2022, CoViTris2022, and Taroxaz-26 could effectively inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of 0.17 and 0.41 μM for ChloViD2022, 0.21 and 0.69 μM for CoViTris2022, and 0.23 and 0.73 μM for Taroxaz-26, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico outcomes greatly supported these biochemical results, proposing that the three molecules potently strike the key catalytic pockets of the SARS-CoV-2 (Omicron variant) RdRp's and ExoN's vital active sites. Moreover, the idealistic pharmacophoric hallmarks of CoViTris2022, Taroxaz-26, and ChloViD2022 molecules relatively make them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading, with their highly flexible structures open for various kinds of chemical derivatization. To cut it short, the present pivotal findings of this comprehensive work disclosed the promising repositioning potentials of the three 2-aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, to successfully interfere with the crucial biological interactions of the coronaviral-2 polymerase/exoribonuclease with the four principal RNA nucleotides, and, as a result, cure COVID-19 infection, encouraging us to rapidly start the three drugs' broad preclinical/clinical anti-COVID-19 evaluations.
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Affiliation(s)
- Amgad M Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City, Mansoura, 35511, Dakahlia Governorate, Egypt.
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City, Dikernis, 35744, Dakahlia Governorate, Egypt.
| | - Wafa A Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi, Nher Anile, Sudan.
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11
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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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12
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Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
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Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
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13
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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14
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Liu C, Huang W, He X, Feng Z, Chen Q. Research Advances on Swine Acute Diarrhea Syndrome Coronavirus. Animals (Basel) 2024; 14:448. [PMID: 38338091 PMCID: PMC10854734 DOI: 10.3390/ani14030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a virulent pathogen that causes acute diarrhea in piglets. The virus was first discovered in Guangdong Province, China, in 2017 and has since emerged in Jiangxi, Fujian, and Guangxi Provinces. The outbreak exhibited a localized and sporadic pattern, with no discernable temporal continuity. The virus can infect human progenitor cells and demonstrates considerable potential for cross-species transmission, representing a potential risk for zoonotic transmission. Therefore, continuous surveillance of and comprehensive research on SADS-CoV are imperative. This review provides an overview of the temporal and evolutionary features of SADS-CoV outbreaks, focusing on the structural characteristics of the virus, which serve as the basis for discussing its potential for interspecies transmission. Additionally, the review summarizes virus-host interactions, including the effects on host cells, as well as apoptotic and autophagic behaviors, and discusses prevention and treatment modalities for this viral infection.
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Affiliation(s)
- Chuancheng Liu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Weili Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Xinyan He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Zhihua Feng
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
| | - Qi Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; (C.L.); (W.H.); (X.H.)
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, Fujian Normal University, Fuzhou 350117, China
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15
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Martin MF, Bonaventure B, McCray NE, Peersen OB, Rozen-Gagnon K, Stapleford KA. Distinct chikungunya virus polymerase palm subdomains contribute to virus replication and virion assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575630. [PMID: 38293111 PMCID: PMC10827052 DOI: 10.1101/2024.01.15.575630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Alphaviruses encode an error-prone RNA-dependent RNA polymerase (RdRp), nsP4, required for genome synthesis, yet how the RdRp functions in the complete alphavirus life cycle is not well-defined. Previous work using chikungunya virus (CHIKV) has established the importance of the nsP4 residue cysteine 483 in maintaining viral genetic fidelity. Given the location of residue C483 in the nsP4 palm domain, we hypothesized that other residues within this domain and surrounding subdomains would also contribute to polymerase function. To test this hypothesis, we designed a panel of nsP4 variants via homology modeling based on the Coxsackievirus B3 3 polymerase. We rescued each variant in both mammalian and mosquito cells and discovered that the palm domain and ring finger subdomain contribute to polymerase host-specific replication and genetic stability. Surprisingly, in mosquito cells, these variants in the ring finger and palm domain were replication competent and produced viral structural proteins, but they were unable to produce infectious progeny, indicating a yet uncharacterized role for the polymerase in viral assembly. Finally, we have identified additional residues in the nsP4 palm domain that influence the genetic diversity of the viral progeny, potentially via an alteration in NTP binding and/or discrimination by the polymerase. Taken together, these studies highlight that distinct nsP4 subdomains regulate multiple processes of the alphavirus life cycle, placing nsP4 in a central role during the switch from RNA synthesis to packaging and assembly.
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Affiliation(s)
- Marie-France Martin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nia E. McCray
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Olve B. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
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16
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Mattiuz G, Di Giorgio S, Conticello SG. An elusive debate on the evidence for RNA editing in SARS-CoV-2. RNA Biol 2024; 21:1-2. [PMID: 38426405 PMCID: PMC10913694 DOI: 10.1080/15476286.2024.2321032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Giorgio Mattiuz
- Department of Experimental and Clinical Medicine, University of Florence, Firenze, Italy
| | - Salvatore Di Giorgio
- German Cancer Research Center (DKFZ) - Division of Immune Diversity, Foundation under Public Law, Heidelberg, Germany
| | - Silvestro G. Conticello
- Core Research Laboratory, ISPRO, Firenze, Italy
- Institute of Clinical Physiology, National Research Council, Pisa, Italy
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17
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Huang C, Mantlo E, Paessler S. Lassa virus NP DEDDh 3'-5' exoribonuclease activity is required for optimal viral RNA replication and mutation control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536665. [PMID: 37090668 PMCID: PMC10120729 DOI: 10.1101/2023.04.12.536665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Lassa virus (LASV), a mammarenavirus from Arenaviridae, is the causative agent of Lassa fever (LF) endemic in West Africa. Currently, there are no vaccines or antivirals approved for LF. The RNA-dependent RNA polymerases (RdRp) of RNA viruses are error-prone. As a negative-sense RNA virus, how LASV copes with errors in RNA synthesis and ensures optimal RNA replication are not well elucidated. LASV nucleoprotein (NP) contains a DEDDH 3'-to-5' exoribonuclease motif (ExoN), which is known to be essential for LASV evasion of the interferon response via its ability to degrade virus-derived double-stranded RNA. Herein, we present evidence that LASV NP ExoN has an additional function important for viral RNA replication. We rescued an ExoN-deficient LASV mutant (ExoN- rLASV) by using a reverse genetics system. Our data indicated that abrogation of NP ExoN led to impaired LASV growth and RNA replication in interferon-deficient cells as compared with wild-type rLASV. By utilizing PacBio Single Molecule, Real-Time (SMRT) long-read sequencing technology, we found that rLASV lacking ExoN activity was prone to producing aberrant viral genomic RNA with structural variations. In addition, NP ExoN deficiency enhanced LASV sensitivity to mutagenic nucleoside analogues in virus titration assay. Next-generation deep sequencing analysis showed increased single nucleotide substitution in ExoN- LASV RNA following mutagenic 5-flurouracil treatment. In conclusion, our study revealed that LASV NP ExoN is required for efficient viral RNA replication and mutation control. Among negative-sense RNA viruses, LASV NP is the first example that a viral protein, other than the RdRp, contributes to reduce errors in RNA replication and maintain genomic RNA integrity. These new findings promote our understanding of the basics of LASV infection and inform antiviral and vaccine development.
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Affiliation(s)
- Cheng Huang
- Department of Pathology, Galveston National Laboratory and
Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
TX, USA
| | - Emily Mantlo
- Department of Pathology, Galveston National Laboratory and
Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
TX, USA
- Current address: Department of Microbiology & Immunology,
Upstate Medical University, Syracuse, NY, USA
| | - Slobodan Paessler
- Department of Pathology, Galveston National Laboratory and
Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston,
TX, USA
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18
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Kurkowiak M, Fletcher S, Daniels A, Mozolewski P, Silvestris DA, Król E, Marek-Trzonkowska N, Hupp T, Tait-Burkard C. Differential RNA editing landscapes in host cell versus the SARS-CoV-2 genome. iScience 2023; 26:108031. [PMID: 37876814 PMCID: PMC10590966 DOI: 10.1016/j.isci.2023.108031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/09/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
The SARS-CoV-2 pandemic was defined by the emergence of new variants formed through virus mutation originating from random errors not corrected by viral proofreading and/or the host antiviral response introducing mutations into the viral genome. While sequencing information hints at cellular RNA editing pathways playing a role in viral evolution, here, we use an in vitro human cell infection model to assess RNA mutation types in two SARS-CoV-2 strains representing the original and the alpha variants. The variants showed both different cellular responses and mutation patterns with alpha showing higher mutation frequency with most substitutions observed being C-U, indicating an important role for apolipoprotein B mRNA editing catalytic polypeptide-like editing. Knockdown of select APOBEC3s through RNAi increased virus production in the original virus, but not in alpha. Overall, these data suggest a deaminase-independent anti-viral function of APOBECs in SARS-CoV-2 while the C-U editing itself might function to enhance genetic diversity enabling evolutionary adaptation.
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Affiliation(s)
- Małgorzata Kurkowiak
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | - Sarah Fletcher
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
| | - Alison Daniels
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
- Infection Medicine, University of Edinburgh, Little France Crescent, UK
| | - Paweł Mozolewski
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
| | | | - Ewelina Król
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine Medical University of Gdańsk, Gdańsk, Poland
| | - Ted Hupp
- International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland
- Cell Signalling Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Christine Tait-Burkard
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK
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19
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Rabie AM, Abdel-Dayem MA, Abdalla M. Promising Experimental Anti-SARS-CoV-2 Agent "SLL-0197800": The Prospective Universal Inhibitory Properties against the Coming Versions of the Coronavirus. ACS OMEGA 2023; 8:35538-35554. [PMID: 37810715 PMCID: PMC10552502 DOI: 10.1021/acsomega.2c08073] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/22/2023] [Indexed: 10/10/2023]
Abstract
Isoquinoline derivatives having some nucleosidic structural features are considered as candidate choices for effective remediation of the different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their following disease, the coronavirus disease 2019 (COVID-19). SLL-0197800 is a recently discovered isoquinoline compound with potential strong universal anticoronaviral activities against SARS-CoV-2 and its previous strains. SLL-0197800 nonspecifically hits the main protease (Mpro) enzyme of the different coronaviruses. Herein in the present study, we tested the probability of the previous findings of this experimental agent to be extended to comprise any coronavirus through concurrently disrupting the mutable-less replication enzymes like the RNA-dependent RNA polymerase (RdRp) protein as well as the 3'-to-5' exoribonuclease (ExoN) protein. The in vitro anti-RdRp/ExoN assay revealed the potent inhibitory activities of SLL-0197800 on the coronaviral replication with minute values of anti-RdRp and anti-RdRp/ExoN EC50 (about 0.16 and 0.27 μM, respectively). The preliminary in silico outcomes significantly supported these biochemical findings. To put it simply, the present important results of these extension efforts greatly reinforce and extend the SLL-0197800's preceding findings, showing that the restraining/blocking actions (i.e., inhibitory activities) of this novel investigational anti-SARS-CoV-2 agent against the Mpro protein could be significantly extended against other copying and multiplication enzymes such as RdRp and ExoN, highlighting the potential use of SLL-0197800 against the coming versions of the homicidal coronavirus (if any), i.e., revealing the probable nonspecific anticoronaviral features and qualities of this golden experimental drug against nearly any coronaviral strain, for instance, SARS-CoV-3.
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Affiliation(s)
- Amgad M. Rabie
- Dr.
Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt
- Head
of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia
Governorate, Egypt
| | - Marwa A. Abdel-Dayem
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Horus University—Egypt (HUE), New Damietta 34518, Damietta Governorate, Egypt
| | - Mohnad Abdalla
- Key
Laboratory of Chemical Biology (Ministry of Education), Department
of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College
of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province 250012, PR China
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20
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Grimes SL, Choi YJ, Banerjee A, Small G, Anderson-Daniels J, Gribble J, Pruijssers AJ, Agostini ML, Abu-Shmais A, Lu X, Darst SA, Campbell E, Denison MR. A mutation in the coronavirus nsp13-helicase impairs enzymatic activity and confers partial remdesivir resistance. mBio 2023; 14:e0106023. [PMID: 37338298 PMCID: PMC10470589 DOI: 10.1128/mbio.01060-23] [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: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 06/21/2023] Open
Abstract
Coronaviruses (CoVs) encode nonstructural proteins 1-16 (nsps 1-16) which form replicase complexes that mediate viral RNA synthesis. Remdesivir (RDV) is an adenosine nucleoside analog antiviral that inhibits CoV RNA synthesis. RDV resistance mutations have been reported only in the nonstructural protein 12 RNA-dependent RNA polymerase (nsp12-RdRp). We here show that a substitution mutation in the nsp13-helicase (nsp13-HEL A335V) of the betacoronavirus murine hepatitis virus (MHV) that was selected during passage with the RDV parent compound confers partial RDV resistance independently and additively when expressed with co-selected RDV resistance mutations in the nsp12-RdRp. The MHV A335V substitution did not enhance replication or competitive fitness compared to WT MHV and remained sensitive to the active form of the cytidine nucleoside analog antiviral molnupiravir (MOV). Biochemical analysis of the SARS-CoV-2 helicase encoding the homologous substitution (A336V) demonstrates that the mutant protein retained the ability to associate with the core replication proteins nsps 7, 8, and 12 but had impaired helicase unwinding and ATPase activity. Together, these data identify a novel determinant of nsp13-HEL enzymatic activity, define a new genetic pathway for RDV resistance, and demonstrate the importance of surveillance for and testing of helicase mutations that arise in SARS-CoV-2 genomes. IMPORTANCE Despite the development of effective vaccines against COVID-19, the continued circulation and emergence of new variants support the need for antivirals such as RDV. Understanding pathways of antiviral resistance is essential for surveillance of emerging variants, development of combination therapies, and for identifying potential new targets for viral inhibition. We here show a novel RDV resistance mutation in the CoV helicase also impairs helicase functions, supporting the importance of studying the individual and cooperative functions of the replicase nonstructural proteins 7-16 during CoV RNA synthesis. The homologous nsp13-HEL mutation (A336V) has been reported in the GISAID database of SARS-CoV-2 genomes, highlighting the importance of surveillance of and genetic testing for nucleoside analog resistance in the helicase.
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Affiliation(s)
- Samantha L. Grimes
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Young J. Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
- Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Gabriel Small
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Jordan Anderson-Daniels
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jennifer Gribble
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrea J. Pruijssers
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
| | - Maria L. Agostini
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandra Abu-Shmais
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Xiaotao Lu
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Elizabeth Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Mark R. Denison
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
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21
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Kawasaki Y, Abe H, Yasuda J. Comparison of genome replication fidelity between SARS-CoV-2 and influenza A virus in cell culture. Sci Rep 2023; 13:13105. [PMID: 37567927 PMCID: PMC10421855 DOI: 10.1038/s41598-023-40463-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/10/2023] [Indexed: 08/13/2023] Open
Abstract
Since the emergence of COVID-19, several SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) variants have emerged and spread widely. These variants are produced through replication errors of the viral genome by viral RNA-dependent RNA polymerase (RdRp). Seasonal epidemics of influenza are also known to occur because of new variants of influenza A virus (IAV), which are generated by the introduction of mutations by viral RdRp with low fidelity. Variants with different antigenicities appear because of mutations in envelope glycoproteins. In this study, we calculated and compared the mutation rates in genome replication of IAV and SARS-CoV-2. Average mutation rates per passage were 9.01 × 10-5 and 3.76 × 10-6 substitutions/site for IAV and SARS-CoV-2, respectively. The mutation rate of SARS-CoV-2 was 23.9-fold lower than that of IAV because of the proofreading activity of the SARS-CoV-2 RdRp complex. Our data could be useful in establishing effective countermeasures against COVID-19.
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Affiliation(s)
- Yoshiko Kawasaki
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Haruka Abe
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
- Graduate School of Biomedical Science, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
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22
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Biancolella M, Colona VL, Luzzatto L, Watt JL, Mattiuz G, Conticello SG, Kaminski N, Mehrian-Shai R, Ko AI, Gonsalves GS, Vasiliou V, Novelli G, Reichardt JKV. COVID-19 annual update: a narrative review. Hum Genomics 2023; 17:68. [PMID: 37488607 PMCID: PMC10367267 DOI: 10.1186/s40246-023-00515-2] [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: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/26/2023] Open
Abstract
Three and a half years after the pandemic outbreak, now that WHO has formally declared that the emergency is over, COVID-19 is still a significant global issue. Here, we focus on recent developments in genetic and genomic research on COVID-19, and we give an outlook on state-of-the-art therapeutical approaches, as the pandemic is gradually transitioning to an endemic situation. The sequencing and characterization of rare alleles in different populations has made it possible to identify numerous genes that affect either susceptibility to COVID-19 or the severity of the disease. These findings provide a beginning to new avenues and pan-ethnic therapeutic approaches, as well as to potential genetic screening protocols. The causative virus, SARS-CoV-2, is still in the spotlight, but novel threatening virus could appear anywhere at any time. Therefore, continued vigilance and further research is warranted. We also note emphatically that to prevent future pandemics and other world-wide health crises, it is imperative to capitalize on what we have learnt from COVID-19: specifically, regarding its origins, the world's response, and insufficient preparedness. This requires unprecedented international collaboration and timely data sharing for the coordination of effective response and the rapid implementation of containment measures.
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Affiliation(s)
| | - Vito Luigi Colona
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy
| | - Lucio Luzzatto
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- University of Florence, 50121, Florence, Italy
| | - Jessica Lee Watt
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, QLD, 4878, Australia
| | | | - Silvestro G Conticello
- Core Research Laboratory, Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Florence, Italy
- Institute of Clinical Physiology - National Council of Research (IFC-CNR), 56124, Pisa, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ruty Mehrian-Shai
- Pediatric Hemato-Oncology, Edmond and Lilly Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 2 Sheba Road, 52621, Ramat Gan, Israel
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Instituto Gonçalo MonizFundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Gregg S Gonsalves
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, USA
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, School of Medicine and Surgery, Tor Vergata University of Rome, Via Montpellier 1, 00133, Rome, Italy.
- IRCCS Neuromed, 86077, Pozzilli, IS, Italy.
- Department of Pharmacology, School of Medicine, University of Nevada, 89557, Reno, NV, USA.
| | - Juergen K V Reichardt
- Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, QLD, 4878, Australia
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23
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Sexton NR, Cline PJ, Gallichotte EN, Fitzmeyer E, Young MC, Janich AJ, Pabilonia KL, Ehrhart N, Ebel GD. SARS-CoV-2 entry into and evolution within a skilled nursing facility. Sci Rep 2023; 13:11657. [PMID: 37468595 DOI: 10.1038/s41598-023-38544-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
SARS-CoV-2 belongs to the family Coronaviridae which includes multiple human pathogens that have an outsized impact on aging populations. As a novel human pathogen, SARS-CoV-2 is undergoing continuous adaptation to this new host species and there is evidence of this throughout the scientific and public literature. However, most investigations of SARS-CoV-2 evolution have focused on large-scale collections of data across diverse populations and/or living environments. Here we investigate SARS-CoV-2 evolution in epidemiologically linked individuals within a single outbreak at a skilled nursing facility beginning with initial introduction of the pathogen. The data demonstrate that SARS-CoV-2 was introduced to the facility multiple times without establishing an interfacility transmission chain, followed by a single introduction that infected many individuals within a week. This large-scale introduction by a single genotype then persisted in the facility. SARS-CoV-2 sequences were investigated at both the consensus and intra-host variation levels. Understanding the variability in SARS-CoV-2 during transmission chains will assist in understanding the spread of this disease and can ultimately inform best practices for mitigation strategies.
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Affiliation(s)
- Nicole R Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68504, USA
| | - Parker J Cline
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Emily N Gallichotte
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Emily Fitzmeyer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael C Young
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ashley J Janich
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Nicole Ehrhart
- Columbine Health Systems Center for Healthy Aging and Department of Clinical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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24
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Lin X, Sha Z, Trimpert J, Kunec D, Jiang C, Xiong Y, Xu B, Zhu Z, Xue W, Wu H. The NSP4 T492I mutation increases SARS-CoV-2 infectivity by altering non-structural protein cleavage. Cell Host Microbe 2023; 31:1170-1184.e7. [PMID: 37402373 DOI: 10.1016/j.chom.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/13/2023] [Accepted: 06/09/2023] [Indexed: 07/06/2023]
Abstract
The historically dominant SARS-CoV-2 Delta variant and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on in silico analyses, we hypothesized that the T492I mutation increases viral transmissibility and adaptability, which we confirmed with competition experiments in hamster and human airway tissue culture models. Furthermore, we showed that the T492I mutation increases the replication capacity and infectiveness of the virus and improves its ability to evade host immune responses. Mechanistically, the T492I mutation increases the cleavage efficiency of the viral main protease NSP5 by enhancing enzyme-substrate binding, which increases production of nearly all non-structural proteins processed by NSP5. Importantly, the T492I mutation suppresses viral-RNA-associated chemokine production in monocytic macrophages, which may contribute to the attenuated pathogenicity of Omicron variants. Our results highlight the importance of NSP4 adaptation in the evolutionary dynamics of SARS-CoV-2.
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Affiliation(s)
- Xiaoyuan Lin
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China; Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Zhou Sha
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Chen Jiang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Binbin Xu
- School of Pharmaceutical Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China
| | - Zhenglin Zhu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China.
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China.
| | - Haibo Wu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Road, Shapingba, Chongqing 401331, China.
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25
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von Delft A, Hall MD, Kwong AD, Purcell LA, Saikatendu KS, Schmitz U, Tallarico JA, Lee AA. Accelerating antiviral drug discovery: lessons from COVID-19. Nat Rev Drug Discov 2023; 22:585-603. [PMID: 37173515 PMCID: PMC10176316 DOI: 10.1038/s41573-023-00692-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2023] [Indexed: 05/15/2023]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, a wave of rapid and collaborative drug discovery efforts took place in academia and industry, culminating in several therapeutics being discovered, approved and deployed in a 2-year time frame. This article summarizes the collective experience of several pharmaceutical companies and academic collaborations that were active in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antiviral discovery. We outline our opinions and experiences on key stages in the small-molecule drug discovery process: target selection, medicinal chemistry, antiviral assays, animal efficacy and attempts to pre-empt resistance. We propose strategies that could accelerate future efforts and argue that a key bottleneck is the lack of quality chemical probes around understudied viral targets, which would serve as a starting point for drug discovery. Considering the small size of the viral proteome, comprehensively building an arsenal of probes for proteins in viruses of pandemic concern is a worthwhile and tractable challenge for the community.
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Affiliation(s)
- Annette von Delft
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Oxford Biomedical Research Centre, National Institute for Health Research, University of Oxford, Oxford, UK.
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | | | | | | | | | | | - Alpha A Lee
- PostEra, Inc., Cambridge, MA, USA.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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26
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Wang H, Liu Y, Li P, Liu C, Li K, Cao L, Zhang Y, Cheng Z, Huang K, Zheng Z, Xin X, Liu Y, Peng X, Liang D, Ke B, Wang T, Chen Q, Luo W, Qin C, Sun L, Chen G, Luo OJ, Li J, Zhang Q, Di B, Zhang Z, Ke C, Jia H, Gao F. Emergence of epidemic variants of SARS-CoV-2 by acquiring combinations of new highly mutable nucleotides in its genome. J Infect 2023; 86:588-592. [PMID: 36889511 PMCID: PMC9987606 DOI: 10.1016/j.jinf.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023]
Affiliation(s)
- Hui Wang
- Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Yuqi Liu
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, 100071, China
| | - Chaowu Liu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangzhou, 510070, Guangdong, China
| | - Kuibiao Li
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, Guangdong, China
| | - Lan Cao
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, Guangdong, China
| | - Ying Zhang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, Guangdong, China
| | - Zichun Cheng
- Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Kailing Huang
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou, 510700, Guangdong, China
| | - Zhouxia Zheng
- Guangzhou Mendel Genomics and Medical Technology Co., Ltd., Guangzhou, 510700, Guangdong, China
| | - Xiaoqian Xin
- Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Yifeng Liu
- Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Xiaofang Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China
| | - Dan Liang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China
| | - Tao Wang
- Shantou University Medical College, Shantou, 515000, Guangdong, China
| | - Qingpei Chen
- Medical Big Data Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
| | - Weihua Luo
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Chaolang Qin
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Lihong Sun
- Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, Guangdong, China
| | - Guobing Chen
- Department of Microbiology and Immunology, Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, Shanghai, 200438, China
| | - Qiao Zhang
- Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China
| | - Biao Di
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, Guangdong, China
| | - Zhoubin Zhang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, Guangdong, China.
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, 511430, Guangdong, China.
| | - Hongling Jia
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
| | - Feng Gao
- Institute of Molecular and Medical Virology, Key Laboratory of Ministry of Education for Viral Pathogenesis & Infection Prevention and Control,School of Medicine, Jinan University, Guangzhou, 510632, Guangdong, China.
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27
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Abdalla M, Rabie AM. Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant. Comput Biol Chem 2023; 104:107768. [PMID: 36842392 PMCID: PMC9450471 DOI: 10.1016/j.compbiolchem.2022.107768] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 09/04/2022] [Indexed: 01/18/2023]
Abstract
Nucleoside analogs/derivatives (NAs/NDs) with potent antiviral activities are now deemed very convenient choices for the treatment of coronavirus disease 2019 (COVID-19) arisen by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. At the same time, the appearance of a new strain of SARS-CoV-2, the Omicron variant, necessitates multiplied efforts in fighting COVID-19. Counteracting the crucial SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) jointly altogether using the same inhibitor is a quite successful new plan to demultiplicate SARS-CoV-2 particles and eliminate COVID-19 whatever the SARS-CoV-2 subtype is (due to the significant conservation nature of RdRps and ExoNs in the different SARS-CoV-2 strains). Successive in silico screening of known NAs finally disclosed six different promising NAs, which are riboprine/forodesine/tecadenoson/nelarabine/vidarabine/maribavir, respectively, that predictably can act through the planned dual-action mode. Further in vitro evaluations affirmed the anti-SARS-CoV-2/anti-COVID-19 potentials of these NAs, with riboprine and forodesine being at the top. The two NAs are able to effectively antagonize the replication of the new virulent SARS-CoV-2 strains with considerably minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of 189 and 408 nM for riboprine and 207 and 657 nM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. Furthermore, the favorable structural characteristics of the two molecules qualify them for varied types of isosteric and analogistic chemical derivatization. In one word, the present important outcomes of this comprehensive dual study revealed the anticipating repurposing potentials of some known nucleosides, led by the two NAs riboprine and forodesine, to successfully discontinue the coronaviral-2 polymerase/exoribonuclease interactions with RNA nucleotides in the SARS-CoV-2 Omicron variant (BA.5 sublineage) and accordingly alleviate COVID-19 infections, motivating us to initiate the two drugs' diverse anti-COVID-19 pharmacological evaluations to add both of them betimes in the COVID-19 therapeutic protocols.
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Affiliation(s)
- Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, PR China.
| | - Amgad M. Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt,Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt,Correspondence to: 16 Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt
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28
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Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene. iScience 2023; 26:106210. [PMID: 36811085 PMCID: PMC9933857 DOI: 10.1016/j.isci.2023.106210] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/23/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), encode a proofreading exonuclease, nonstructural protein 14 (nsp14), that helps ensure replication competence at a low evolutionary rate compared with other RNA viruses. In the current pandemic, SARS-CoV-2 has accumulated diverse genomic mutations including in nsp14. Here, to clarify whether amino acid substitutions in nsp14 affect the genomic diversity and evolution of SARS-CoV-2, we searched for amino acid substitutions in nature that may interfere with nsp14 function. We found that viruses carrying a proline-to-leucine change at position 203 (P203L) have a high evolutionary rate and that a recombinant SARS-CoV-2 virus with the P203L mutation acquired more diverse genomic mutations than wild-type virus during its replication in hamsters. Our findings suggest that substitutions, such as P203L, in nsp14 may accelerate the genomic diversity of SARS-CoV-2, contributing to virus evolution during the pandemic.
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29
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Cable J, Denison MR, Kielian M, Jackson WT, Bartenschlager R, Ahola T, Mukhopadhyay S, Fremont DH, Kuhn RJ, Shannon A, Frazier MN, Yuen KY, Coyne CB, Wolthers KC, Ming GL, Guenther CS, Moshiri J, Best SM, Schoggins JW, Jurado KA, Ebel GD, Schäfer A, Ng LFP, Kikkert M, Sette A, Harris E, Wing PAC, Eggenberger J, Krishnamurthy SR, Mah MG, Meganck RM, Chung D, Maurer-Stroh S, Andino R, Korber B, Perlman S, Shi PY, Bárcena M, Aicher SM, Vu MN, Kenney DJ, Lindenbach BD, Nishida Y, Rénia L, Williams EP. Positive-strand RNA viruses-a Keystone Symposia report. Ann N Y Acad Sci 2023; 1521:46-66. [PMID: 36697369 PMCID: PMC10347887 DOI: 10.1111/nyas.14957] [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] [Indexed: 01/27/2023]
Abstract
Positive-strand RNA viruses have been the cause of several recent outbreaks and epidemics, including the Zika virus epidemic in 2015, the SARS outbreak in 2003, and the ongoing SARS-CoV-2 pandemic. On June 18-22, 2022, researchers focusing on positive-strand RNA viruses met for the Keystone Symposium "Positive-Strand RNA Viruses" to share the latest research in molecular and cell biology, virology, immunology, vaccinology, and antiviral drug development. This report presents concise summaries of the scientific discussions at the symposium.
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Affiliation(s)
| | - Mark R Denison
- Department of Pediatrics and Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center; and Vanderbilt Institute for Infection, Immunology, and Inflammation, Nashville, Tennessee, USA
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - William T Jackson
- Department of Microbiology and Immunology and Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University and German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg, Germany
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | | | - Daved H Fremont
- Department of Pathology & Immunology; Department of Molecular Microbiology; and Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ashleigh Shannon
- Architecture et Fonction des Macromolécules Biologiques, CNRS and Aix Marseille Université, Marseille, France
| | - Meredith N Frazier
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, People's Republic of China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong, People's Republic of China
| | - Carolyn B Coyne
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, USA
| | - Katja C Wolthers
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam and Amsterdam Institute for Infection and Immunity, OrganoVIR Labs, Amsterdam, The Netherlands
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jasmine Moshiri
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - John W Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kellie Ann Jurado
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory D Ebel
- Center for Vector-borne Infectious Diseases, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lisa F P Ng
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Peter A C Wing
- Nuffield Department of Medicine and Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology and NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marcus G Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore City, Singapore
| | - Rita M Meganck
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Donghoon Chung
- Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, Texas, USA
| | - Sebastian Maurer-Stroh
- Yong Loo Lin School of Medicine and Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore City, Singapore
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, and Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Montserrat Bárcena
- Section Electron Microscopy, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sophie-Marie Aicher
- Institut Pasteurgrid, Université de Paris Cité, Virus Sensing and Signaling Unit, Paris, France
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Devin J Kenney
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yukiko Nishida
- Chugai Pharmaceutical, Co., Tokyo, Japan
- Lee Kong Chian School of Medicine and School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Laurent Rénia
- ASTAR Infectious Diseases Labs (A*STAR ID Labs), Agency for Science Technology and Research (A*STAR), Singapore City, Singapore
| | - Evan P Williams
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
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30
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Abbasian MH, Mahmanzar M, Rahimian K, Mahdavi B, Tokhanbigli S, Moradi B, Sisakht MM, Deng Y. Global landscape of SARS-CoV-2 mutations and conserved regions. J Transl Med 2023; 21:152. [PMID: 36841805 PMCID: PMC9958328 DOI: 10.1186/s12967-023-03996-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management. METHODS 10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence. RESULTS Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508-635(0.77%) and aa 381-508 (0.43%). The highest frequency of mutation was observed in aa 66-88 (2.19%), aa 7-14, and aa 164-246 (2.92%) in M, E, and N proteins, respectively. CONCLUSION Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS-CoV-2 diagnostic efficiency and design safe and effective vaccines against emerging variants.
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Affiliation(s)
- Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Karim Rahimian
- Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Samaneh Tokhanbigli
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, Australia
| | - Bahman Moradi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, 2040, 3000 CA, Rotterdam, The Netherlands
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA.
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31
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Takahata N, Sugawara H. Role of error catastrophe in transmission ability of virus. Genes Genet Syst 2023; 97:237-246. [PMID: 36709980 DOI: 10.1266/ggs.22-00096] [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: 01/28/2023] Open
Abstract
The role played by error catastrophe is explicitly taken into account in a mathematical formulation to analyze COVID-19 data. The idea is to combine the mathematical genetics formalism of the error catastrophe of mutations in virus gene loci with the standard model of epidemics, which lacks the explicit incorporation of the effect of mutation on the spreading of viruses. We apply this formalism to the case of SARS-CoV-2 virus. We assume the universality of the error catastrophe in the process of analyzing the data. This means that some basic parameter to describe the error catastrophe is independent of which group (country or city) we deal with. Concretely, we analyze Omicron variant data from South Africa and then analyze cases from Japan using the same value of the basic parameter derived in the South Africa analysis. The excellent fit between the two sets of data, one from South Africa and the other from Japan, using the common values of genetic parameters, justifies our assumption of the universality of these parameters.
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32
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Eltayb WA, Abdalla M, Rabie AM. Novel Investigational Anti-SARS-CoV-2 Agent Ensitrelvir "S-217622": A Very Promising Potential Universal Broad-Spectrum Antiviral at the Therapeutic Frontline of Coronavirus Species. ACS OMEGA 2023; 8:5234-5246. [PMID: 36798145 PMCID: PMC9897045 DOI: 10.1021/acsomega.2c03881] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/05/2022] [Indexed: 06/06/2023]
Abstract
Lately, nitrogenous heterocyclic antivirals, such as nucleoside-like compounds, oxadiazoles, thiadiazoles, triazoles, quinolines, and isoquinolines, topped the therapeutic scene as promising agents of choice for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying ailment, the coronavirus disease 2019 (COVID-19). At the same time, the continuous emergence of new strains of SARS-CoV-2, like the Omicron variant and its multiple sublineages, resulted in a new defiance in the enduring COVID-19 battle. Ensitrelvir (S-217622) is a newly discovered orally active noncovalent nonpeptidic agent with potential strong broad-spectrum anticoronaviral activities, exhibiting promising nanomolar potencies against the different SARS-CoV-2 variants. S-217622 effectively and nonspecifically hits the main protease (Mpro) enzyme of a broad scope of coronaviruses. Herein, in the present computational/biological study, we tried to extend these previous findings to prove the universal activities of this investigational agent against any coronavirus, irrespective of its type, through synchronously acting on most of its main unchanged replication enzymes/proteins, including (in addition to the Mpro), e.g., the highly conserved RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN). Biochemical evaluation proved, using the in vitro anti-RdRp/ExoN bioassay, that S-217622 can potently inhibit the replication of coronaviruses, including the new virulent strains of SARS-CoV-2, with extremely minute in vitro anti-RdRp and anti-RdRp/ExoN half-maximal effective concentration (EC50) values of 0.17 and 0.27 μM, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico results greatly supported these biochemical results, proposing that the S-217622 molecule strongly and stabilizingly strikes the key catalytic pockets of the SARS-CoV-2 RdRp's and ExoN's principal active sites predictably via the nucleoside analogism mode of anti-RNA action (since the S-217622 molecule can be considered as a uridine analog). Moreover, the idealistic druglikeness and pharmacokinetic characteristics of S-217622 make it ready for pharmaceutical formulation with the expected very good clinical behavior as a drug for the infections caused by coronaviruses, e.g., COVID-19. To cut it short, the current critical findings of this extension work significantly potentiate and extend the S-217622's previous in vitro/in vivo (preclinical) results since they showed that the striking inhibitory activities of this novel anti-SARS-CoV-2 agent on the Mpro could be extended to other replication enzymes like RdRp and ExoN, unveiling the possible universal use of the compound against the next versions of the virus (i.e., disclosing the nonspecific anticoronaviral properties of this compound against almost any coronavirus strain), e.g., SARS-CoV-3, and encouraging us to rapidly start the compound's vast clinical anti-COVID-19 evaluations.
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Affiliation(s)
- Wafa A. Eltayb
- Biotechnology
Department, Faculty of Science and Technology, Shendi University, Shendi 11111, River Nile State, Sudan
| | - Mohnad Abdalla
- Key
Laboratory of Chemical Biology (Ministry of Education), Department
of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College
of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province 250012, P. R. China
| | - Amgad M. Rabie
- Dr.
Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt
- Drug
Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia
Governorate, Egypt
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33
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Shannon A, Canard B. Kill or corrupt: Mechanisms of action and drug-resistance of nucleotide analogues against SARS-CoV-2. Antiviral Res 2023; 210:105501. [PMID: 36567022 PMCID: PMC9773703 DOI: 10.1016/j.antiviral.2022.105501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Nucleoside/tide analogues (NAs) have long been used in the fight against viral diseases, and now present a promising option for the treatment of COVID-19. Once activated to the 5'-triphosphate state, NAs act by targeting the viral RNA-dependent RNA-polymerase for incorporation into the viral RNA genome. Incorporated analogues can either 'kill' (terminate) synthesis, or 'corrupt' (genetically or chemically) the RNA. Against coronaviruses, the use of NAs has been further complicated by the presence of a virally encoded exonuclease domain (nsp14) with proofreading and repair capacities. Here, we describe the mechanism of action of four promising anti-COVID-19 NAs; remdesivir, molnupiravir, favipiravir and bemnifosbuvir. Their distinct mechanisms of action best exemplify the concept of 'killers' and 'corruptors'. We review available data regarding their ability to be incorporated and excised, and discuss the specific structural features that dictate their overall potency, toxicity, and mutagenic potential. This should guide the synthesis of novel analogues, lend insight into the potential for resistance mutations, and provide a rational basis for upcoming combinations therapies.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.
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34
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Ma H, Zong HF, Liu JJ, Yue YL, Ke Y, Liao YJ, Tang HN, Wang L, Wang SS, Yuan YS, Wu MY, Bian YL, Zhang BH, Yin HY, Jiang H, Sun T, Han L, Xie YQ, Zhu JW. Long-term passaging of pseudo-typed SARS-CoV-2 reveals the breadth of monoclonal and bispecific antibody cocktails. Acta Pharmacol Sin 2023:10.1038/s41401-022-01043-w. [PMID: 36707721 PMCID: PMC9880922 DOI: 10.1038/s41401-022-01043-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/13/2022] [Indexed: 01/28/2023] Open
Abstract
The continuous emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses challenges to the effectiveness of neutralizing antibodies. Rational design of antibody cocktails is a realizable approach addressing viral immune evasion. However, evaluating the breadth of antibody cocktails is essential for understanding the development potential. Here, based on a replication competent vesicular stomatitis virus model that incorporates the spike of SARS-CoV-2 (VSV-SARS-CoV-2), we evaluated the breadth of a number of antibody cocktails consisting of monoclonal antibodies and bispecific antibodies by long-term passaging the virus in the presence of the cocktails. Results from over two-month passaging of the virus showed that 9E12 + 10D4 + 2G1 and 7B9-9D11 + 2G1 from these cocktails were highly resistant to random mutation, and there was no breakthrough after 30 rounds of passaging. As a control, antibody REGN10933 was broken through in the third passage. Next generation sequencing was performed and several critical mutations related to viral evasion were identified. These mutations caused a decrease in neutralization efficiency, but the reduced replication rate and ACE2 susceptibility of the mutant virus suggested that they might not have the potential to become epidemic strains. The 9E12 + 10D4 + 2G1 and 7B9-9D11 + 2G1 cocktails that picked from the VSV-SARS-CoV-2 system efficiently neutralized all current variants of concern and variants of interest including the most recent variants Delta and Omicron, as well as SARS-CoV-1. Our results highlight the feasibility of using the VSV-SARS-CoV-2 system to develop SARS-CoV-2 antibody cocktails and provide a reference for the clinical selection of therapeutic strategies to address the mutational escape of SARS-CoV-2.
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Affiliation(s)
- Hang Ma
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China ,grid.263906.80000 0001 0362 4044School of Pharmaceutical Sciences, Southwest University, Chongqing, 400715 China
| | - Hui-fang Zong
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China ,Jecho Institute, Co., Ltd., Shanghai, 200240 China
| | - Jun-jun Liu
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Ya-li Yue
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yong Ke
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yun-ji Liao
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Hao-neng Tang
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lei Wang
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | | | - Yun-sheng Yuan
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Ming-yuan Wu
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yan-lin Bian
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Bao-hong Zhang
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Hai-yang Yin
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Hua Jiang
- Jecho Laboratories, Inc., Frederick, MD 21704 USA
| | - Tao Sun
- grid.16821.3c0000 0004 0368 8293School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240 China ,Shanghai Municipal Veterinary Key Laboratory, Shanghai, 200240 China
| | - Lei Han
- Jecho Institute, Co., Ltd., Shanghai, 200240 China
| | - Yue-qing Xie
- Jecho Laboratories, Inc., Frederick, MD 21704 USA
| | - Jian-wei Zhu
- grid.419897.a0000 0004 0369 313XEngineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, Shanghai, 200240 China ,grid.16821.3c0000 0004 0368 8293School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240 China
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Rabie AM, Eltayb WA. Strong Dual Antipolymerase/Antiexonuclease Actions of Some Aminothiadiazole Antioxidants: A Promising In-Silico/ In-Vitro Repurposing Research Study against the COVID-19 Omicron Virus (B.1.1.529.3 Lineage). ADVANCES IN REDOX RESEARCH 2023:100064. [PMID: 36776420 PMCID: PMC9907022 DOI: 10.1016/j.arres.2023.100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/03/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
Currently, nitrogen-containing heterocyclic virucides take the lead as top options for treating the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their escorting disease, the coronavirus disease 2019 (COVID-19). But unfortunately, the sudden emergence of a new strain of SARS-CoV-2, the Omicron variant and its lineages, complicated matters in the incessant COVID-19 battle. Goaling the two paramount coronaviral-2 multiplication enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) at synchronous times using single ligand is a quite effective new binary avenue to restrain SARS-CoV-2 reproduction and cease COVID-19 progression irrespective of the SARS-CoV-2 strain type, as RdRps and ExoNs are vastly conserved in all SARS-CoV-2 strains. The presented in-silico/in-vitro research winnowed our own small libraries of antioxidant nitrogenous heterocyclic compounds, inspecting for the utmost convenient drug candidates expectedly capable of effectively working through this dual tactic. Computational screening afforded three promising compounds of the antioxidant 1,3,4-thiadiazole class, which were named ChloViD2022, Taroxaz-26, and CoViTris2022. Subsequent biological examination, employing the in-vitro anti-RdRp/anti-ExoN and anti-SARS-CoV-2 assays, exclusively demonstrated that ChloViD2022, CoViTris2022, and Taroxaz-26 could efficiently block the replication of the new lineages of SARS-CoV-2 with considerably minute anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.18 and 0.44 μM for ChloViD2022, 0.22 and 0.72 μM for CoViTris2022, and 0.25 and 0.78 μM for Taroxaz-26, in the order, overtaking the standard anti-SARS-CoV-2 drug molnupiravir. These biochemical findings were optimally presupported by the results of the prior in-silico screening, suggesting that the three compounds might potently hit the catalytic active sites of the virus's RdRp and ExoN enzymes. Furthermore, the perfect pharmacophoric features of ChloViD2022, Taroxaz-26, and CoViTris2022 molecules make them typical dual inhibitors of SARS-CoV-2 replication and proofreading, with their relatively flexible structures eligible for diverse forms of chemical modification. In sum, the current important results of this thorough research work exposed the interesting repurposing potential of the three 2-amino-1,3,4-thiadiazole ligands, ChloViD2022, Taroxaz-26, and CoViTris2022, to effectively conflict with the vital biointeractions between the coronavirus's polymerase/exoribonuclease and the four essential RNA nucleotides, and, accordingly, arrest COVID-19 disease, persuading the relevant investigators to quickly begin the three agents' comprehensive preclinical and clinical anti-COVID-19 assessments.
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Affiliation(s)
- Amgad M Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt
| | - Wafa A Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi 11111, River Nile State, Sudan
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Zapata-Cardona MI, Florez-Alvarez L, Guerra-Sandoval AL, Chvatal-Medina M, Guerra-Almonacid CM, Hincapie-Garcia J, Hernandez JC, Rugeles MT, Zapata-Builes W. In vitro and in silico evaluation of antiretrovirals against SARS-CoV-2: A drug repurposing approach. AIMS Microbiol 2023; 9:20-40. [PMID: 36891537 PMCID: PMC9988408 DOI: 10.3934/microbiol.2023002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/26/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
Background Drug repurposing is a valuable strategy for rapidly developing drugs for treating COVID-19. This study aimed to evaluate the antiviral effect of six antiretrovirals against SARS-CoV-2 in vitro and in silico. Methods The cytotoxicity of lamivudine, emtricitabine, tenofovir, abacavir, efavirenz and raltegravir on Vero E6 was evaluated by MTT assay. The antiviral activity of each of these compounds was evaluated via a pre-post treatment strategy. The reduction in the viral titer was assessed by plaque assay. In addition, the affinities of the antiretroviral interaction with viral targets RdRp (RNA-dependent RNA polymerase), ExoN-NSP10 (exoribonuclease and its cofactor, the non-structural protein 10) complex and 3CLpro (3-chymotrypsin-like cysteine protease) were evaluated by molecular docking. Results Lamivudine exhibited antiviral activity against SARS-CoV-2 at 200 µM (58.3%) and 100 µM (66.7%), while emtricitabine showed anti-SARS-CoV-2 activity at 100 µM (59.6%), 50 µM (43.4%) and 25 µM (33.3%). Raltegravir inhibited SARS-CoV-2 at 25, 12.5 and 6.3 µM (43.3%, 39.9% and 38.2%, respectively). The interaction between the antiretrovirals and SARS-CoV-2 RdRp, ExoN-NSP10 and 3CLpro yielded favorable binding energies (from -4.9 kcal/mol to -7.7 kcal/mol) using bioinformatics methods. Conclusion Lamivudine, emtricitabine and raltegravir showed in vitro antiviral effects against the D614G strain of SARS-CoV-2. Raltegravir was the compound with the greatest in vitro antiviral potential at low concentrations, and it showed the highest binding affinities with crucial SARS-CoV-2 proteins during the viral replication cycle. However, further studies on the therapeutic utility of raltegravir in patients with COVID-19 are required.
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Affiliation(s)
- Maria I. Zapata-Cardona
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Lizdany Florez-Alvarez
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
- Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Mateo Chvatal-Medina
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Jaime Hincapie-Garcia
- Grupo de investigacion, Promocion y prevencion farmaceutica, Facultad de ciencias farmaceuticas yalimentarias, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Juan C. Hernandez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellin, Colombia
| | - Maria T. Rugeles
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellin, Colombia
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Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa I, Passow K, Kennelly S, Moorthy R, Dulin D, Feng J, Harki D, Kirchdoerfer R, Cameron C, Arnold J. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res 2023; 51:315-336. [PMID: 36546762 PMCID: PMC9841423 DOI: 10.1093/nar/gkac1177] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Srivastava
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas K Anderson
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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Nakata Y, Ode H, Kubota M, Kasahara T, Matsuoka K, Sugimoto A, Imahashi M, Yokomaku Y, Iwatani Y. Cellular APOBEC3A deaminase drives mutations in the SARS-CoV-2 genome. Nucleic Acids Res 2023; 51:783-795. [PMID: 36610792 PMCID: PMC9881129 DOI: 10.1093/nar/gkac1238] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
The number of genetic variations in the SARS-CoV-2 genome has been increasing primarily due to continuous viral mutations. Here, we report that the human APOBEC3A (A3A) cytidine deaminase plays a critical role in the induction of C-to-U substitutions in the SARS-CoV-2 genome. Bioinformatic analysis of the chronological genetic changes in a sequence database indicated that the largest UC-to-UU mutation signature, consistent with APOBEC-recognized nucleotide motifs, was predominant in single-stranded RNA regions of the viral genome. In SARS-CoV-2-infected cells, exogenous expression of A3A but not expression of other APOBEC proteins induced UC-to-UU mutations in viral RNA (vRNA). Additionally, the mutated C bases were often located at the tips in bulge or loop regions in the vRNA secondary structure. Interestingly, A3A mRNA expression was drastically increased by interferons (IFNs) and tumour necrosis factor-α (TNF-α) in epithelial cells derived from the respiratory system, a site of efficient SARS-CoV-2 replication. Moreover, the UC-to-UU mutation rate was increased in SARS-CoV-2 produced from lung epithelial cells treated with IFN-ß and TNF-α, but not from CRISPR/Cas9-based A3A knockout cells. Collectively, these findings demonstrate that A3A is a primary host factor that drives mutations in the SARS-CoV-2 RNA genome via RNA editing.
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Affiliation(s)
- Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan,Department of AIDS Research, Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Takaaki Kasahara
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan,Department of Respiratory Medicine, Division of Internal Medicine, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Atsuko Sugimoto
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Aichi 460-0001, Japan
| | - Yasumasa Iwatani
- To whom correspondence should be addressed. Tel: +81 52 951 1111; Fax: +81 52 963 3970;
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39
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Naidu SAG, Mustafa G, Clemens RA, Naidu AS. Plant-Derived Natural Non-Nucleoside Analog Inhibitors (NNAIs) against RNA-Dependent RNA Polymerase Complex (nsp7/nsp8/nsp12) of SARS-CoV-2. J Diet Suppl 2023; 20:254-283. [PMID: 34850656 DOI: 10.1080/19390211.2021.2006387] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of fast-spreading SARS-CoV-2 mutants has sparked a new phase of COVID-19 pandemic. There is a dire necessity for antivirals targeting highly conserved genomic domains on SARS-CoV-2 that are less prone to mutation. The nsp12, also known as the RNA-dependent RNA-polymerase (RdRp), the core component of 'SARS-CoV-2 replication-transcription complex', is a potential well-conserved druggable antiviral target. Several FDA-approved RdRp 'nucleotide analog inhibitors (NAIs)' such as remdesivir, have been repurposed to treat COVID-19 infections. The NAIs target RdRp protein translation and competitively block the nucleotide insertion into the RNA chain, resulting in the inhibition of viral replication. However, the replication proofreading function of nsp14-ExoN could provide resistance to SARS-CoV-2 against many NAIs. Conversely, the 'non-nucleoside analog inhibitors (NNAIs)' bind to allosteric sites on viral polymerase surface, change the redox state; thereby, exert antiviral activity by altering interactions between the enzyme substrate and active core catalytic site of the RdRp. NNAIs neither require metabolic activation (unlike NAIs) nor compete with intracellular pool of nucleotide triphosphates (NTPs) for anti-RdRp activity. The NNAIs from phytonutrient origin are potential antiviral candidates compared to their synthetic counterparts. Several in-silico studies reported the antiviral spectrum of natural phytonutrient-NNAIs such as Suramin, Silibinin (flavonolignan), Theaflavin (tea polyphenol), Baicalein (5,6,7-trihydroxyflavone), Corilagin (gallotannin), Hesperidin (citrus bioflavonoid), Lycorine (pyrrolidine alkaloid), with superior redox characteristics (free binding energy, hydrogen-bonds, etc.) than antiviral drugs (i.e. remdesivir, favipiravir). These phytonutrient-NNAIs also exert anti-inflammatory, antioxidant, immunomodulatory and cardioprotective functions, with multifunctional therapeutic benefits in the clinical management of COVID-19.
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Affiliation(s)
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, CA, USA
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40
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Domingo E, García-Crespo C, Soria ME, Perales C. Viral Fitness, Population Complexity, Host Interactions, and Resistance to Antiviral Agents. Curr Top Microbiol Immunol 2023; 439:197-235. [PMID: 36592247 DOI: 10.1007/978-3-031-15640-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fitness of viruses has become a standard parameter to quantify their adaptation to a biological environment. Fitness determinations for RNA viruses (and some highly variable DNA viruses) meet with several uncertainties. Of particular interest are those that arise from mutant spectrum complexity, absence of population equilibrium, and internal interactions among components of a mutant spectrum. Here, concepts, fitness measurements, limitations, and current views on experimental viral fitness landscapes are discussed. The effect of viral fitness on resistance to antiviral agents is covered in some detail since it constitutes a widespread problem in antiviral pharmacology, and a challenge for the design of effective antiviral treatments. Recent evidence with hepatitis C virus suggests the operation of mechanisms of antiviral resistance additional to the standard selection of drug-escape mutants. The possibility that high replicative fitness may be the driver of such alternative mechanisms is considered. New broad-spectrum antiviral designs that target viral fitness may curtail the impact of drug-escape mutants in treatment failures. We consider to what extent fitness-related concepts apply to coronaviruses and how they may affect strategies for COVID-19 prevention and treatment.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 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.
| | - Carlos García-Crespo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 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
| | - María Eugenia Soria
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 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.,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
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 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.,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.,Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
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41
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Petushkov I, Esyunina D, Kulbachinskiy A. Effects of natural RNA modifications on the activity of SARS-CoV-2 RNA-dependent RNA polymerase. FEBS J 2023; 290:80-92. [PMID: 35916766 PMCID: PMC9538676 DOI: 10.1111/febs.16587] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/17/2022] [Accepted: 08/01/2022] [Indexed: 01/18/2023]
Abstract
RNA-dependent RNA polymerase (RdRp) plays a key role in the replication of RNA viruses, including SARS-CoV-2. Processive RNA synthesis by RdRp is crucial for successful genome replication and expression, especially in the case of very long coronaviral genomes. Here, we analysed the activity of SARS-CoV-2 RdRp (the nsp12-nsp7-nsp8 complex) on synthetic primer-templates of various structures, including substrates with mismatched primers or template RNA modifications. It has been shown that RdRp cannot efficiently extend RNA primers containing mismatches and has no intrinsic RNA cleavage activity to remove the primer 3'-end, thus necessitating the action of exoribonuclease for proofreading. Similar to DNA-dependent RNA polymerases, RdRp can perform processive pyrophosphorolysis of the nascent RNA product but this reaction is also blocked in the presence of mismatches. Furthermore, we have demonstrated that several natural post-transcriptional modifications in the RNA template, which do not prevent complementary interactions (N6-methyladenosine, 5-methylcytosine, inosine and pseudouridine), do not change RdRp processivity. At the same time, certain modifications of RNA bases and ribose residues strongly block RNA synthesis, either prior to nucleotide incorporation (3-methyluridine and 1-methylguanosine) or immediately after it (2'-O-methylation). The results demonstrate that the activity of SARS-CoV-2 RdRp can be strongly inhibited by common modifications of the RNA template suggesting a way to design novel antiviral compounds.
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Affiliation(s)
- Ivan Petushkov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
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42
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Rabie AM, Abdalla M. Evaluation of a series of nucleoside analogs as effective anticoronaviral-2 drugs against the Omicron-B.1.1.529/BA.2 subvariant: A repurposing research study. Med Chem Res 2022; 32:326-341. [PMID: 36593869 PMCID: PMC9797896 DOI: 10.1007/s00044-022-02970-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/06/2022] [Indexed: 12/30/2022]
Abstract
Mysterious evolution of a new strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the Omicron variant, led to a new challenge in the persistent coronavirus disease 2019 (COVID-19) battle. Objecting the conserved SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) together using one ligand is a successful new tactic to stop SARS-CoV-2 multiplication and COVID-19 progression. The current comprehensive study investigated most nucleoside analogs (NAs) libraries, searching for the most ideal drug candidates expectedly able to act through this double tactic. Gradual computational filtration afforded six different promising NAs, riboprine/forodesine/tecadenoson/nelarabine/vidarabine/maribavir. Further biological assessment proved that riboprine and forodesine are able to powerfully inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.21 and 0.45 μM for riboprine and about 0.23 and 0.70 μM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. These biochemical findings were supported by the prior in silico data. Additionally, the ideal pharmacophoric features of riboprine and forodesine molecules render them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading. These findings suggest that riboprine and forodesine could serve as prospective lead compounds against COVID-19. Graphical abstract.
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Affiliation(s)
- Amgad M. Rabie
- Dr. Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate Egypt
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate Egypt
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province 250012 PR China
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43
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Rabie AM, Abdalla M. Forodesine and Riboprine Exhibit Strong Anti-SARS-CoV-2 Repurposing Potential: In Silico and In Vitro Studies. ACS BIO & MED CHEM AU 2022; 2:565-585. [PMID: 37582236 PMCID: PMC9631343 DOI: 10.1021/acsbiomedchemau.2c00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 11/07/2022]
Abstract
Lately, nucleos(t)ide antivirals topped the scene as top options for the treatment of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Targeting the two broadly conserved SARS-CoV-2 enzymes, RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN), together using only one shot is a very successful new tactic to stop SARS-CoV-2 multiplication irrespective of the SARS-CoV-2 variant type. Herein, the current studies investigated most nucleoside analogue (NA) libraries, searching for the ideal drug candidates expectedly able to act through this double tactic. Gradual computational filtration gave rise to six different promising NAs along with their corresponding triphosphate (TP) nucleotides. The subsequent biological assessment proved for the first time that, among the six NAs, riboprine and forodesine are able to hyperpotently inhibit the replication of the Omicron strain of SARS-CoV-2 with extremely low in vitro anti-RdRp, anti-ExoN, and anti-SARS-CoV-2 EC50 values of about 0.18, 0.28, and 0.40 μM for riboprine and about 0.20, 0.31, and 0.65 μM for forodesine, respectively, surpassing remdesivir and molnupiravir. The significant probability that both compounds may also act as prodrugs for their final TP nucleotides in vivo pushed us to examine the same activities for forodesine-TP and riboprine-TP. Both nucleotides similarly displayed very promising results, respectively, which are much better than those for the two reference TP nucleotides, GS-443902 and β-d-N4-hydroxycytidine 5'-TP (NHC-TP). The prior in silico data supported these biochemical findings, suggesting that riboprine and forodesine molecules and their expected active TP metabolites strongly hit the key catalytic pockets of the SARS-CoV-2 RdRp's and ExoN's main active sites. In brief, the current important results of this comprehensive study revealed the interesting repurposing potentials of, mainly, the two bioactive nucleosides forodesine and riboprine and their TP nucleotides to effectively shut down the polymerase/exoribonuclease-RNA nucleotide interactions of SARS-CoV-2 and consequently treat COVID-19 infections.
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Affiliation(s)
- Amgad M. Rabie
- Dr.
Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City35511,Mansoura, Dakahlia Governorate, Egypt
- Head
of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City35744,Dikernis, Dakahlia Governorate, Egypt
| | - Mohnad Abdalla
- Key
Laboratory of Chemical Biology (Ministry of Education), Department
of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College
of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province250012, P. R. China
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44
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Rabie AM, Abdalla M. A Series of Adenosine Analogs as the First Efficacious Anti-SARS-CoV-2 Drugs against the B.1.1.529.4 Lineage: A Preclinical Repurposing Research Study. ChemistrySelect 2022; 7:e202201912. [PMID: 36718467 PMCID: PMC9877610 DOI: 10.1002/slct.202201912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/30/2022] [Indexed: 12/13/2022]
Abstract
Given the rapid progression of the coronavirus disease 2019 (COVID-19) pandemic, an ultrafast response was urgently required to handle this major public crisis. To contain the pandemic, investments are required to develop diagnostic tests, prophylactic vaccines, and novel therapies. Lately, nucleoside analog (NA) antivirals topped the scene as top options for the treatment of COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Meanwhile, the continuous generation of new lineages of the SARS-CoV-2 Omicron variant caused a new challenge in the persistent COVID-19 battle. Hitting the two crucial SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) collectively together using only one single ligand is a very successful new approach to stop SARS-CoV-2 multiplication and combat COVID-19 irrespective of the SARS-CoV-2 variant type because RdRps and ExoNs are broadly conserved among all SARS-CoV-2 strains. Herein, the current comprehensive study investigated most NAs libraries, searching for the most ideal drug candidates expectedly able to perfectly act through this double tactic. Gradual computational filtration gave rise to six different promising NAs, which are riboprine, forodesine, tecadenoson, nelarabine, vidarabine, and maribavir, respectively. Further biological assessment proved for the first time, using the in vitro anti-RdRp/ExoN and anti-SARS-CoV-2 bioassays, that riboprine and forodesine, among all the six tested NAs, are able to powerfully inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.22 and 0.49 μM for riboprine and about 0.25 and 0.73 μM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. The prior in silico data supported these biochemical findings, suggesting that riboprine and forodesine molecules strongly hit the key catalytic pockets of the SARS-CoV-2 (Omicron variant) RdRp's and ExoN's main active sites. Additionally, the ideal pharmacophoric features of riboprine and forodesine molecules render them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading, with their relatively flexible structures open for diverse types of chemical derivatization. In Brief, the current important results of this comprehensive study revealed the interesting repurposing potentials of, mainly, the two nucleosides riboprine and forodesine to effectively shut down the polymerase/exoribonuclease-RNA nucleotides interactions of the SARS-CoV-2 Omicron variant and consequently treat COVID-19 infections, motivating us to rapidly begin the two drugs' broad preclinical/clinical anti-COVID-19 bioevaluations, hoping to combine both drugs soon in the COVID-19 treatment protocols.
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Affiliation(s)
- Amgad M. Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD)35511MansouraDakahlia GovernorateEgypt,Head of Drug Discovery & Clinical Research Department Dikernis General Hospital (DGH)Magliss El-Madina Street Dikernis35744DikernisDakahlia GovernorateEgypt
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education)Department of PharmaceuticsSchool of Pharmaceutical SciencesCheeloo College of MedicineShandong University44 Cultural West RoadShandong Province250012PR China
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45
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Wang W, Li W, Wen Z, Wang C, Liu W, Zhang Y, Liu J, Ding T, Shuai L, Zhong G, Bu Z, Qu L, Ren M, Li F. Gossypol Broadly Inhibits Coronaviruses by Targeting RNA-Dependent RNA Polymerases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203499. [PMID: 36266926 PMCID: PMC9762316 DOI: 10.1002/advs.202203499] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/10/2022] [Indexed: 05/03/2023]
Abstract
Outbreaks of coronaviruses (CoVs), especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have posed serious threats to humans and animals, which urgently calls for effective broad-spectrum antivirals. RNA-dependent RNA polymerase (RdRp) plays an essential role in viral RNA synthesis and is an ideal pan-coronaviral therapeutic target. Herein, based on cryo-electron microscopy and biochemical approaches, gossypol (GOS) is identified from 881 natural products to directly block SARS-CoV-2 RdRp, thus inhibiting SARS-CoV-2 replication in both cellular and mouse infection models. GOS also acts as a potent inhibitor against the SARS-CoV-2 variant of concern (VOC) and exerts same inhibitory effects toward mutated RdRps of VOCs as the RdRp of the original SARS-CoV-2. Moreover, that the RdRp inhibitor GOS has broad-spectrum anti-coronavirus activity against alphacoronaviruses (porcine epidemic diarrhea virus and swine acute diarrhea syndrome coronavirus), betacoronaviruses (SARS-CoV-2), gammacoronaviruses (avian infectious bronchitis virus), and deltacoronaviruses (porcine deltacoronavirus) is showed. The findings demonstrate that GOS may serve as a promising lead compound for combating the ongoing COVID-19 pandemic and other coronavirus outbreaks.
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Affiliation(s)
- Wenjing Wang
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
- Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan455000P. R. China
- Hainan Yazhou Bay Seed LaboratorySanyaHainan572025P. R. China
| | - Wenkang Li
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
- Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan455000P. R. China
| | - Zhiyuan Wen
- State Key Laboratory of Veterinary BiotechnologyHarbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbinHeilongjiang150069P. R. China
| | - Chong Wang
- State Key Laboratory of Veterinary BiotechnologyHarbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbinHeilongjiang150069P. R. China
| | - Weilong Liu
- Institute for HepatologyNational Clinical Research Center for Infectious DiseaseShenzhen Third People's HospitalThe Second Affiliated HospitalSchool of MedicineSouthern University of Science and TechnologyShenzhenGuangdong518112P. R. China
| | - Yufang Zhang
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
- Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan455000P. R. China
| | - Juncheng Liu
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
- Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan455000P. R. China
| | - Tianze Ding
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
- Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan455000P. R. China
| | - Lei Shuai
- State Key Laboratory of Veterinary BiotechnologyHarbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbinHeilongjiang150069P. R. China
| | - Gongxun Zhong
- State Key Laboratory of Veterinary BiotechnologyHarbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbinHeilongjiang150069P. R. China
| | - Zhigao Bu
- State Key Laboratory of Veterinary BiotechnologyHarbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbinHeilongjiang150069P. R. China
| | - Lingbo Qu
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
| | - Maozhi Ren
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
- Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan455000P. R. China
- Institute of Urban AgricultureChinese Academy of Agricultural SciencesChengduSichuan610213P. R. China
- Hainan Yazhou Bay Seed LaboratorySanyaHainan572025P. R. China
| | - Fuguang Li
- Zhengzhou Research BaseState Key Laboratory of Cotton BiologySchool of Agricultural SciencesZhengzhou UniversityZhengzhouHenan450001P. R. China
- Institute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangHenan455000P. R. China
- Hainan Yazhou Bay Seed LaboratorySanyaHainan572025P. R. China
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Jaiswal D, Verma S, Nair DT, Salunke DM. Antibody multispecificity: A necessary evil? Mol Immunol 2022; 152:153-161. [DOI: 10.1016/j.molimm.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
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Luo WR, Wu XM. Novel coronavirus mutations: Vaccine development and challenges. Microb Pathog 2022; 173:105828. [PMID: 36243381 PMCID: PMC9561474 DOI: 10.1016/j.micpath.2022.105828] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 10/09/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
The ongoing global pandemic of novel coronavirus pneumonia (COVID-19) caused by the SARS-CoV-2 has a significant impact on global health and economy system. In this context, there have been some landmark advances in vaccine development. Over 100 new coronavirus vaccine candidates have been approved for clinical trials, with ten WHO-approved vaccines including four inactivated virus vaccines, two mRNA vaccines, three recombinant viral vectored vaccines and one protein subunit vaccine on the "Emergency Use Listing". Although the SARS-CoV-2 has an internal proofreading mechanism, there have been a number of mutations emerged in the pandemic affecting its transmissibility, pathogenicity and immunogenicity. Of these, mutations in the spike (S) protein and the resultant mutant variants have posed new challenges for vaccine development and application. In this review article, we present an overview of vaccine development, the prevalence of new coronavirus variants and their impact on protective efficacy of existing vaccines and possible immunization strategies coping with the viral mutation and diversity.
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Maltsev OV, Kasyanenko KV, Kozlov KV, Zhdanov KV, Lapikov II. Prospects of using the nucleoside analogue riamilovir in patients with SARS-CoV-2 infection. TERAPEVT ARKH 2022; 94:1171-1176. [DOI: 10.26442/00403660.2022.10.201920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022]
Abstract
Aim. To evaluate clinical efficacy of nucleoside analogues in therapy of moderate COVID-19 in in-patients.
Materials and methods. Retrospective processing of 108 completed clinical cases with moderate novel coronavirus disease was carried out for the period 20202021. The duration of the disease at the time of admission did not exceed three days. Experimental group consisted of 53 patients who, in addition to standard therapy, were prescribed off-label riamilovir at a daily dosage of 1250 mg for 5 days by the decision of the medical commission. Comparison group included 55 patients who received a combination of umifenovir and ribavirin as antiviral therapy for 5 days. The duration of the main clinical manifestations of the disease, the indicators of clinical and biochemical blood tests, results of the SARS-CoV-2 virus RNA study using the nucleic acid amplification method (NAAT diagnostics).
Results. Significantly faster achievement of clinical improvement in the group of patients treated with riamilovir was shown, as well as faster sanitation from SARS-CoV-2 virus based on the results of etiological testing.
Conclusion. The use of riamilovir for the treatment of patients with moderate novel coronavirus infection (COVID-19) resulted in a significant reduction of general infectious syndromes and respiratory symptoms. Patients from the experimental group significantly faster achieved clinical recovery and sanitation from the pathogen according to the results of NAAT diagnostics.
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Solomon M, Liang C. Human coronaviruses: The emergence of SARS-CoV-2 and management of COVID-19. Virus Res 2022; 319:198882. [PMID: 35934258 PMCID: PMC9351210 DOI: 10.1016/j.virusres.2022.198882] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/12/2022]
Abstract
To date, a total of seven human coronaviruses (HCoVs) have been identified, all of which are important respiratory pathogens. Recently, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has led to a global pandemic causing millions of infections and deaths. Here, we summarize the discovery and fundamental virology of HCoVs, discuss their zoonotic transmission and highlight the weak species barrier of SARS-CoV-2. We also discuss the possible origins of SARS-CoV-2 variants of concern identified to date and discuss the experimental challenges in characterizing mutations of interest and propose methods to circumvent them. As the COVID-19 treatment and prevention landscape rapidly evolves, we summarize current therapeutics and vaccines, and their implications on SARS-CoV-2 variants. Finally, we explore how interspecies transmission of SARS-CoV-2 may drive the emergence of novel strains, how disease severity may evolve and how COVID-19 will likely continue to burden healthcare systems globally.
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Affiliation(s)
- Magan Solomon
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Chen Liang
- Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
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Scott TM, Solis-Leal A, Lopez JB, Robison RA, Berges BK, Pickett BE. Comparison of Intracellular Transcriptional Response of NHBE Cells to Infection with SARS-CoV-2 Washington and New York Strains. Front Cell Infect Microbiol 2022; 12:1009328. [PMID: 36204651 PMCID: PMC9530606 DOI: 10.3389/fcimb.2022.1009328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/26/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China in December 2019 and caused a global pandemic resulting in millions of deaths and tens of millions of patients positive tests. While studies have shown a D614G mutation in the viral spike protein are more transmissible, the effects of this and other mutations on the host response, especially at the cellular level, are yet to be fully elucidated. In this experiment we infected normal human bronchial epithelial (NHBE) cells with the Washington (D614) strain or the New York (G614) strains of SARS-CoV-2. We generated RNA sequencing data at 6, 12, and 24 hours post-infection (hpi) to improve our understanding of how the intracellular host response differs between infections with these two strains. We analyzed these data with a bioinformatics pipeline that identifies differentially expressed genes (DEGs), enriched Gene Ontology (GO) terms and dysregulated signaling pathways. We detected over 2,000 DEGs, over 600 GO terms, and 29 affected pathways between the two infections. Many of these entities play a role in immune signaling and response. A comparison between strains and time points showed a higher similarity between matched time points than across different time points with the same strain in DEGs and affected pathways, but found more similarity between strains across different time points when looking at GO terms. A comparison of the affected pathways showed that the 24hpi samples of the New York strain were more similar to the 12hpi samples of the Washington strain, with a large number of pathways related to translation being inhibited in both strains. These results suggest that the various mutations contained in the genome of these two viral isolates may cause distinct effects on the host transcriptional response in infected host cells, especially relating to how quickly translation is dysregulated after infection. This comparison of the intracellular host response to infection with these two SARS-CoV-2 isolates suggest that some of the mechanisms associated with more severe disease from these viruses could include virus replication, metal ion usage, host translation shutoff, host transcript stability, and immune inhibition.
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Affiliation(s)
- Tiana M. Scott
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Antonio Solis-Leal
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
- Population Health and Host-pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - J. Brandon Lopez
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Richard A. Robison
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Bradford K. Berges
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brett E. Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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