1
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Danda M, Klimešová A, Kušková K, Dostálková A, Pagáčová A, Prchal J, Kapisheva M, Ruml T, Rumlová M. Biochemical characterization of naturally occurring mutations in SARS-CoV-2 RNA-dependent RNA polymerase. Protein Sci 2024; 33:e5103. [PMID: 39145418 PMCID: PMC11325161 DOI: 10.1002/pro.5103] [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: 02/24/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 08/16/2024]
Abstract
Since the emergence of SARS-CoV-2, mutations in all subunits of the RNA-dependent RNA polymerase (RdRp) of the virus have been repeatedly reported. Although RdRp represents a primary target for antiviral drugs, experimental studies exploring the phenotypic effect of these mutations have been limited. This study focuses on the phenotypic effects of substitutions in the three RdRp subunits: nsp7, nsp8, and nsp12, selected based on their occurrence rate and potential impact. We employed nano-differential scanning fluorimetry and microscale thermophoresis to examine the impact of these mutations on protein stability and RdRp complex assembly. We observed diverse impacts; notably, a single mutation in nsp8 significantly increased its stability as evidenced by a 13°C increase in melting temperature, whereas certain mutations in nsp7 and nsp8 reduced their binding affinity to nsp12 during RdRp complex formation. Using a fluorometric enzymatic assay, we assessed the overall effect on RNA polymerase activity. We found that most of the examined mutations altered the polymerase activity, often as a direct result of changes in stability or affinity to the other components of the RdRp complex. Intriguingly, a combination of nsp8 A21V and nsp12 P323L mutations resulted in a 50% increase in polymerase activity. To our knowledge, this is the first biochemical study to demonstrate the impact of amino acid mutations across all components constituting the RdRp complex in emerging SARS-CoV-2 subvariants.
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Affiliation(s)
- Matěj Danda
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Anna Klimešová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Klára Kušková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Aneta Pagáčová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Jan Prchal
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Marina Kapisheva
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
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2
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Snyder LR, Kilde I, Nemudryi A, Wiedenheft B, Koutmos M, Koutmou KS. Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription. RNA (NEW YORK, N.Y.) 2024; 30:1141-1150. [PMID: 38942480 PMCID: PMC11331411 DOI: 10.1261/rna.079991.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/20/2024] [Indexed: 06/30/2024]
Abstract
SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA life cycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or antiviral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N 6-methyladenosine and 2'-O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.
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Affiliation(s)
- Laura R Snyder
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ingrid Kilde
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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3
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Deng H, Cao H, Wang Y, Li J, Dai J, Li LF, Qiu HJ, Li S. Viral replication organelles: the highly complex and programmed replication machinery. Front Microbiol 2024; 15:1450060. [PMID: 39144209 PMCID: PMC11322364 DOI: 10.3389/fmicb.2024.1450060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
Viral infections usually induce the rearrangement of cellular cytoskeletal proteins and organelle membrane structures, thus creating independent compartments [termed replication organelles (ROs)] to facilitate viral genome replication. Within the ROs, viral replicases, including polymerases, helicases, and ligases, play functional roles during viral replication. These viral replicases are pivotal in the virus life cycle, and numerous studies have demonstrated that the viral replicases could be the potential targets for drugs development. Here, we summarize primarily the key replicases within viral ROs and emphasize the advancements of antiviral drugs targeting crucial viral replicases, providing novel insights into the future development of antiviral strategies.
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Affiliation(s)
| | | | | | | | | | | | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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4
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Hoferle PJ, Anderson TK, Kirchdoerfer RN. A genus-specific nsp12 region impacts polymerase assembly in Alpha- and Gammacoronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604833. [PMID: 39091740 PMCID: PMC11291119 DOI: 10.1101/2024.07.23.604833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Coronavirus relevancy for human health has surged over the past 20 years as they have a propensity for spillover into humans from animal reservoirs resulting in pandemics such as COVID-19. The diversity within the Coronavirinae subfamily and high infection frequency in animal species worldwide creates a looming threat that calls for research across all genera within the Coronavirinae subfamily. We sought to contribute to the limited structural knowledge within the Gammacoronavirus genera and determined the structure of the viral core replication-transcription complex (RTC) from Infectious Bronchitis Virus (IBV) using single-particle cryo-EM. Comparison between our IBV structure with published RTC structures from other Coronavirinae genera reveals structural differences across genera. Using in vitro biochemical assays, we characterized these differences and revealed their differing involvement in core RTC formation across different genera. Our findings highlight the value of cross-genera Coronavirinae studies, as they show genera specific features in coronavirus genome replication. A broader knowledge of coronavirus replication will better prepare us for future coronavirus spillovers.
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Affiliation(s)
- Peter J. Hoferle
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Thomas K. Anderson
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
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5
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Ferrer-Orta C, Vázquez-Monteagudo S, Ferrero DS, Martínez-González B, Perales C, Domingo E, Verdaguer N. Point mutations at specific sites of the nsp12-nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2. Proc Natl Acad Sci U S A 2024; 121:e2317977121. [PMID: 38990941 PMCID: PMC11260105 DOI: 10.1073/pnas.2317977121] [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: 10/16/2023] [Accepted: 06/04/2024] [Indexed: 07/13/2024] Open
Abstract
In a recent characterization of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variability present in 30 diagnostic samples from patients of the first COVID-19 pandemic wave, 41 amino acid substitutions were documented in the RNA-dependent RNA polymerase (RdRp) nsp12. Eight substitutions were selected in this work to determine whether they had an impact on the RdRp activity of the SARS-CoV-2 nsp12-nsp8-nsp7 replication complex. Three of these substitutions were found around the polymerase central cavity, in the template entry channel (D499G and M668V), and within the motif B (V560A), and they showed polymerization rates similar to the wild type RdRp. The remaining five mutations (P323L, L372F, L372P, V373A, and L527H) were placed near the nsp12-nsp8F contact surface; residues L372, V373, and L527 participated in a large hydrophobic cluster involving contacts between two helices in the nsp12 fingers and the long α-helix of nsp8F. The presence of any of these five amino acid substitutions resulted in important alterations in the RNA polymerization activity. Comparative primer elongation assays showed different behavior depending on the hydrophobicity of their side chains. The substitution of L by the bulkier F side chain at position 372 slightly promoted RdRp activity. However, this activity was dramatically reduced with the L372P, and L527H mutations, and to a lesser extent with V373A, all of which weaken the hydrophobic interactions within the cluster. Additional mutations, specifically designed to disrupt the nsp12-nsp8F interactions (nsp12-V330S, nsp12-V341S, and nsp8-R111A/D112A), also resulted in an impaired RdRp activity, further illustrating the importance of this contact interface in the regulation of RNA synthesis.
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Affiliation(s)
- Cristina Ferrer-Orta
- Structural and Molecular Biology Department, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | - Sergi Vázquez-Monteagudo
- Structural and Molecular Biology Department, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | - Diego S. Ferrero
- Structural and Molecular Biology Department, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid28040, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid28040, Spain
| | - Esteban Domingo
- Microbes in Health and Welfare Program, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid28049, Spain
| | - Nuria Verdaguer
- Structural and Molecular Biology Department, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
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6
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Anderson TK, Hoferle PJ, Chojnacki KJ, Lee K, Coon J, Kirchdoerfer R. An alphacoronavirus polymerase structure reveals conserved replication factor functions. Nucleic Acids Res 2024; 52:5975-5986. [PMID: 38442273 PMCID: PMC11162792 DOI: 10.1093/nar/gkae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine structures of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. One structure shows an unexpected nsp8 stoichiometry despite remaining bound to RNA. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha- and betacoronaviruses. Our work demonstrates the importance of studying diverse coronaviruses in revealing aspects of coronavirus replication and identifying areas of conservation to be targeted by antiviral drugs.
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Affiliation(s)
- Thomas K Anderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter J Hoferle
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kennan J Chojnacki
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kenneth W Lee
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Robert N Kirchdoerfer
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
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7
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Li CW, Chao TL, Lai CL, Lin CC, Pan MYC, Cheng CL, Kuo CJ, Wang LHC, Chang SY, Liang PH. Systematic Studies on the Anti-SARS-CoV-2 Mechanisms of Tea Polyphenol-Related Natural Products. ACS OMEGA 2024; 9:23984-23997. [PMID: 38854515 PMCID: PMC11154727 DOI: 10.1021/acsomega.4c02392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
The causative pathogen of COVID-19, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), utilizes the receptor-binding domain (RBD) of the spike protein to bind to human receptor angiotensin-converting enzyme 2 (ACE2). Further cleavage of spike by human proteases furin, TMPRSS2, and/or cathepsin L facilitates viral entry into the host cells for replication, where the maturation of polyproteins by 3C-like protease (3CLpro) and papain-like protease (PLpro) yields functional nonstructural proteins (NSPs) such as RNA-dependent RNA polymerase (RdRp) to synthesize mRNA of structural proteins. By testing the tea polyphenol-related natural products through various assays, we found that the active antivirals prevented SARS-CoV-2 entry by blocking the RBD/ACE2 interaction and inhibiting the relevant human proteases, although some also inhibited the viral enzymes essential for replication. Due to their multitargeting properties, these compounds were often misinterpreted for their antiviral mechanisms. In this study, we provide a systematic protocol to check and clarify their anti-SARS-CoV-2 mechanisms, which should be applicable for all of the antivirals.
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Affiliation(s)
- Chen-Wei Li
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Tai-Ling Chao
- Department
of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan
| | - Chin-Lan Lai
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Cheng-Chin Lin
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Max Yu-Chen Pan
- Institute
of Molecular and Cellular Biology, National
Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chieh-Ling Cheng
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Chih-Jung Kuo
- Department
of Veterinary Medicine, National Chung Hsing
University, Taichung 40227, Taiwan
| | - Lily Hui-Ching Wang
- Institute
of Molecular and Cellular Biology, National
Tsing Hua University, Hsinchu 30013, Taiwan
| | - Sui-Yuan Chang
- Department
of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan
- Department
of Laboratory Medicine, National Taiwan
University Hospital, Taipei 10002, Taiwan
| | - Po-Huang Liang
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
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8
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Kenward C, Vuckovic M, Paetzel M, Strynadka NCJ. Kinetic comparison of all eleven viral polyprotein cleavage site processing events by SARS-CoV-2 main protease using a linked protein FRET platform. J Biol Chem 2024; 300:107367. [PMID: 38750796 PMCID: PMC11209022 DOI: 10.1016/j.jbc.2024.107367] [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: 02/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
The main protease (Mpro) remains an essential therapeutic target for COVID-19 post infection intervention given its critical role in processing the majority of viral proteins encoded by the genome of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2). Upon viral entry, the +ssRNA genome is translated into two long polyproteins (pp1a or the frameshift-dependent pp1ab) containing all the nonstructural proteins (nsps) required by the virus for immune modulation, replication, and ultimately, virion assembly. Included among these nsps is the cysteine protease Mpro (nsp5) which self-excises from the polyprotein, dimerizes, then sequentially cleaves 11 of the 15 cut-site junctions found between each nsp within the polyprotein. Many structures of Mpro (often bound to various small molecule inhibitors or peptides) have been detailed recently, including structures of Mpro bound to each of the polyprotein cleavage sequences, showing that Mpro can accommodate a wide range of targets within its active site. However, to date, kinetic characterization of the interaction of Mpro with each of its native cleavage sequences remains incomplete. Here, we present a robust and cost-effective FRET based system that benefits from a more consistent presentation of the substrate that is also closer in organization to the native polyprotein environment compared to previously reported FRET systems that use chemically modified peptides. Using this system, we were able to show that while each site maintains a similar Michaelis constant, the catalytic efficiency of Mpro varies greatly between cut-site sequences, suggesting a clear preference for the order of nsp processing.
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Affiliation(s)
- Calem Kenward
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marija Vuckovic
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Paetzel
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, The University of British Columbia, Vancouver, British Columbia, Canada.
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9
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Ge X, Zhou H, Shen F, Yang G, Zhang Y, Zhang X, Li H. SARS-CoV-2 subgenomic RNA: formation process and rapid molecular diagnostic methods. Clin Chem Lab Med 2024; 62:1019-1028. [PMID: 38000044 DOI: 10.1515/cclm-2023-0846] [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: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus disease-2019 (COVID-19) is spreading worldwide and posing enormous losses to human health and socio-economic. Due to the limitations of medical and health conditions, it is still a huge challenge to develop appropriate discharge standards for patients with COVID-19 and to use medical resources in a timely and effective manner. Similar to other coronaviruses, SARS-CoV-2 has a very complex discontinuous transcription process to generate subgenomic RNA (sgRNA). Some studies support that sgRNA of SARS-CoV-2 can only exist when the virus is active and is an indicator of virus replication. The results of sgRNA detection in patients can be used to evaluate the condition of hospitalized patients, which is expected to save medical resources, especially personal protective equipment. There have been numerous investigations using different methods, especially molecular methods to detect sgRNA. Here, we introduce the process of SARS-CoV-2 sgRNA formation and the commonly used molecular diagnostic methods to bring a new idea for clinical detection in the future.
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Affiliation(s)
- Xiao Ge
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Huizi Zhou
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Fangyuan Shen
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Guimao Yang
- Department of Medical Laboratory, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P.R. China
| | - Yubo Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Xiaoyu Zhang
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
| | - Heng Li
- Department of Medical Laboratory, Weifang Medical University, Weifang, Shandong, P.R. China
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10
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Israr J, Alam S, Kumar A. Drug repurposing for respiratory infections. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 207:207-230. [PMID: 38942538 DOI: 10.1016/bs.pmbts.2024.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Respiratory infections such as Coronavirus disease 2019 are a substantial worldwide health challenge, frequently resulting in severe sickness and death, especially in susceptible groups. Conventional drug development for respiratory infections faces obstacles such as extended timescales, substantial expenses, and the rise of resistance to current treatments. Drug repurposing is a potential method that has evolved to quickly find and reuse existing medications for treating respiratory infections. Drug repurposing utilizes medications previously approved for different purposes, providing a cost-effective and time-efficient method to tackle pressing medical needs. This chapter summarizes current progress and obstacles in repurposing medications for respiratory infections, focusing on notable examples of repurposed pharmaceuticals and their probable modes of action. The text also explores the significance of computational approaches, high-throughput screening, and preclinical investigations in identifying potential candidates for repurposing. The text delves into the significance of regulatory factors, clinical trial structure, and actual data in confirming the effectiveness and safety of repurposed medications for respiratory infections. Drug repurposing is a valuable technique for quickly increasing the range of treatments for respiratory infections, leading to better patient outcomes and decreasing the worldwide disease burden.
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Affiliation(s)
- Juveriya Israr
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, India; Department of Biotechnology, Era University, Lucknow, Uttar Pradesh, India
| | - Shabroz Alam
- Department of Biotechnology, Era University, Lucknow, Uttar Pradesh, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, Mandhana, Kanpur, Uttar Pradesh, India.
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11
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Yadav AJ, Kumar S, Maurya S, Bhagat K, Padhi AK. Interface design of SARS-CoV-2 symmetrical nsp7 dimer and machine learning-guided nsp7 sequence prediction reveals physicochemical properties and hotspots for nsp7 stability, adaptation, and therapeutic design. Phys Chem Chem Phys 2024; 26:14046-14061. [PMID: 38686454 DOI: 10.1039/d4cp01014k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The COVID-19 pandemic, driven by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates a profound understanding of the virus and its lifecycle. As an RNA virus with high mutation rates, SARS-CoV-2 exhibits genetic variability leading to the emergence of variants with potential implications. Among its key proteins, the RNA-dependent RNA polymerase (RdRp) is pivotal for viral replication. Notably, RdRp forms dimers via non-structural protein (nsp) subunits, particularly nsp7, crucial for efficient viral RNA copying. Similar to the main protease (Mpro) of SARS-CoV-2, there is a possibility that the nsp7 might also undergo mutational selection events to generate more stable and adaptable versions of nsp7 dimer during virus evolution. However, efforts to obtain such cohesive and comprehensive information are lacking. To address this, we performed this study focused on deciphering the molecular intricacies of nsp7 dimerization using a multifaceted approach. Leveraging computational protein design (CPD), machine learning (ML), AlphaFold v2.0-based structural analysis, and several related computational approaches, we aimed to identify critical residues and mutations influencing nsp7 dimer stability and adaptation. Our methodology involved identifying potential hotspot residues within the dimeric nsp7 interface using an interface-based CPD approach. Through Rosetta-based symmetrical protein design, we designed and modulated nsp7 dimerization, considering selected interface residues. Analysis of physicochemical features revealed acceptable structural changes and several structural and residue-specific insights emphasizing the intricate nature of such protein-protein complexes. Our ML models, particularly the random forest regressor (RFR), accurately predicted binding affinities and ML-guided sequence predictions corroborated CPD findings, elucidating potential nsp7 mutations and their impact on binding affinity. Validation against clinical sequencing data demonstrated the predictive accuracy of our approach. Moreover, AlphaFold v2.0 structural analyses validated optimal dimeric configurations of affinity-enhancing designs, affirming methodological precision. Affinity-enhancing designs exhibited favourable energetics and higher binding affinity as compared to their counterparts. The obtained physicochemical properties, molecular interactions, and sequence predictions advance our understanding of SARS-CoV-2 evolution and inform potential avenues for therapeutic intervention against COVID-19.
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Affiliation(s)
- Amar Jeet Yadav
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Shivank Kumar
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Khushboo Bhagat
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
| | - Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi 221005, Uttar Pradesh, India.
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12
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Kuzikov M, Reinshagen J, Wycisk K, Corona A, Esposito F, Malune P, Manelfi C, Iaconis D, Beccari A, Tramontano E, Nowotny M, Windshügel B, Gribbon P, Zaliani A. Drug repurposing screen to identify inhibitors of the RNA polymerase (nsp12) and helicase (nsp13) from SARS-CoV-2 replication and transcription complex. Virus Res 2024; 343:199356. [PMID: 38490582 PMCID: PMC10958470 DOI: 10.1016/j.virusres.2024.199356] [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: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Coronaviruses contain one of the largest genomes among the RNA viruses, coding for 14-16 non-structural proteins (nsp) that are involved in proteolytic processing, genome replication and transcription, and four structural proteins that build the core of the mature virion. Due to conservation across coronaviruses, nsps form a group of promising drug targets as their inhibition directly affects viral replication and, therefore, progression of infection. A minimal but fully functional replication and transcription complex was shown to be formed by one RNA-dependent RNA polymerase (nsp12), one nsp7, two nsp8 accessory subunits, and two helicase (nsp13) enzymes. Our approach involved, targeting nsp12 and nsp13 to allow multiple starting point to interfere with virus infection progression. Here we report a combined in-vitro repurposing screening approach, identifying new and confirming reported SARS-CoV-2 nsp12 and nsp13 inhibitors.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany.
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Krzysztof Wycisk
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Paolo Malune
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Daniela Iaconis
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Andrea Beccari
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Marcin Nowotny
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
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13
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Ohyama T, Osawa T, Sekine SI, Ishii Y. NMR Studies of Genomic RNA in 3' Untranslated Region Unveil Pseudoknot Structure that Initiates Viral RNA Replication in SARS-CoV-2. JACS AU 2024; 4:1323-1333. [PMID: 38665648 PMCID: PMC11041675 DOI: 10.1021/jacsau.3c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/20/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024]
Abstract
In the 3' untranslated region of the SARS-CoV-2 virus RNA genome, genomic RNA replication is initiated in the highly conserved region called 3'PK, containing three stem structures (P1pk, P2, and P5). According to one proposed mechanism, P1pk and distal P2 stems switch their structure to a pseudoknot through base-pairing, thereby initiating transcription by recruiting RNA-dependent RNA polymerase complexed with nonstructural proteins (nsp)7 and nsp8. However, experimental evidence of pseudoknot formation or structural switching is unavailable. Using SARS-CoV-2 3'PK fragments, we show that 3'PK adopted stem-loop and pseudoknot forms in a mutually exclusive manner. When P1pk and P2 formed a pseudoknot, the P5 stem, which includes a sequence at the 3' end, exited from the stem-loop structure and opened up. Interaction with the nsp7/nsp8 complex destabilized the stem-loop form but did not alter the pseudoknot form. These results suggest that the interaction between the pseudoknot and nsp7/nsp8 complex transformed the 3' end of viral genomic RNA into single-stranded RNA ready for synthesis, presenting the unique pseudoknot structure as a potential pharmacological target.
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Affiliation(s)
- Takako Ohyama
- Laboratory for Advanced NMR Application and
Development, Center for Biosystems Dynamics Research, RIKEN,
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa,
Japan
- School of Life Science and Technology,
Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku,
Yokohama 226-8503, Kanagawa, Japan
| | - Takuo Osawa
- Laboratory for Transcription Structural Biology,
Center for Biosystems Dynamics Research, RIKEN, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Shun-ichi Sekine
- Laboratory for Transcription Structural Biology,
Center for Biosystems Dynamics Research, RIKEN, 1-7-22
Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan
| | - Yoshitaka Ishii
- Laboratory for Advanced NMR Application and
Development, Center for Biosystems Dynamics Research, RIKEN,
1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa,
Japan
- School of Life Science and Technology,
Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku,
Yokohama 226-8503, Kanagawa, Japan
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14
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Tang WF, Chang YH, Lin CC, Jheng JR, Hsieh CF, Chin YF, Chang TY, Lee JC, Liang PH, Lin CY, Lin GH, Cai JY, Chen YL, Chen YS, Tsai SK, Liu PC, Yang CM, Shadbahr T, Tang J, Hsu YL, Huang CH, Wang LY, Chen CC, Kau JH, Hung YJ, Lee HY, Wang WC, Tsai HP, Horng JT. BPR3P0128, a non-nucleoside RNA-dependent RNA polymerase inhibitor, inhibits SARS-CoV-2 variants of concern and exerts synergistic antiviral activity in combination with remdesivir. Antimicrob Agents Chemother 2024; 68:e0095623. [PMID: 38446062 PMCID: PMC10989008 DOI: 10.1128/aac.00956-23] [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: 07/20/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024] Open
Abstract
Viral RNA-dependent RNA polymerase (RdRp), a highly conserved molecule in RNA viruses, has recently emerged as a promising drug target for broad-acting inhibitors. Through a Vero E6-based anti-cytopathic effect assay, we found that BPR3P0128, which incorporates a quinoline core similar to hydroxychloroquine, outperformed the adenosine analog remdesivir in inhibiting RdRp activity (EC50 = 0.66 µM and 3 µM, respectively). BPR3P0128 demonstrated broad-spectrum activity against various severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern. When introduced after viral adsorption, BPR3P0128 significantly decreased SARS-CoV-2 replication; however, it did not affect the early entry stage, as evidenced by a time-of-drug-addition assay. This suggests that BPR3P0128's primary action takes place during viral replication. We also found that BPR3P0128 effectively reduced the expression of proinflammatory cytokines in human lung epithelial Calu-3 cells infected with SARS-CoV-2. Molecular docking analysis showed that BPR3P0128 targets the RdRp channel, inhibiting substrate entry, which implies it operates differently-but complementary-with remdesivir. Utilizing an optimized cell-based minigenome RdRp reporter assay, we confirmed that BPR3P0128 exhibited potent inhibitory activity. However, an enzyme-based RdRp assay employing purified recombinant nsp12/nsp7/nsp8 failed to corroborate this inhibitory activity. This suggests that BPR3P0128 may inhibit activity by targeting host-related RdRp-associated factors. Moreover, we discovered that a combination of BPR3P0128 and remdesivir had a synergistic effect-a result likely due to both drugs interacting with separate domains of the RdRp. This novel synergy between the two drugs reinforces the potential clinical value of the BPR3P0128-remdesivir combination in combating various SARS-CoV-2 variants of concern.
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Affiliation(s)
- Wen-Fang Tang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Yu-Hsiu Chang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Chin Lin
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Jia-Rong Jheng
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Chung-Fan Hsieh
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yuan-Fan Chin
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
| | - Tein-Yao Chang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Department of Pathology and Graduate Institute of Pathology and Parasitology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Jin-Ching Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Yi Lin
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Guan-Hua Lin
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Jie-Yun Cai
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Yu-Li Chen
- Research Center for Industry of Human Ecology and Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Yuan-Siao Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Shan-Ko Tsai
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Ping-Cheng Liu
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Chuen-Mi Yang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Tolou Shadbahr
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Jing Tang
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Yu-Lin Hsu
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Chih-Heng Huang
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Department of Microbiology and Immunology, National Defense Medical Center, Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Ling-Yu Wang
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Division of Medical Oncology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng Cheung Chen
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Jyh-Hwa Kau
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Yi-Jen Hung
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Hsin-Yi Lee
- Institute of Biotechnology and Pharmaceutical Research, Value-Added MedChem Innovation Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wen-Chieh Wang
- Institute of Biotechnology and Pharmaceutical Research, Value-Added MedChem Innovation Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Hui-Ping Tsai
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei, Taiwan
| | - Jim-Tong Horng
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Biochemistry and Molecular Biology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Research Center for Industry of Human Ecology and Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
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15
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Subong BJJ, Ozawa T. Bio-Chemoinformatics-Driven Analysis of nsp7 and nsp8 Mutations and Their Effects on Viral Replication Protein Complex Stability. Curr Issues Mol Biol 2024; 46:2598-2619. [PMID: 38534781 DOI: 10.3390/cimb46030165] [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: 02/20/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/28/2024] Open
Abstract
The nonstructural proteins 7 and 8 (nsp7 and nsp8) of SARS-CoV-2 are highly important proteins involved in the RNA-dependent polymerase (RdRp) protein replication complex. In this study, we analyzed the global mutation of nsp7 and nsp8 in 2022 and 2023 and analyzed the effects of mutation on the viral replication protein complex using bio-chemoinformatics. Frequently occurring variants are found to be single amino acid mutations for both nsp7 and nsp8. The most frequently occurring mutations for nsp7 which include L56F, L71F, S25L, M3I, D77N, V33I and T83I are predicted to cause destabilizing effects, whereas those in nsp8 are predicted to cause stabilizing effects, with the threonine to isoleucine mutation (T89I, T145I, T123I, T148I, T187I) being a frequent mutation. A conserved domain database analysis generated critical interaction residues for nsp7 (Lys-7, His-36 and Asn-37) and nsp8 (Lys-58, Pro-183 and Arg-190), which, according to thermodynamic calculations, are prone to destabilization. Trp-29, Phe-49 of nsp7 and Trp-154, Tyr-135 and Phe-15 of nsp8 cause greater destabilizing effects to the protein complex based on a computational alanine scan suggesting them as possible new target sites. This study provides an intensive analysis of the mutations of nsp7 and nsp8 and their possible implications for viral complex stability.
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Affiliation(s)
- Bryan John J Subong
- Department of Chemistry, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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16
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Hassan SS, Bhattacharya T, Nawn D, Jha I, Basu P, Redwan EM, Lundstrom K, Barh D, Andrade BS, Tambuwala MM, Aljabali AA, Hromić-Jahjefendić A, Baetas-da-Cruz W, Serrano-Aroca Á, Uversky VN. SARS-CoV-2 NSP14 governs mutational instability and assists in making new SARS-CoV-2 variants. Comput Biol Med 2024; 170:107899. [PMID: 38232455 DOI: 10.1016/j.compbiomed.2023.107899] [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: 09/26/2023] [Revised: 12/03/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional Nonstructural protein 14 (NSP14) enzyme, possessing exonuclease and messenger RNA (mRNA) capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscoresthe dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Tanishta Bhattacharya
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, IISER Berhampur Transit campus (Govt. ITI Building), Engg. School Junction, Berhampur, 760010, Odisha, India.
| | - Debaleena Nawn
- Indian Research Institute for Integrated Medicine (IRIIM), Unsani, Howrah, 711302, West Bengal, India.
| | - Ishana Jha
- Department of Bioinformatics, Pondicherry University, Chinna Kalapet, Kalapet, Puducherry 605014, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa; Adjunct Faculty, Woxsen School of Sciences, Woxsen University, Telangana, 500 033, India.
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
| | | | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié 45083-900, Brazil.
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK; College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Alaa A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan.
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka cesta 15, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Wagner Baetas-da-Cruz
- Centre for Experimental Surgery, Translational Laboratory in Molecular Physiology, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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17
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Vijay A, Sreyas Adury VS, Mukherjee A. Targeting RdRp of SARS-CoV-2 with De Novo Molecule Generation. ACS APPLIED BIO MATERIALS 2024; 7:609-616. [PMID: 37566736 DOI: 10.1021/acsabm.3c00339] [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: 08/13/2023]
Abstract
Viruses are known for their extremely high mutation rates, allowing them to evade both the human immune system and many forms of standard medicine. Despite this, the RNA dependent RNA polymerase (RdRp) of the RNA viruses has been largely conserved, and any significant mutation of this protein is unlikely. The recent COVID-19 pandemic presents a need for therapeutics. We have designed a de novo drug design algorithm that generates strong binding ligands from scratch, based on only the structure of the target protein's receptor. In this paper, we applied our method to target SARS-CoV-2 RdRp and generated several de novo molecules. We then chose some drug molecules based on the structural similarity to some of our strongest binding de novo molecules. Subsequently, we showed, using rigorous all-atom explicit-water free energy calculations in near-microsecond time scales using state-of-the-art well-tempered metadynamics simulations, that some of our de novo generated ligands bind more strongly to RdRp than the recent FDA approved drug remdesivir in its active form, remdesivir triphosphate (RTP). We elucidated the binding mechanism for some of the top binders and compared it with RTP. We believe that this work will be useful both by presenting lead structures for RdRp inhibition and by delivering key insights into the residues of the protein potentially involved in the binding/unbinding of these small molecule drugs, leading to more targeted studies in the future.
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Affiliation(s)
- Amal Vijay
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | | | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
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18
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Chen H, Wan J, Wei M, Liu P, Kong L, Xin X. Expression and immunogenicity of non-structural protein 8 of porcine epidemic diarrhea virus. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2024; 15:65-73. [PMID: 38465319 PMCID: PMC10924293 DOI: 10.30466/vrf.2023.2009322.3977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/05/2023] [Indexed: 03/12/2024]
Abstract
The non-structural protein (nsp) 8 of the porcine epidemic diarrhea virus (PEDV) is highly stable across different PEDV strains and plays an important role in PEDV virulence. In current study, nsp8 prokaryotic expression vectors were constructed based on parental vectors pMAL-c2x-maltose binding protein (MBP) and pET-28a (+). Subsequently, the optimization of expression conditions in Escherichia coli, including induced temperature, time and isopropyl β-D-thiogalactopyranoside concentration were performed to obtain a stable expression of MBP-nsp8 and nsp8. The nsp8 fused with MBP increased the water solubility of the expressed products. Target proteins were further purified from E. coli culture and their immunogenicities were evaluated in vivo by mice. The antibody titers of serum from nsp8 immunized mice were up to 1:7,750,000 when measured by indirect enzyme-linked immunosorbent assay; meanwhile, the mice immunized with MBP-nsp8 gave an antibody titer reaching 1:1,000,000. In all, the expression and purification system of PEDV nsp8 and MBP-nsp8 were successfully established in this work and a strong immune response was elicited in mice by both purified nsp8 and MBP-nsp8, providing a basis for the study of the structure and function of PEDV nsp8.
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Affiliation(s)
- Hong Chen
- Institute of Pathogenic Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China;
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China.
| | - Jiawu Wan
- Institute of Pathogenic Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China;
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China.
| | - Meihua Wei
- Institute of Pathogenic Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China;
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China.
| | - Ping Liu
- Institute of Pathogenic Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China;
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China.
| | - Lingbao Kong
- Institute of Pathogenic Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China;
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China.
| | - Xiu Xin
- Institute of Pathogenic Microbiology, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China;
- Nanchang Key Laboratory of Animal Virus and Genetic Engineering, College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China.
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19
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [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: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Lima Neto JX, Bezerra KS, Barbosa ED, Araujo RL, Galvão DS, Lyra ML, Oliveira JIN, Akash S, Jardan YAB, Nafidi HA, Bourhia M, Fulco UL. Investigation of protein-protein interactions and hotspot region on the NSP7-NSP8 binding site in NSP12 of SARS-CoV-2. Front Mol Biosci 2024; 10:1325588. [PMID: 38304231 PMCID: PMC10830813 DOI: 10.3389/fmolb.2023.1325588] [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: 10/21/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024] Open
Abstract
Background: The RNA-dependent RNA polymerase (RdRp) complex, essential in viral transcription and replication, is a key target for antiviral therapeutics. The core unit of RdRp comprises the nonstructural protein NSP12, with NSP7 and two copies of NSP8 (NSP81 and NSP82) binding to NSP12 to enhance its affinity for viral RNA and polymerase activity. Notably, the interfaces between these subunits are highly conserved, simplifying the design of molecules that can disrupt their interaction. Methods: We conducted a detailed quantum biochemical analysis to characterize the interactions within the NSP12-NSP7, NSP12-NSP81, and NSP12-NSP82 dimers. Our objective was to ascertain the contribution of individual amino acids to these protein-protein interactions, pinpointing hotspot regions crucial for complex stability. Results: The analysis revealed that the NSP12-NSP81 complex possessed the highest total interaction energy (TIE), with 14 pairs of residues demonstrating significant energetic contributions. In contrast, the NSP12-NSP7 complex exhibited substantial interactions in 8 residue pairs, while the NSP12-NSP82 complex had only one pair showing notable interaction. The study highlighted the importance of hydrogen bonds and π-alkyl interactions in maintaining these complexes. Intriguingly, introducing the RNA sequence with Remdesivir into the complex resulted in negligible alterations in both interaction energy and geometric configuration. Conclusion: Our comprehensive analysis of the RdRp complex at the protein-protein interface provides invaluable insights into interaction dynamics and energetics. These findings can guide the design of small molecules or peptide/peptidomimetic ligands to disrupt these critical interactions, offering a strategic pathway for developing effective antiviral drugs.
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Affiliation(s)
- José Xavier Lima Neto
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Katyanna Sales Bezerra
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Emmanuel Duarte Barbosa
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Roniel Lima Araujo
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | | | | | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal, Brazil
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Wang T, Zheng G, Chen Z, Wang Y, Zhao C, Li Y, Yuan Y, Duan H, Zhu H, Yang X, Li W, Du W, Li Y, Li D. Drug repurposing screens identify Tubercidin as a potent antiviral agent against porcine nidovirus infections. Virus Res 2024; 339:199275. [PMID: 38008220 PMCID: PMC10730850 DOI: 10.1016/j.virusres.2023.199275] [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: 09/07/2023] [Revised: 10/18/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
The emergence of new coronaviruses poses a significant threat to animal husbandry and human health. Porcine epidemic diarrhea virus (PEDV) is considered a re-emerging porcine enteric coronavirus, which causes fatal watery diarrhea in piglets. Currently, there are no effective drugs to combat PEDV. Drug repurposing screens have emerged as an attractive strategy to accelerate antiviral drug discovery and development. Here, we screened 206 natural products for antiviral activity using live PEDV infection in Vero cells and identified ten candidate antiviral agents. Among them, Tubercidin, a nucleoside analog derived from Streptomyces tubercidicus, showed promising antiviral activity against PEDV infection. Furthermore, we demonstrated that Tubercidin exhibited significant antiviral activity against both classical and variant PEDV. Time of addition assay showed that Tubercidin displayed a significant inhibitory effect on viral post-entry events but not during other periods. Molecular docking analysis indicated that Tubercidin had better docking efficiency and formed hydrophobic interactions with the active pocket of RNA-dependent RNA polymerase (RdRp) of PEDV and other nidoviruses. Additionally, Tubercidin can effectively suppress other porcine nidoviruses, such as SADS-CoV and PRRSV, demonstrating its broad-spectrum antiviral properties. In summary, our findings provide valuable evidence for the antiviral activity of Tubercidin and offer insights into the development of new strategies for the prevention and treatment of coronavirus infections.
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Affiliation(s)
- Tianliang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Guanmin Zheng
- School of Medicine, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Zilu Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yue Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenxu Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqin Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yixin Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong Duan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China
| | - Hongsen Zhu
- School of Medicine, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China
| | - Wentao Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wenjuan Du
- Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CL, the Netherlands
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China.
| | - Dongliang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China.
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22
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Zargari F, Mohammadi M, Nowroozi A, Morowvat MH, Nakhaei E, Rezagholi F. The Inhibitory Effects of the Herbals Secondary Metabolites (7α-acetoxyroyleanone, Curzerene, Incensole, Harmaline, and Cannabidiol) on COVID-19: A Molecular Docking Study. Recent Pat Biotechnol 2024; 18:316-331. [PMID: 38817009 DOI: 10.2174/0118722083246773231108045238] [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: 04/04/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 06/01/2024]
Abstract
BACKGROUND Since the COVID-19 outbreak in early 2020, researchers and studies are continuing to find drugs and/or vaccines against the disease. As shown before, medicinal plants can be very good sources against viruses because of their secondary compounds which may cure diseases and help in survival of patients. There is a growing trend in the filed patents in this field. AIMS In the present study, we test and suggest the inhibitory potential of five herbal based extracts including 7α-acetoxyroyleanone, Curzerene, Incensole, Harmaline, and Cannabidiol with antivirus activity on the models of the significant antiviral targets for COVID-19 like spike glycoprotein, Papain-like protease (PLpro), non-structural protein 15 (NSP15), RNA-dependent RNA polymerase and core protease by molecular docking study. METHODS The Salvia rythida root was extracted, dried, and pulverized by a milling machine. The aqueous phase and the dichloromethane phase of the root extractive were separated by two-phase extraction using a separatory funnel. The separation was performed using the column chromatography method. The model of the important antivirus drug target of COVID-19 was obtained from the Protein Data Bank (PDB) and modified. TO study the binding difference between the studied molecules, the docking study was performed. RESULTS These herbal compounds are extracted from Salvia rhytidea, Curcuma zeodaria, Frankincense, Peganum harmala, and Cannabis herbs, respectively. The binding energies of all compounds on COVID-19 main targets are located in the limited area of 2.22-5.30 kcal/mol. This range of binding energies can support our hypothesis for the presence of the inhibitory effects of the secondary metabolites of mentioned structures on COVID-19. Generally, among the investigated herbal structures, Cannabidiol and 7α- acetoxyroyleanone compounds with the highest binding energy have the most inhibitory potential. The least inhibitory effects are related to the Curzerene and Incensole structures by the lowest binding affinity. CONCLUSION The general arrangement of the basis of the potential barrier of binding energies is in the order below: Cannabidiol > 7α-acetoxyroyleanone > Harmaline> Incensole > Curzerene. Finally, the range of docking scores for investigated herbal compounds on the mentioned targets indicates that the probably inhibitory effects on these targets obey the following order: main protease> RNA-dependent RNA polymerase> PLpro> NSP15> spike glycoprotein.
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Affiliation(s)
- Farshid Zargari
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Mehdi Mohammadi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Mohammad Hossein Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
| | - Ebrahim Nakhaei
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Fatemeh Rezagholi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
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Mia ME, Howlader M, Akter F, Hossain MM. Preclinical and Clinical Investigations of Potential Drugs and Vaccines for COVID-19 Therapy: A Comprehensive Review With Recent Update. CLINICAL PATHOLOGY (THOUSAND OAKS, VENTURA COUNTY, CALIF.) 2024; 17:2632010X241263054. [PMID: 39070952 PMCID: PMC11282570 DOI: 10.1177/2632010x241263054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 06/03/2024] [Indexed: 07/30/2024]
Abstract
The COVID-19 pandemic-led worldwide healthcare crisis necessitates prompt societal, ecological, and medical efforts to stop or reduce the rising number of fatalities. Numerous mRNA based vaccines and vaccines for viral vectors have been licensed for use in emergencies which showed 90% to 95% efficacy in preventing SARS-CoV-2 infection. However, safety issues, vaccine reluctance, and skepticism remain major concerns for making mass vaccination a successful approach to treat COVID-19. Hence, alternative therapeutics is needed for eradicating the global burden of COVID-19 from developed and low-resource countries. Repurposing current medications and drug candidates could be a more viable option for treating SARS-CoV-2 as these therapies have previously passed a number of significant checkpoints for drug development and patient care. Besides vaccines, this review focused on the potential usage of alternative therapeutic agents including antiviral, antiparasitic, and antibacterial drugs, protease inhibitors, neuraminidase inhibitors, and monoclonal antibodies that are currently undergoing preclinical and clinical investigations to assess their effectiveness and safety in the treatment of COVID-19. Among the repurposed drugs, remdesivir is considered as the most promising agent, while favipiravir, molnupiravir, paxlovid, and lopinavir/ritonavir exhibited improved therapeutic effects in terms of elimination of viruses. However, the outcomes of treatment with oseltamivir, umifenovir, disulfiram, teicoplanin, and ivermectin were not significant. It is noteworthy that combining multiple drugs as therapy showcases impressive effectiveness in managing individuals with COVID-19. Tocilizumab is presently employed for the treatment of patients who exhibit COVID-19-related pneumonia. Numerous antiviral drugs such as galidesivir, griffithsin, and thapsigargin are under clinical trials which could be promising for treating COVID-19 individuals with severe symptoms. Supportive treatment for patients of COVID-19 may involve the use of corticosteroids, convalescent plasma, stem cells, pooled antibodies, vitamins, and natural substances. This study provides an updated progress in SARS-CoV-2 medications and a crucial guide for inventing novel interventions against COVID-19.
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Affiliation(s)
- Md. Easin Mia
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mithu Howlader
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Farzana Akter
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Murad Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
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24
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Alshahrani MM. Inhibition of SARS-CoV-2 NSP-15 by Uridine-5'-Monophosphate Analogues Using QSAR Modelling, Molecular Dynamics Simulations, and Free Energy Landscape. Saudi Pharm J 2024; 32:101914. [PMID: 38111672 PMCID: PMC10727945 DOI: 10.1016/j.jsps.2023.101914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/09/2023] [Indexed: 12/20/2023] Open
Abstract
SARS-CoV-2 is accountable for severe social and economic disruption around the world causing COVID-19. Non-structural protein-15 (NSP15) possesses a domain that is vital to the viral life cycle and is known as uridylate-specific endoribonuclease (EndoU). This domain binds to the uridine 5'-monophosphate (U5P) so that the protein may carry out its native activity. It is considered a vital drug target to inhibit the growth of the virus. Thus, in this current study, ML-based QSAR and virtual screening of U5P analogues targeting Nsp15 were performed to identify potential molecules against SARS-CoV-2. Screening of 816 unique U5P analogues using ML-based QSAR identified 397 compounds ranked on their predicted bioactivity (pIC50). Further, molecular docking and hydrogen bond interaction analysis resulted in the selection of the top three compounds (53309102, 57398422, and 76314921). Molecular dynamics simulation of the most promising compounds showed that two molecules 53309102 and 57398422 acted as potential binders of Nsp15. The compound was able to inhibit nsp15 activity as it was successfully bound to the active site of the nsp15 protein. This was achieved by the formation of relevant contacts with enzymatically critical amino acid residues (His235, His250, and Lys290). Principal component analysis and free energy landscape studies showed stable complex formation while MM/GBSA calculation showed lower binding energies for 53309102 (ΔGTOTAL = -29.4 kcal/mol) and 57398422 (ΔGTOTAL = -39.4 kcal/mol) compared to the control U5P (ΔGTOTAL = -18.8 kcal/mol). This study aimed to identify analogues of U5P inhibiting the NSP15 function that potentially could be used for treating COVID-19.
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Affiliation(s)
- Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran 61441, Saudi Arabia
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25
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Islam MA. A review of SARS-CoV-2 variants and vaccines: Viral properties, mutations, vaccine efficacy, and safety. INFECTIOUS MEDICINE 2023; 2:247-261. [PMID: 38205179 PMCID: PMC10774670 DOI: 10.1016/j.imj.2023.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/09/2023] [Accepted: 08/28/2023] [Indexed: 01/12/2024]
Abstract
The severe acute respiratory syndrome coronavirus disease 2 instigated by coronavirus disease of 2019 (COVID-19) has delivered an unfathomable obstruction that has touched all sectors worldwide. Despite new vaccine technologies and mass administration of booster doses, the virus persists, and unknown the ending of the pandemic for new variants and sub-variants. Moreover, whether leaning on home medications or using plant extracts is sufficient often to combat the virus has generated tremendous interest in the scientific fraternity. Different databases including PubMed, Scopus, Web of Science, and Google Scholar used to find published articles linked with related topics. Currently, COVID-19 third and fourth shots of vaccines are progressively administered worldwide, where some countries trail others by a significant margin. Many proteins related to viral activity have changed, possibly boosting the virus infectivity and making antibodies ineffective. This study will reminisce the viral genome, associated pathways for viral protein functions, variants, and their mutations. The current, comprehensive review will also provide information on vaccine technologies developed by several biotech companies and the efficacy of their doses, costs including boosters on a mass level. As no vaccine is working to protect fully against all the variants, the new proactive vaccine research needs to be conducted based on all variants, their sub-lineage, and mutations.
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Affiliation(s)
- Md. Aminul Islam
- Advanced Molecular Lab, Department of Microbiology, President Abdul Hamid Medical College, Karimganj 2310, Bangladesh
- COVID-19 Diagnostic lab, Department of Microbiology, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
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26
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Comunale BA, Larson RJ, Jackson-Ward E, Singh A, Koback FL, Engineer LD. The Functional Implications of Broad Spectrum Bioactive Compounds Targeting RNA-Dependent RNA Polymerase (RdRp) in the Context of the COVID-19 Pandemic. Viruses 2023; 15:2316. [PMID: 38140557 PMCID: PMC10747147 DOI: 10.3390/v15122316] [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: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND As long as COVID-19 endures, viral surface proteins will keep changing and new viral strains will emerge, rendering prior vaccines and treatments decreasingly effective. To provide durable targets for preventive and therapeutic agents, there is increasing interest in slowly mutating viral proteins, including non-surface proteins like RdRp. METHODS A scoping review of studies was conducted describing RdRp in the context of COVID-19 through MEDLINE/PubMed and EMBASE. An iterative approach was used with input from content experts and three independent reviewers, focused on studies related to either RdRp activity inhibition or RdRp mechanisms against SARS-CoV-2. RESULTS Of the 205 records screened, 43 studies were included in the review. Twenty-five evaluated RdRp activity inhibition, and eighteen described RdRp mechanisms of existing drugs or compounds against SARS-CoV-2. In silico experiments suggested that RdRp inhibitors developed for other RNA viruses may be effective in disrupting SARS-CoV-2 replication, indicating a possible reduction of disease progression from current and future variants. In vitro, in vivo, and human clinical trial studies were largely consistent with these findings. CONCLUSIONS Future risk mitigation and treatment strategies against forthcoming SARS-CoV-2 variants should consider targeting RdRp proteins instead of surface proteins.
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Affiliation(s)
- Brittany A. Comunale
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robin J. Larson
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Department of Palliative Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Erin Jackson-Ward
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aditi Singh
- Department of Biological Sciences, University of California San Diego, La Jolla, CA 92161, USA
| | | | - Lilly D. Engineer
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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27
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Bag SS, Sinha S, Dutta S, Baishya HJ, Paul S. Targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) with synthetic/designer unnatural nucleoside analogs: an in silico study. J Mol Model 2023; 29:366. [PMID: 37950101 DOI: 10.1007/s00894-023-05767-2] [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: 02/16/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
CONTEXT Since the outbreak of COVID-19 in December 2019, it developed into a pandemic affecting all the countries and millions of people around the globe. Until now, there is no medicine available to contain the spread of the virus. As an aid to drug discovery, the molecular docking and molecular dynamic tools were applied extensively. In silico studies made it possible for rapid screening of potential molecules as possible inhibitors/drugs against the targeted proteins. As a continuation of our drug discovery research, we have carried out molecular docking studies of our 12 reported unnatural nucleosides and 14 designer Avigan analogs with SARS-CoV-2, RNA-dependent RNA polymerase (RdRp), which we want to report herein. The same calculation was also carried out, taking 11 known/under trail/commercial nucleoside drug molecules for a comparison of the binding interactions in the catalytic site of RdRp. The docking results and binding efficiencies of our reported nucleosides and designer nucleosidic were compared with the binding energy of commercially available drugs such as remdesevir and favipiravir. Furthermore, we evaluated the protein-drug binding efficiency and stability of the best docked molecules by molecular dynamic studies (MD). From our study, we have found that few of our proposed drugs show promising binding efficiency at the catalytic pocket of SARS-CoV-2 RdRp and can be a promising RdRp inhibitor drug candidate. Hence, this study will be of importance to make progress toward developing successful nucleoside-based drugs and conduct the antiviral test in the wet lab to understand their efficacy against COVID-19. METHOD All the docking studies were carried out with AutoDock 4.2, AutoDock Vina and Molegro Virtual Docker. Following the docking studies, the MD simulations were carried out following the standard protocol with the GROMACS ver. 2019.6. by applying the CHARMM36 all-atom biomolecular force field. The drug-protein interaction was studied using the Biovia Discovery Studio suite, Ligplot software, and Protein-Ligand Interaction Profiler (PLIP).
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Affiliation(s)
- Subhendu Sekhar Bag
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039.
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039.
| | - Sayantan Sinha
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
| | - Soumya Dutta
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
| | - Hirak Jyoti Baishya
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
| | - Suravi Paul
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
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Gabbianelli R, Shahar E, de Simone G, Rucci C, Bordoni L, Feliziani G, Zhao F, Ferrati M, Maggi F, Spinozzi E, Mahajna J. Plant-Derived Epi-Nutraceuticals as Potential Broad-Spectrum Anti-Viral Agents. Nutrients 2023; 15:4719. [PMID: 38004113 PMCID: PMC10675658 DOI: 10.3390/nu15224719] [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: 10/17/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Although the COVID-19 pandemic appears to be diminishing, the emergence of SARS-CoV-2 variants represents a threat to humans due to their inherent transmissibility, immunological evasion, virulence, and invulnerability to existing therapies. The COVID-19 pandemic affected more than 500 million people and caused over 6 million deaths. Vaccines are essential, but in circumstances in which vaccination is not accessible or in individuals with compromised immune systems, drugs can provide additional protection. Targeting host signaling pathways is recommended due to their genomic stability and resistance barriers. Moreover, targeting host factors allows us to develop compounds that are effective against different viral variants as well as against newly emerging virus strains. In recent years, the globe has experienced climate change, which may contribute to the emergence and spread of infectious diseases through a variety of factors. Warmer temperatures and changing precipitation patterns can increase the geographic range of disease-carrying vectors, increasing the risk of diseases spreading to new areas. Climate change may also affect vector behavior, leading to a longer breeding season and more breeding sites for disease vectors. Climate change may also disrupt ecosystems, bringing humans closer to wildlife that transmits zoonotic diseases. All the above factors may accelerate the emergence of new viral epidemics. Plant-derived products, which have been used in traditional medicine for treating pathological conditions, offer structurally novel therapeutic compounds, including those with anti-viral activity. In addition, plant-derived bioactive substances might serve as the ideal basis for developing sustainable/efficient/cost-effective anti-viral alternatives. Interest in herbal antiviral products has increased. More than 50% of approved drugs originate from herbal sources. Plant-derived compounds offer diverse structures and bioactive molecules that are candidates for new drug development. Combining these therapies with conventional drugs could improve patient outcomes. Epigenetics modifications in the genome can affect gene expression without altering DNA sequences. Host cells can use epigenetic gene regulation as a mechanism to silence incoming viral DNA molecules, while viruses recruit cellular epitranscriptomic (covalent modifications of RNAs) modifiers to increase the translational efficiency and transcript stability of viral transcripts to enhance viral gene expression and replication. Moreover, viruses manipulate host cells' epigenetic machinery to ensure productive viral infections. Environmental factors, such as natural products, may influence epigenetic modifications. In this review, we explore the potential of plant-derived substances as epigenetic modifiers for broad-spectrum anti-viral activity, reviewing their modulation processes and anti-viral effects on DNA and RNA viruses, as well as addressing future research objectives in this rapidly emerging field.
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Affiliation(s)
- Rosita Gabbianelli
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Ehud Shahar
- Department of Nutrition and Natural Products, Migal—Galilee Research Institute, Kiryat Shmona 11016, Israel;
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona 1220800, Israel
| | - Gaia de Simone
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Chiara Rucci
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Laura Bordoni
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Giulia Feliziani
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Fanrui Zhao
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Marta Ferrati
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Filippo Maggi
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Eleonora Spinozzi
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Jamal Mahajna
- Department of Nutrition and Natural Products, Migal—Galilee Research Institute, Kiryat Shmona 11016, Israel;
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona 1220800, Israel
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol Cell 2023; 83:3921-3930.e7. [PMID: 37890482 PMCID: PMC10843261 DOI: 10.1016/j.molcel.2023.10.001] [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: 06/07/2023] [Revised: 08/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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30
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait B, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558837. [PMID: 37808858 PMCID: PMC10557602 DOI: 10.1101/2023.09.25.558837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5'-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Chemistry and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Present address: University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Lead contact:
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Aleebrahim-Dehkordi E, Ghoshouni H, Koochaki P, Esmaili-Dehkordi M, Aleebrahim E, Chichagi F, Jafari A, Hanaei S, Heidari-Soureshjani E, Rezaei N. Targeting the vital non-structural proteins (NSP12, NSP7, NSP8 and NSP3) from SARS-CoV-2 and inhibition of RNA polymerase by natural bioactive compound naringenin as a promising drug candidate against COVID-19. J Mol Struct 2023; 1287:135642. [PMID: 37131962 PMCID: PMC10131750 DOI: 10.1016/j.molstruc.2023.135642] [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: 04/24/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023]
Abstract
The prevalence of SARS-CoV-2-induced respiratory infections is now a major challenge worldwide. There is currently no specific antiviral drug to prevent or treat this disease. Infection with COVID-19 seriously needs to find effective therapeutic agents. In the present study, naringenin, as a potential inhibitor candidate for RNA Polymerase SARS-CoV-2 was compared with remdesivir (FDA-approved drug) and GS-441,524 (Derivative of the drug remdesivir) by screening with wild-type and mutant SARS-CoV-2 NSP12 (NSP7-NSP8) and NSP3 interfaces, then complexes were simulated by molecular dynamics (MD) simulations to gain their stabilities. The docking results displayed scores of -3.45 kcal/mol and -4.32 kcal/mol against NSP12 and NSP3, respectively. Our results showed that naringenin had ΔG values more negative than the ΔG values of Remdesivir (RDV) and GS-441,524. Hence, naringenin was considered to be a potential inhibitor. Also, the number of hydrogen bonds of naringenin with NSP3 and later NSP12 are more than Remdesivir and its derivative. In this research, Mean root mean square deviation (RMSD) values of NSP3 and NSP12with naringenin ligand (5.55±1.58 nm to 3.45±0.56 nm and 0.238±0.01 to 0.242±0.021 nm, respectively showed stability in the presence of ligand. The root mean square fluctuations (RMSF) values of NSP3 and NSP12 amino acid units in the presence of naringenin in were 1.5 ± 0.31 nm and 0.118±0.058, respectively. Pharmacokinetic properties and prediction of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of naringenin and RDV showed that these two compounds had no potential cytotoxicity.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamed Ghoshouni
- Medical student, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Pooneh Koochaki
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Elham Aleebrahim
- PhD Student in Food Sciences and Engineering, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Fatemeh Chichagi
- Research Development Center, Sina Hospital, Tehran University of Medical Science, Tehran, Iran
| | - Ali Jafari
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Student Research Committee, Department of Nutrition, School of Health, Golestan University of Medical Sciences, Gorgan, Iran
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sara Hanaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ehsan Heidari-Soureshjani
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box. 115, Iran
- Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Nima Rezaei
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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32
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Xu T, Zhang L. Current understanding of nucleoside analogs inhibiting the SARS-CoV-2 RNA-dependent RNA polymerase. Comput Struct Biotechnol J 2023; 21:4385-4394. [PMID: 37711189 PMCID: PMC10498173 DOI: 10.1016/j.csbj.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Since the outbreak of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has become a main target for antiviral therapeutics due to its essential role in viral replication and transcription. Thus, nucleoside analogs structurally resemble the natural RdRp substrate and hold great potential as inhibitors. Until now, extensive experimental investigations have been performed to explore nucleoside analogs to inhibit the RdRp, and concerted efforts have been made to elucidate the underlying molecular mechanisms further. This review begins by discussing the nucleoside analogs that have demonstrated inhibition in the experiments. Second, we examine the current understanding of the molecular mechanisms underlying the action of nucleoside analogs on the SARS-CoV-2 RdRp. Recent findings in structural biology and computational research are presented through the classification of inhibitory mechanisms. This review summarizes previous experimental findings and mechanistic investigations of nucleoside analogs inhibiting SARS-CoV-2 RdRp. It would guide the rational design of antiviral medications and research into viral transcriptional mechanisms.
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Affiliation(s)
- Tiantian Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fujian 361005, China
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Pattaro-Júnior JR, Araújo IG, Moraes CB, Barbosa CG, Philippsen GS, Freitas-Junior LH, Guidi AC, de Mello JCP, Peralta RM, Fernandez MA, Teixeira RR, Seixas FAV. Antiviral activity of Cenostigma pluviosum var. peltophoroides extract and fractions against SARS-CoV-2. J Biomol Struct Dyn 2023; 41:7297-7308. [PMID: 36069130 DOI: 10.1080/07391102.2022.2120078] [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: 06/21/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Few extracts of plant species from the Brazilian flora have been validated from a pharmacological and clinical point of view, and it is important to determine whether their traditional use is proven by pharmacological effects. Cenostigma pluviosum var. peltophoroides is one of those plants, which belongs to the Fabaceae family that is widely used in traditional medicine and is very rich in tannins. Due to the lack of effective drugs to treat severe cases of Covid-19, the main protease of SARS-CoV-2 (Mpro) becomes an attractive target in the research for new antivirals since this enzyme is crucial for virus replication and does not have homologs in humans. This study aimed to prospect inhibitor candidates among the compounds from C. pluviosum extract, by virtual screening simulations using SARS-CoV-2 Mpro as target. Experimental validation was made by inhibitory proteolytic assays of recombinant Mpro and by antiviral activity with infected Vero cells. Docking simulations identify four compounds with potential inhibitory activity of Mpro present in the extract. The compound pentagalloylglucose showed the best result in proteolytic kinetics experiments, with suppression of recombinant Mpro activity by approximately 60%. However, in experiments with infected cells ethyl acetate fraction and sub-fractions, F2 and F4 of C. pluviosum extract performed better than pentagalloylglucose, reaching close to 100% of antiviral activity. The prominent activity of the extract fractions in infected cells may be a result of a synergistic effect from the different hydrolyzable tannins present, performing simultaneous action on Mpro and other targets from SARS-CoV-2 and host.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- José Renato Pattaro-Júnior
- Laboratory of Structural Biochemistry, Departamento de Tecnologia, Universidade Estadual de Maringá, Umuarama, PR, Brazil
| | - Ingrid Garcia Araújo
- Laboratory of Structural Biochemistry, Departamento de Tecnologia, Universidade Estadual de Maringá, Umuarama, PR, Brazil
| | | | | | | | | | - Ana Carolina Guidi
- PalaFito Laboratory, Departamento de Farmácia, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | | | - Rosane Marina Peralta
- Laboratory of Biochemistry and Physiology of Microorganisms, Departamento de Bioquímica, Universidade Estadual de Maringá, PR, Brazil
| | - Maria Aparecida Fernandez
- Laboratório de Organização Funcional do Núcleo, Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Róbson Ricardo Teixeira
- Laboratory of Organic Chemistry, Departamento de Química, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Flavio Augusto Vicente Seixas
- Laboratory of Structural Biochemistry, Departamento de Tecnologia, Universidade Estadual de Maringá, Umuarama, PR, Brazil
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Das T, Sikdar S, Chowdhury MHU, Nyma KJ, Adnan M. SARS-CoV-2 prevalence in domestic and wildlife animals: A genomic and docking based structural comprehensive review. Heliyon 2023; 9:e19345. [PMID: 37662720 PMCID: PMC10474441 DOI: 10.1016/j.heliyon.2023.e19345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/05/2023] Open
Abstract
The SARS-CoV-2 virus has been identified as the infectious agent that led to the COVID-19 pandemic, which the world has seen very recently. Researchers have linked the SARS-CoV-2 outbreak to bats for the zoonotic spread of the virus to humans. Coronaviruses have a crown-like shape and positive-sense RNA nucleic acid. It attaches its spike glycoprotein to the host angiotensin-converting enzyme 2 (ACE2) receptor. Coronavirus genome comprises 14 ORFs and 27 proteins, spike glycoprotein being one of the most critical proteins for viral pathogenesis. Many mammals and reptiles, including bats, pangolins, ferrets, snakes, and turtles, serve as the principal reservoirs for this virus. But many experimental investigations have shown that certain domestic animals, including pigs, chickens, dogs, cats, and others, may also be able to harbor this virus, whether they exhibit any symptoms. These animals act as reservoirs for SARS-CoV, facilitating its zoonotic cross-species transmission to other species, including humans. In this review, we performed a phylogenetic analysis with multiple sequence alignment and pairwise evolutionary distance analysis, which revealed the similarity of ACE2 receptors in humans, chimpanzees, domestic rabbits, house mice, and golden hamsters. Pairwise RMSD analysis of the spike protein from some commonly reported SARS-CoV revealed that bat and pangolin coronavirus shared the highest structural similarity with human coronavirus. In a further experiment, molecular docking confirmed a higher affinity of pig, bat, and pangolin coronavirus spike proteins' affinity to the human ACE2 receptor. Such comprehensive structural and genomic analysis can help us to forecast the next likely animal source of these coronaviruses that may infect humans. To combat these zoonotic illnesses, we need a one health strategy that considers the well-being of people and animals and the local ecosystem.
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Affiliation(s)
- Tuhin Das
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Suranjana Sikdar
- Department of Microbiology, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md. Helal Uddin Chowdhury
- Ethnobotany and Pharmacognosy Lab, Department of Botany, University of Chittagong, Chattogram, 4331, Bangladesh
| | | | - Md. Adnan
- Department of Molecular Pharmaceutics, University of Utah, Salt Lake City, 84112, United States
- Department of Pharmacy, International Islamic University Chittagong, Chattogram, 4318, Bangladesh
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Chenna A, Khan WH, Dash R, Saraswat S, Chugh A, Rathore AS, Goel G. An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins. Proteins 2023; 91:1222-1234. [PMID: 37283297 DOI: 10.1002/prot.26511] [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: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) complex of SARS-CoV-2 lies at the core of its replication and transcription processes. The interfaces between holo-RdRp subunits are highly conserved, facilitating the design of inhibitors with high affinity for the interaction interface hotspots. We, therefore, take this as a model protein complex for the application of a structural bioinformatics protocol to design peptides that inhibit RdRp complexation by preferential binding at the interface of its core subunit nonstructural protein, nsp12, with accessory factor nsp7. Here, the interaction hotspots of the nsp7-nsp12 subunit of RdRp, determined from a long molecular dynamics trajectory, are used as a template. A large library of peptide sequences constructed from multiple hotspot motifs of nsp12 is screened in-silico to determine sequences with high geometric complementarity and interaction specificity for the binding interface of nsp7 (target) in the complex. Two lead designed peptides are extensively characterized using orthogonal bioanalytical methods to determine their suitability for inhibition of RdRp complexation. Binding affinity of these peptides to accessory factor nsp7, determined using a surface plasmon resonance (SPR) assay, is slightly better than that of nsp12: dissociation constant of 133nM and 167nM, respectively, compared to 473nM for nsp12. A competitive ELISA is used to quantify inhibition of nsp7-nsp12 complexation, with one of the lead peptides giving an IC50 of 25μM . Cell penetrability and cytotoxicity are characterized using a cargo delivery assay and MTT cytotoxicity assay, respectively. Overall, this work presents a proof-of-concept of an approach for rational discovery of peptide inhibitors of SARS-CoV-2 protein-protein interactions.
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Affiliation(s)
- Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Wajihul Hasan Khan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
- Virology Unit, Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rozaleen Dash
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Saurabh Saraswat
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
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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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37
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Tam D, Lorenzo-Leal AC, Hernández LR, Bach H. Targeting SARS-CoV-2 Non-Structural Proteins. Int J Mol Sci 2023; 24:13002. [PMID: 37629182 PMCID: PMC10455537 DOI: 10.3390/ijms241613002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped respiratory β coronavirus that causes coronavirus disease (COVID-19), leading to a deadly pandemic that has claimed millions of lives worldwide. Like other coronaviruses, the SARS-CoV-2 genome also codes for non-structural proteins (NSPs). These NSPs are found within open reading frame 1a (ORF1a) and open reading frame 1ab (ORF1ab) of the SARS-CoV-2 genome and encode NSP1 to NSP11 and NSP12 to NSP16, respectively. This study aimed to collect the available literature regarding NSP inhibitors. In addition, we searched the natural product database looking for similar structures. The results showed that similar structures could be tested as potential inhibitors of the NSPs.
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Affiliation(s)
- Donald Tam
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Ana C. Lorenzo-Leal
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
| | - Luis Ricardo Hernández
- Laboratorio de Investigación Fitoquímica, Departamento de Ciencias Químico Biológicas, Universidad de las Américas Puebla, Ex Hacienda Sta. Catarina Mártir S/N, San Andrés Cholula 72810, Mexico;
| | - Horacio Bach
- Division of Infectious Disease, Department of Medicine, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada; (D.T.); (A.C.L.-L.)
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38
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Gratteri C, Ambrosio FA, Lupia A, Moraca F, Catalanotti B, Costa G, Bellocchi M, Carioti L, Salpini R, Ceccherini-Silberstein F, Frazia SL, Malagnino V, Sarmati L, Svicher V, Bryant S, Artese A, Alcaro S. Molecular and Structural Aspects of Clinically Relevant Mutations of SARS-CoV-2 RNA-Dependent RNA Polymerase in Remdesivir-Treated Patients. Pharmaceuticals (Basel) 2023; 16:1143. [PMID: 37631058 PMCID: PMC10459223 DOI: 10.3390/ph16081143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target to fight COVID-19, and many RdRp inhibitors nucleotide/nucleoside analogs, such as remdesivir, have been identified or are in clinical studies. However, the appearance of resistant mutations could reduce their efficacy. In the present work, we structurally evaluated the impact of RdRp mutations found at baseline in 39 patients treated with remdesivir and associated with a different degree of antiviral response in vivo. (2) Methods: A refined bioinformatics approach was applied to assign SARS-CoV-2 clade and lineage, and to define RdRp mutational profiles. In line with such a method, the same mutations were built and analyzed by combining docking and thermodynamics evaluations with both molecular dynamics and representative pharmacophore models. (3) Results: Clinical studies revealed that patients bearing the most prevalent triple mutant P323L+671S+M899I, which was present in 41% of patients, or the more complex mutational profile P323L+G671S+L838I+D738Y+K91E, which was found with a prevalence of 2.6%, showed a delayed reduced response to remdesivir, as confirmed by the increase in SARS-CoV-2 viral load and by a reduced theoretical binding affinity versus RdRp (ΔGbindWT = -122.70 kcal/mol; ΔGbindP323L+671S+M899I = -84.78 kcal/mol; ΔGbindP323L+G671S+L838I+D738Y+K91E = -96.74 kcal/mol). Combined computational approaches helped to rationalize such clinical observations, offering a mechanistic understanding of the allosteric effects of mutants on the global motions of the viral RNA synthesis machine and in the changes of the interactions patterns of remdesivir during its binding.
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Affiliation(s)
- Carmen Gratteri
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy;
| | - Antonio Lupia
- Dipartimento di Scienze della vita e dell’ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy;
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Federica Moraca
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Maria Bellocchi
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Luca Carioti
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Francesca Ceccherini-Silberstein
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Simone La Frazia
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Vincenzo Malagnino
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Loredana Sarmati
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Valentina Svicher
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Sharon Bryant
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, 1070 Vienna, Austria;
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
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Slanina H, Madhugiri R, Wenk K, Reinke T, Schultheiß K, Schultheis J, Karl N, Linne U, Ziebuhr J. Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains. J Virol 2023; 97:e0046523. [PMID: 37199624 PMCID: PMC10308930 DOI: 10.1128/jvi.00465-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents the central functional subunit. It harbors the RNA-directed RNA polymerase (RdRp) domain and contains, at its N terminus, an additional domain called NiRAN which is widely conserved in coronaviruses and other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate and compare NiRAN-mediated NMPylation activities from representative alpha- and betacoronaviruses. We found that the four coronavirus NiRAN domains characterized to date have a number of conserved properties, including (i) robust nsp9-specific NMPylation activities that appear to operate largely independently of the C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed by ATP and other nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, and (iv) a key role of N-terminal residues (particularly Asn2) of nsp9 for efficient formation of a covalent phosphoramidate bond between NMP and the N-terminal amino group of nsp9. In this context, a mutational analysis confirmed the conservation and critical role of Asn2 across different subfamilies of the family Coronaviridae, as shown by studies using chimeric coronavirus nsp9 variants in which six N-terminal residues were replaced with those from other corona-, pito- and letovirus nsp9 homologs. The combined data of this and previous studies reveal a remarkable degree of conservation among coronavirus NiRAN-mediated NMPylation activities, supporting a key role of this enzymatic activity in viral RNA synthesis and processing. IMPORTANCE There is strong evidence that coronaviruses and other large nidoviruses evolved a number of unique enzymatic activities, including an additional RdRp-associated NiRAN domain, that are conserved in nidoviruses but not in most other RNA viruses. Previous studies of the NiRAN domain mainly focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and suggested different functions for this domain, such as NMPylation/RNAylation of nsp9, RNA guanylyltransferase activities involved in canonical and/or unconventional RNA capping pathways, and other functions. To help resolve partly conflicting information on substrate specificities and metal ion requirements reported previously for the SARS-CoV-2 NiRAN NMPylation activity, we extended these earlier studies by characterizing representative alpha- and betacoronavirus NiRAN domains. The study revealed that key features of NiRAN-mediated NMPylation activities, such as protein and nucleotide specificity and metal ion requirements, are very well conserved among genetically divergent coronaviruses, suggesting potential avenues for future antiviral drug development targeting this essential viral enzyme.
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Affiliation(s)
- Heiko Slanina
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - Kai Wenk
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Tess Reinke
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Karin Schultheiß
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Julia Schultheis
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Philipps University, Marburg, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
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40
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Cordsmeier A, Jungnickl D, Herrmann A, Korn K, Ensser A. Analysis of SARS-CoV-2 Spike Protein Variants with Recombinant Reporter Viruses Created from a Bacmid System. Int J Mol Sci 2023; 24:ijms24098156. [PMID: 37175863 PMCID: PMC10179725 DOI: 10.3390/ijms24098156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 04/28/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, has spread around the world with more than 700 million cases and 6.8 million deaths. Various variants of concern (VoC) have emerged due to mutations and recombination and concurrent selection for increased viral fitness and immune evasion. The viral protein that primarily determines the pathogenicity, infectivity, and transmissibility is the Spike protein. To analyze the specific impact of variant Spike proteins on infection dynamics, we constructed SARS-CoV-2 with a uniform B.1 backbone but with alternative Spike proteins. In addition, ORF6 was replaced by EYFP as a biological safety measure, and for use of this well-established reporter. We show that namely the delta variant Spike proteins cause a distinct phenotype from the wild type (B.1, D614G) and other variants of concern. Furthermore, we demonstrate that the omicron BA.1 Spike results in lower viral loads and a less efficient spread in vitro. Finally, we utilized viruses with the two different reporters EYFP and mCherry to establish a competitive growth assay, demonstrating that most but not all Spike variant viruses were able to outcompete wild type SARS-CoV-2 B.1.
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Affiliation(s)
- Arne Cordsmeier
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Doris Jungnickl
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Alexandra Herrmann
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Klaus Korn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Armin Ensser
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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41
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Chen TH, Chang CJ, Hung PH. Possible Pathogenesis and Prevention of Long COVID: SARS-CoV-2-Induced Mitochondrial Disorder. Int J Mol Sci 2023; 24:8034. [PMID: 37175745 PMCID: PMC10179190 DOI: 10.3390/ijms24098034] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/27/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Patients who have recovered from coronavirus disease 2019 (COVID-19) infection may experience chronic fatigue when exercising, despite no obvious heart or lung abnormalities. The present lack of effective treatments makes managing long COVID a major challenge. One of the underlying mechanisms of long COVID may be mitochondrial dysfunction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections can alter the mitochondria responsible for energy production in cells. This alteration leads to mitochondrial dysfunction which, in turn, increases oxidative stress. Ultimately, this results in a loss of mitochondrial integrity and cell death. Moreover, viral proteins can bind to mitochondrial complexes, disrupting mitochondrial function and causing the immune cells to over-react. This over-reaction leads to inflammation and potentially long COVID symptoms. It is important to note that the roles of mitochondrial damage and inflammatory responses caused by SARS-CoV-2 in the development of long COVID are still being elucidated. Targeting mitochondrial function may provide promising new clinical approaches for long-COVID patients; however, further studies are needed to evaluate the safety and efficacy of such approaches.
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Affiliation(s)
- Tsung-Hsien Chen
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
| | - Chia-Jung Chang
- Division of Critical Care Medicine, Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan
| | - Peir-Haur Hung
- Department of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan;
- Department of Life and Health Science, Chia-Nan University of Pharmacy and Science, Tainan 717301, Taiwan
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42
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Apostle A, Yin Y, Chillar K, Eriyagama AMDN, Arneson R, Burke E, Fang S, Yuan Y. Effects of Epitranscriptomic RNA Modifications on the Catalytic Activity of the SARS-CoV-2 Replication Complex. Chembiochem 2023; 24:e202300095. [PMID: 36752976 PMCID: PMC10121919 DOI: 10.1002/cbic.202300095] [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: 02/06/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 causes individualized symptoms. Many reasons have been given. We propose that an individual's epitranscriptomic system could be responsible as well. The viral RNA genome can be subject to epitranscriptomic modifications, which can be different for different individuals, and thus epitranscriptomics can affect many events including RNA replication differently. In this context, we studied the effects of modifications including pseudouridine (Ψ), 5-methylcytosine (m5 C), N6-methyladenosine (m6 A), N1-methyladenosine (m1 A) and N3-methylcytosine (m3 C) on the activity of SARS-CoV-2 replication complex (SC2RC). We found that Ψ, m5 C, m6 A and m3 C had little effect, whereas m1 A inhibited the enzyme. Both m1 A and m3 C disrupt canonical base pairing, but they had different effects. The fact that m1 A inhibits SC2RC implies that the modification can be difficult to detect. This fact also implies that individuals with upregulated m1 A including cancer, obesity and diabetes patients might have milder symptoms. However, this contradicts clinical observations. Relevant discussions are provided.
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Affiliation(s)
- Alexander Apostle
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Yipeng Yin
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Komal Chillar
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Adikari M D N Eriyagama
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Reed Arneson
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Emma Burke
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Shiyue Fang
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Yinan Yuan
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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43
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Gu Y, Liu M, Staker BL, Buchko GW, Quinn RJ. Drug-Repurposing Screening Identifies a Gallic Acid Binding Site on SARS-CoV-2 Non-structural Protein 7. ACS Pharmacol Transl Sci 2023; 6:578-586. [PMID: 37082753 PMCID: PMC10111621 DOI: 10.1021/acsptsci.2c00225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 03/09/2023]
Abstract
SARS-CoV-2 is the agent responsible for acute respiratory disease COVID-19 and the global pandemic initiated in early 2020. While the record-breaking development of vaccines has assisted the control of COVID-19, there is still a pressing global demand for antiviral drugs to halt the destructive impact of this disease. Repurposing clinically approved drugs provides an opportunity to expediate SARS-CoV-2 treatments into the clinic. In an effort to facilitate drug repurposing, an FDA-approved drug library containing 2400 compounds was screened against the SARS-CoV-2 non-structural protein 7 (nsp7) using a native mass spectrometry-based assay. Nsp7 is one of the components of the SARS-CoV-2 replication/transcription complex essential for optimal viral replication, perhaps serving to off-load RNA from nsp8. From this library, gallic acid was identified as a compound that bound tightly to nsp7, with an estimated K d of 15 μM. NMR chemical shift perturbation experiments were used to map the ligand-binding surface of gallic acid on nsp7, indicating that the compound bound to a surface pocket centered on one of the protein's four α-helices (α2). The identification of the gallic acid-binding site on nsp7 may allow development of a SARS-CoV-2 therapeutic via artificial-intelligence-based virtual docking and other strategies.
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Affiliation(s)
- Yushu Gu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Miaomiao Liu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Bart L. Staker
- Seattle
Children’s Research Institute, Seattle, Washington 98101, United States
| | - Garry W. Buchko
- Earth
and Biological Sciences Directorate, Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
- School of
Molecular Biosciences, Washington State
University, Pullman, Washington 99164, United States
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
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Preparation and characterization of nanobodies targeting SARS-CoV-2 papain-like protease. Protein Expr Purif 2023; 207:106267. [PMID: 37030644 PMCID: PMC10076250 DOI: 10.1016/j.pep.2023.106267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Coronavirus Papain-like protease (PLpro) mediates the cleavage of viral polyproteins and assists the virus escaping from innate immune response. Thus, PLpro is an attractive target for the development of broad-spectrum drugs as it has a conserved structure across different coronaviruses. In this study, we purified SARS-CoV-2 PLpro as an immune antigen, constructed a nanobody phage display library, and identified a set of nanobodies with high affinity for SARS-CoV-2. In addition, enzyme activity experiments demonstrated that two nanobodies had a significant inhibitory effect on the PLpro. These nanobodies should therefore be investigated as candidates for the treatment of coronaviruses.
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45
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Anderson TK, Hoferle PJ, Lee KW, Coon JJ, Kirchdoerfer RN. An alphacoronavirus polymerase structure reveals conserved co-factor functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532841. [PMID: 36993498 PMCID: PMC10055115 DOI: 10.1101/2023.03.15.532841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from the betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine the structure of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. Our structure shows an unexpected nsp8 stoichiometry in comparison to other published coronavirus polymerase structures. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha and betacoronaviruses as previously hypothesized. Our work shows the importance of studying diverse coronaviruses to reveal aspects of coronavirus replication while also identifying areas of conservation to be targeted by antiviral drugs.
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Affiliation(s)
- Thomas K. Anderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
| | - Peter J. Hoferle
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
| | - Kenneth W. Lee
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Joshua J. Coon
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Robert N. Kirchdoerfer
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706
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Rabaan AA, Halwani MA, Aljeldah M, Al Shammari BR, Garout M, Aldali J, Alawfi A, Alshengeti A, Alsulaiman AM, Alsayyah A. Exploration of potent antiviral phytomedicines from Lauraceae family plants against SARS-CoV-2 RNA-dependent RNA polymerase. J Biomol Struct Dyn 2023; 41:15085-15105. [PMID: 36883874 DOI: 10.1080/07391102.2023.2186720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
RNA-dependent RNA polymerase, also known as RdRp, is a possible therapeutic target that could be used to suppress the proliferation of RNA viruses such as SARS-CoV-2. This protein has two major functional sites (a) catalytic and (b) substrate entry, which regulate the natural substrate entry and its corresponding interaction with the protein. In this study, a computational drug design pipeline was applied to investigate potential inhibitors against SARS-CoV-2 RdRp from Lauraceae plants, and five top hits were selected based on the docked score (< -7 kcal/mol). The docking study suggested that the Glochidioboside had a minimum binding score of -7.8 kcal/mol. This compound showed total five hydrogen bonds while two of them were with catalytic residues Asp618 and Asp760. However, another compound, Sitogluside showed a binding score of -7.3 kcal/mol with four hydrogen bonds targeting three functional residues (Arg555, Ser759, and Asp760). Later, 100 ns explicit solvent molecular dynamics (MD) simulation was performed to evaluate the stability of the protein-ligand docked system. These compounds translocated their positions from the catalytic site to the substrate entry site, as observed in the MD simulation trajectory. However, translocation did not affect the binding strength of these compounds, and they retained the strong binding affinity (ΔG < -11.5 kcal/mol), estimated using the MM/GBSA method. In general, the findings of this study indicated the potential therapeutic compounds that may be used targeting SARS-CoV-2 RdRp. However, these compounds still need to be validated by experimentation in order to determine their inhibitory function.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Al Baha, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Basim R Al Shammari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Jehad Aldali
- Pathology Organization, Imam Mohammed Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdulsalam Alawfi
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah, Saudi Arabia
| | | | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Miropolskaya N, Kozlov M, Petushkov I, Prostova M, Pupov D, Esyunina D, Kochetkov S, Kulbachinskiy A. Effects of natural polymorphisms in SARS-CoV-2 RNA-dependent RNA polymerase on its activity and sensitivity to inhibitors in vitro. Biochimie 2023; 206:81-88. [PMID: 36252889 PMCID: PMC9568283 DOI: 10.1016/j.biochi.2022.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/02/2022] [Accepted: 10/11/2022] [Indexed: 11/02/2022]
Abstract
SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is the key enzyme required for viral replication and mRNA synthesis. RdRp is one of the most conserved viral proteins and a promising target for antiviral drugs and inhibitors. At the same time, analysis of public databases reveals multiple variants of SARS-CoV-2 genomes with substitutions in the catalytic RdRp subunit nsp12. Structural mapping of these mutations suggests that some of them may affect the interactions of nsp12 with its cofactors nsp7/nsp8 as well as with RNA substrates. We have obtained several mutations of these types and demonstrated that some of them decrease specific activity of RdRp in vitro, possibly by changing RdRp assembly and/or its interactions with RNA. Therefore, natural polymorphisms in RdRp may potentially affect viral replication. Furthermore, we have synthesized a series of polyphenol and diketoacid derivatives based on previously studied inhibitors of hepatitis C virus RdRp and found that several of them can inhibit SARS-CoV-2 RdRp. Tested mutations in RdRp do not have strong effects on the efficiency of inhibition. Further development of more efficient non-nucleoside inhibitors of SARS-CoV-2 RdRp should take into account the existence of multiple polymorphic variants of RdRp.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Maxim Kozlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Maria Prostova
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Danil Pupov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
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Severe acute respiratory syndrome coronaviruses contributing to mitochondrial dysfunction: Implications for post-COVID complications. Mitochondrion 2023; 69:43-56. [PMID: 36690315 PMCID: PMC9854144 DOI: 10.1016/j.mito.2023.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/21/2023]
Abstract
Mitochondria play a central role in oxidative phosphorylation (OXPHOS), bioenergetics linked with ATP production, fatty acids biosynthesis, calcium signaling, cell cycle regulation, apoptosis, and innate immune response. Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection manipulates the host cellular machinery for its survival and replication in the host cell. The infectiaon causes perturbed the cellular metabolism that favours viral replication leading to mitochondrial dysfunction and chronic inflammation. By localizing to the mitochondria, SARS CoV proteins increase reactive oxygen species (ROS) levels, perturbation of Ca2+ signaling, changes in mtDNA copy number, mitochondrial membrane potential (MMP), mitochondrial mass, and induction of mitophagy. These proteins also influence the fusion and fission kinetics, size, structure, and distribution of mitochondria in the infected host cells. This results in compromised bioenergetics, altered metabolism, and innate immune signaling, and hence can be a key player in determining the outcome of SARS-CoV infection. SARS-CoV infection contributes to stress and activates apoptotic pathways. This review summarizes how mitochondrial function and dynamics are affected by SARS-CoV and how the mitochondria-SARS-CoV interaction benefits viral survival and growth by evading innate host immunity. We also highlight how the SARS-CoV-mediated mitochondrial dysfunction contributes to post-COVID complications. Besides, a discussion on targeting virus-mitochondria interactions as a therapeutic strategy is presented.
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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50
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Ghelichkhani F, Gonzalez FA, Kapitonova MA, Rozovsky S. Selenoprotein S Interacts with the Replication and Transcription Complex of SARS-CoV-2 by Binding nsp7. J Mol Biol 2023; 435:168008. [PMID: 36773692 PMCID: PMC9911985 DOI: 10.1016/j.jmb.2023.168008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/05/2022] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replicates and evades detection using ER membranes and their associated protein machinery. Among these hijacked human proteins is selenoprotein S (selenos). This selenoprotein takes part in the protein quality control, signaling, and the regulation of cytokine secretion. While the role of selenos in the viral life cycle is not yet known, it has been reported to interact with SARS-CoV-2 nonstructural protein 7 (nsp7), a viral protein essential for the replication of the virus. We set to study whether selenos and nsp7 interact directly and if they can still bind when nsp7 is bound to the replication and transcription complex of the virus. Using biochemical assays, we show that selenos binds directly to nsp7. In addition, we found that selenos can bind to nsp7 when it is in a complex with the coronavirus's minimal replication and transcription complex, comprised of nsp7, nsp8, and the RNA-dependent RNA polymerase nsp12. In addition, through crosslinking experiments, we mapped the interaction sites of selenos and nsp7 in the replication complex and showed that the hydrophobic segment of selenos is essential for binding to nsp7. This arrangement leaves an extended helix and the intrinsically disordered segment of selenos-including the reactive selenocysteine-exposed and free to potentially recruit additional proteins to the replication and transcription complex.
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Affiliation(s)
- Farid Ghelichkhani
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Fabio A Gonzalez
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Mariia A Kapitonova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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