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Latimer-Smith M, Salgado PS, Forsyth I, Makeyev E, Poranen MM, Stuart DI, Grimes JM, El Omari K. Structure of the RNA-dependent RNA polymerase P2 from the cystovirus φ8. Sci Rep 2024; 14:23540. [PMID: 39384884 PMCID: PMC11464883 DOI: 10.1038/s41598-024-75213-7] [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: 05/23/2024] [Accepted: 10/03/2024] [Indexed: 10/11/2024] Open
Abstract
The replication of RNA viruses relies on the activity of RNA-dependent RNA polymerases (RdRps). Despite large variations in their genomic sequences, viral RdRps share a common architecture generally known as a closed right hand. The P2 polymerase of cystovirus φ6 is currently among the best characterized viral RdRps. This polymerase is responsible for carrying out both replication and transcription of the viral double-stranded RNA genome using de novo initiation. Despite the extensive biochemical and structural studies conducted on φ6 P2, further structural information on other cystoviral RdRps is crucial to elucidate the structural and functional diversity of viral RdRps. Here, we have determined the atomic X-ray structure of the RdRp P2 from the φ6-related cystovirus φ8 at 3Å resolution. This structure completes the existing set of structural information on the φ8 polymerase complex and sheds light on the difference and similarities with related cystoviral RdRps.
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Affiliation(s)
- Merlyn Latimer-Smith
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX110DE, UK
| | - Paula S Salgado
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ismay Forsyth
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX110DE, UK
| | - Eugene Makeyev
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Centre for Developmental Neurobiology, Kings College London, London, SE1 1UL, UK
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX110DE, UK.
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, OX11 0FA, UK.
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2
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Mäkinen JJ, Rosenqvist P, Virta P, Metsä-Ketelä M, Belogurov GA. Probing the nucleobase selectivity of RNA polymerases with dual-coding substrates. J Biol Chem 2024; 300:107755. [PMID: 39260691 DOI: 10.1016/j.jbc.2024.107755] [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: 05/17/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/13/2024] Open
Abstract
Formycin A (FOR) and pyrazofurin A (PYR) are nucleoside analogs with antiviral and antitumor properties. They are known to interfere with nucleic acid metabolism, but their direct effect on transcription is less understood. We explored how RNA polymerases (RNAPs) from bacteria, mitochondria, and viruses utilize FOR, PYR, and oxidized purine nucleotides. All tested polymerases incorporated FOR in place of adenine and PYR in place of uridine. FOR also exhibited surprising dual-coding behavior, functioning as a cytosine substitute, particularly for viral RNAP. In contrast, 8-oxoadenine and 8-oxoguanine were incorporated in place of uridine in addition to their canonical Watson-Crick codings. Our data suggest that the interconversion of canonical anti and alternative syn conformers underlies dual-coding abilities of FOR and oxidized purines. Structurally distinct RNAPs displayed varying abilities to utilize syn conformers during transcription. By examining base pairings that led to substrate incorporation and the entire spectrum of geometrically compatible pairings, we have gained new insights into the nucleobase selection processes employed by structurally diverse RNAPs. These insights may pave the way for advancements in antiviral therapies.
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Affiliation(s)
- Janne J Mäkinen
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Pasi Virta
- Department of Chemistry, University of Turku, Turku, Finland
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Kleiner VA, Fearns R. How does the polymerase of non-segmented negative strand RNA viruses commit to transcription or genome replication? J Virol 2024; 98:e0033224. [PMID: 39078194 PMCID: PMC11334523 DOI: 10.1128/jvi.00332-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024] Open
Abstract
The Mononegavirales, or non-segmented negative-sense RNA viruses (nsNSVs), includes significant human pathogens, such as respiratory syncytial virus, parainfluenza virus, measles virus, Ebola virus, and rabies virus. Although these viruses differ widely in their pathogenic properties, they are united by each having a genome consisting of a single strand of negative-sense RNA. Consistent with their shared genome structure, the nsNSVs have evolved similar ways to transcribe their genome into mRNAs and replicate it to produce new genomes. Importantly, both mRNA transcription and genome replication are performed by a single virus-encoded polymerase. A fundamental and intriguing question is: how does the nsNSV polymerase commit to being either an mRNA transcriptase or a replicase? The polymerase must become committed to one process or the other either before it interacts with the genome template or in its initial interactions with the promoter sequence at the 3´ end of the genomic RNA. This review examines the biochemical, molecular biology, and structural biology data regarding the first steps of transcription and RNA replication that have been gathered over several decades for different families of nsNSVs. These findings are discussed in relation to possible models that could explain how an nsNSV polymerase initiates and commits to either transcription or genome replication.
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Affiliation(s)
- Victoria A. Kleiner
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
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4
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Yuan H, Liu RD, Gao ZY, Zhong LT, Zhou YC, Tan JH, Huang ZS, Li Z, Chen SB. Targeting ATP-binding site of WRN Helicase: Identification of novel inhibitors through pocket analysis and Molecular Dynamics-Enhanced virtual screening. Bioorg Med Chem Lett 2024; 104:129711. [PMID: 38521175 DOI: 10.1016/j.bmcl.2024.129711] [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: 08/16/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
WRN helicase is a critical protein involved in maintaining genomic stability, utilizing ATP hydrolysis to dissolve DNA secondary structures. It has been identified as a promising synthetic lethal target for microsatellite instable (MSI) cancers. However, few WRN helicase inhibitors have been discovered, and their potential binding sites remain unexplored. In this study, we analyzed potential binding sites for WRN inhibitors and focused on the ATP-binding site for screening new inhibitors. Through molecular dynamics-enhanced virtual screening, we identified two compounds, h6 and h15, which effectively inhibited WRN's helicase and ATPase activity in vitro. Importantly, these compounds selectively targeted WRN's ATPase activity, setting them apart from other non-homologous proteins with ATPase activity. In comparison to the homologous protein BLM, h6 exhibits some degree of selectivity towards WRN. We also investigated the binding mode of these compounds to WRN's ATP-binding sites. These findings offer a promising strategy for discovering new WRN inhibitors and present two novel scaffolds, which might be potential for the development of MSI cancer treatment.
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Affiliation(s)
- Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Run-Duo Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhuo-Yu Gao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Li-Ting Zhong
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Ying-Chen Zhou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhe Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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Wang X, Jing X, Shi J, Liu Q, Shen S, Cheung PPH, Wu J, Deng F, Gong P. A jingmenvirus RNA-dependent RNA polymerase structurally resembles the flavivirus counterpart but with different features at the initiation phase. Nucleic Acids Res 2024; 52:3278-3290. [PMID: 38296832 PMCID: PMC11014250 DOI: 10.1093/nar/gkae042] [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: 10/09/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
Jingmenviruses are a category of emerging segmented viruses that have garnered global attention in recent years, and are close relatives of the flaviviruses in the Flaviviridae family. One of their genome segments encodes NSP1 homologous to flavivirus NS5. NSP1 comprises both the methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRP) modules playing essential roles in viral genome replication and capping. Here we solved a 1.8-Å resolution crystal structure of the NSP1 RdRP module from Jingmen tick virus (JMTV), the type species of jingmenviruses. The structure highly resembles flavivirus NS5 RdRP despite a sequence identity less than 30%. NSP1 RdRP enzymatic properties were dissected in a comparative setting with several representative Flaviviridae RdRPs included. Our data indicate that JMTV NSP1 produces characteristic 3-mer abortive products similar to the hepatitis C virus RdRP, and exhibits the highest preference of terminal initiation and shorter-primer usage. Unlike flavivirus NS5, JMTV RdRP may require the MTase for optimal transition from initiation to elongation, as an MTase-less NSP1 construct produced more 4-5-mer intermediate products than the full-length protein. Taken together, this work consolidates the evolutionary relationship between the jingmenvirus group and the Flaviviridae family, providing a basis to the further understanding of their viral replication/transcription process.
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Affiliation(s)
- Xinyu Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuping Jing
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Junming Shi
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Qiaojie Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Shu Shen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China
| | - Jiqin Wu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.262 Jin Long Street, Wuhan, Hubei 430207, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No. 262 Jin Long Street, Wuhan, Hubei 430207, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin 300350, China
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An H, Yu X, Li J, Shi F, Liu Y, Shu M, Li Z, Li X, Li W, Chen J. Interleukin-2 enhancer binding factor 2 negatively regulates the replication of duck hepatitis A virus type 1 by disrupting the RNA-dependent RNA polymerase activity of 3D polymerase. Vet Res 2024; 55:40. [PMID: 38532469 DOI: 10.1186/s13567-024-01294-x] [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: 09/28/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
The interaction between viral components and cellular proteins plays a crucial role in viral replication. In a previous study, we showed that the 3'-untranslated region (3'-UTR) is an essential element for the replication of duck hepatitis A virus type 1 (DHAV-1). However, the underlying mechanism is still unclear. To gain a deeper understanding of this mechanism, we used an RNA pull-down and a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assay to identify new host factors that interact with the 3'-UTR. We selected interleukin-2 enhancer binding factor 2 (ILF2) for further analysis. We showed that ILF2 interacts specifically with both the 3'-UTR and the 3D polymerase (3Dpol) of DHAV-1 through in vitro RNA pull-down and co-immunoprecipitation assays, respectively. We showed that ILF2 negatively regulates viral replication in duck embryo fibroblasts (DEFs), and that its overexpression in DEFs markedly suppresses DHAV-1 replication. Conversely, ILF2 silencing resulted in a significant increase in viral replication. In addition, the RNA-dependent RNA polymerase (RdRP) activity of 3Dpol facilitated viral replication by enhancing viral RNA translation efficiency, whereas ILF2 disrupted the role of RdRP in viral RNA translation efficiency to suppress DHAV-1 replication. At last, DHAV-1 replication markedly suppressed the expression of ILF2 in DEFs, duck embryo hepatocytes, and different tissues of 1 day-old ducklings. A negative correlation was observed between ILF2 expression and the viral load in primary cells and different organs of young ducklings, suggesting that ILF2 may affect the viral load both in vitro and in vivo.
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Affiliation(s)
- Hao An
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Xiaoli Yu
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Jing Li
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Fuyan Shi
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Yumei Liu
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Ming Shu
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Zihan Li
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Xiaohong Li
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Wanwei Li
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China
| | - Junhao Chen
- School of Public Health, Weifang Medical University, Weifang, 261042, Shandong, China.
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7
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Levanova AA, Poranen MM. Utilization of Bacteriophage phi6 for the Production of High-Quality Double-Stranded RNA Molecules. Viruses 2024; 16:166. [PMID: 38275976 PMCID: PMC10818839 DOI: 10.3390/v16010166] [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: 12/24/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Double-stranded RNA (dsRNA) molecules are mediators of RNA interference (RNAi) in eukaryotic cells. RNAi is a conserved mechanism of post-transcriptional silencing of genes cognate to the sequences of the applied dsRNA. RNAi-based therapeutics for the treatment of rare hereditary diseases have recently emerged, and the first sprayable dsRNA biopesticide has been proposed for registration. The range of applications of dsRNA molecules will likely expand in the future. Therefore, cost-effective methods for the efficient large-scale production of high-quality dsRNA are in demand. Conventional approaches to dsRNA production rely on the chemical or enzymatic synthesis of single-stranded (ss)RNA molecules with a subsequent hybridization of complementary strands. However, the yield of properly annealed biologically active dsRNA molecules is low. As an alternative approach, we have developed methods based on components derived from bacteriophage phi6, a dsRNA virus encoding RNA-dependent RNA polymerase (RdRp). Phi6 RdRp can be harnessed for the enzymatic production of high-quality dsRNA molecules. The isolated RdRp efficiently synthesizes dsRNA in vitro on a heterologous ssRNA template of any length and sequence. To scale up dsRNA production, we have developed an in vivo system where phi6 polymerase complexes produce target dsRNA molecules inside Pseudomonas cells.
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Affiliation(s)
- Alesia A. Levanova
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland;
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8
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Latosińska M, Latosińska JN. Favipiravir Analogues as Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase, Combined Quantum Chemical Modeling, Quantitative Structure-Property Relationship, and Molecular Docking Study. Molecules 2024; 29:441. [PMID: 38257352 PMCID: PMC10818557 DOI: 10.3390/molecules29020441] [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: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Our study was motivated by the urgent need to develop or improve antivirals for effective therapy targeting RNA viruses. We hypothesized that analogues of favipiravir (FVP), an inhibitor of RNA-dependent RNA polymerase (RdRp), could provide more effective nucleic acid recognition and binding processes while reducing side effects such as cardiotoxicity, hepatotoxicity, teratogenicity, and embryotoxicity. We proposed a set of FVP analogues together with their forms of triphosphate as new SARS-CoV-2 RdRp inhibitors. The main aim of our study was to investigate changes in the mechanism and binding capacity resulting from these modifications. Using three different approaches, QTAIM, QSPR, and MD, the differences in the reactivity, toxicity, binding efficiency, and ability to be incorporated by RdRp were assessed. Two new quantum chemical reactivity descriptors, the relative electro-donating and electro-accepting power, were defined and successfully applied. Moreover, a new quantitative method for comparing binding modes was developed based on mathematical metrics and an atypical radar plot. These methods provide deep insight into the set of desirable properties responsible for inhibiting RdRp, allowing ligands to be conveniently screened. The proposed modification of the FVP structure seems to improve its binding ability and enhance the productive mode of binding. In particular, two of the FVP analogues (the trifluoro- and cyano-) bind very strongly to the RNA template, RNA primer, cofactors, and RdRp, and thus may constitute a very good alternative to FVP.
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Heymann JB. Structural Studies of Bacteriophage Φ6 and Its Transformations during Its Life Cycle. Viruses 2023; 15:2404. [PMID: 38140645 PMCID: PMC10747372 DOI: 10.3390/v15122404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
From the first isolation of the cystovirus bacteriophage Φ6 from Pseudomonas syringae 50 years ago, we have progressed to a better understanding of the structure and transformations of many parts of the virion. The three-layered virion, encapsulating the tripartite double-stranded RNA (dsRNA) genome, breaches the cell envelope upon infection, generates its own transcripts, and coopts the bacterial machinery to produce its proteins. The generation of a new virion starts with a procapsid with a contracted shape, followed by the packaging of single-stranded RNA segments with concurrent expansion of the capsid, and finally replication to reconstitute the dsRNA genome. The outer two layers are then added, and the fully formed virion released by cell lysis. Most of the procapsid structure, composed of the proteins P1, P2, P4, and P7 is now known, as well as its transformations to the mature, packaged nucleocapsid. The outer two layers are less well-studied. One additional study investigated the binding of the host protein YajQ to the infecting nucleocapsid, where it enhances the transcription of the large RNA segment that codes for the capsid proteins. Finally, I relate the structural aspects of bacteriophage Φ6 to those of other dsRNA viruses, noting the similarities and differences.
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Affiliation(s)
- J. Bernard Heymann
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Dr., Bethesda, MD 20892, USA; ; Tel.: +1-301-846-6924
- National Cryo-EM Program, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
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10
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Mäntynen S, Salomaa MM, Poranen MM. Diversity and Current Classification of dsRNA Bacteriophages. Viruses 2023; 15:2154. [PMID: 38005832 PMCID: PMC10674327 DOI: 10.3390/v15112154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Half a century has passed since the discovery of Pseudomonas phage phi6, the first enveloped dsRNA bacteriophage to be isolated. It remained the sole known dsRNA phage for a quarter of a century and the only recognised member of the Cystoviridae family until the year 2018. After the initial discovery of phi6, additional dsRNA phages have been isolated from globally distant locations and identified in metatranscriptomic datasets, suggesting that this virus type is more ubiquitous in nature than previously acknowledged. Most identified dsRNA phages infect Pseudomonas strains and utilise either pilus or lipopolysaccharide components of the host as the primary receptor. In addition to the receptor-mediated strictly lytic lifestyle, an alternative persistent infection strategy has been described for some dsRNA phages. To date, complete genome sequences of fourteen dsRNA phage isolates are available. Despite the high sequence diversity, similar sets of genes can typically be found in the genomes of dsRNA phages, suggesting shared evolutionary trajectories. This review provides a brief overview of the recognised members of the Cystoviridae virus family and related dsRNA phage isolates, outlines the current classification of dsRNA phages, and discusses their relationships with eukaryotic RNA viruses.
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Affiliation(s)
- Sari Mäntynen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland; (M.M.S.); (M.M.P.)
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11
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Abstract
The nonsegmented, negative-strand RNA viruses (nsNSVs), also known as the order Mononegavirales, have a genome consisting of a single strand of negative-sense RNA. Integral to the nsNSV replication cycle is the viral polymerase, which is responsible for transcribing the viral genome, to produce an array of capped and polyadenylated messenger RNAs, and replicating it to produce new genomes. To perform the different steps that are necessary for these processes, the nsNSV polymerases undergo a series of coordinated conformational transitions. While much is still to be learned regarding the intersection of nsNSV polymerase dynamics, structure, and function, recently published polymerase structures, combined with a history of biochemical and molecular biology studies, have provided new insights into how nsNSV polymerases function as dynamic machines. In this review, we consider each of the steps involved in nsNSV transcription and replication and suggest how these relate to solved polymerase structures.
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Affiliation(s)
- Mohamed Ouizougun-Oubari
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
| | - Rachel Fearns
- Department of Virology, Immunology & Microbiology, National Emerging Infectious Diseases Laboratories, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA;
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12
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Kumar G, Singh AK, Agarwal D. Structural and functional characterization of RNA dependent RNA polymerase of Macrobrachium rosenbergii nodavirus (MnRdRp). J Biomol Struct Dyn 2023; 41:12825-12837. [PMID: 36757137 DOI: 10.1080/07391102.2023.2175384] [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: 07/21/2022] [Accepted: 01/07/2023] [Indexed: 02/10/2023]
Abstract
Macrobrachium rosenbergii is a highly valued farmed freshwater species and its production has been affected globally by white tail disease caused by M. rosenbergii nodavirus (MrNV). MrNV is a single stranded positive sense RNA virus encoding RNA-dependent RNA polymerase (RdRp) for genome replication. Due to its essentiality for pathogenesis, it is an important drug target. The domain prediction of the complete sequence revealed the presence of two enzymatic regions namely methyl transferase and RdRp separated by transmembrane region. The predicted three-dimensional (3D) structure of MnRdRp using AlphaFold 2 shows that the structure is composed of three major sub-domains common for other polymerases namely fingers, palm and thumb. Structural similarity search revealed its similarity with other flaviviridea members especially with BVDV RdRp (BvdvRdRp). The structure of fingers and palm sub-domains is more conserved than the thumb sub-domain. A small α-helix named 'priming helix' having conserve Tyr was identified at position 829-833 with a potential role in de novo initiation. Analysis of electrostatic potential revealed that nucleotide and template channels are electropositive. Metal binding residues were identified as Asp599, Asp704 and Asp705. The α and β phosphates of incoming nucleotide interact with two Mn2+, Arg455 and Arg537. For recognition of 2'-OH of incoming rNTP, Asp604, Ser661 and Asn670 were identified which can form H-bond network with 2'-OH group. Docking study revealed that Dasabuvir can potentially inhibit MnRdRp. The study concluded that the overall structure and function of MnRdRp are similar to Flaviviridae polymerases and their inhibitors can work against this enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gulshan Kumar
- College of Fisheries Science Gunla, Birsa Agricultural University, Ranchi, Jharkhand, India
| | - A K Singh
- College of Fisheries Science Gunla, Birsa Agricultural University, Ranchi, Jharkhand, India
| | - Deepak Agarwal
- TNJFU, Institute of Fisheries Post Graduate Studies, OMR, Chennai, Tamil Nadu, India
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13
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Cancela F, Rendon-Marin S, Quintero-Gil C, Houston DR, Gumbis G, Panzera Y, Pérez R, Arbiza J, Mirazo S. Modelling of Hepatitis E virus RNA-dependent RNA polymerase genotype 3 from a chronic patient and in silico interaction analysis by molecular docking with Ribavirin. J Biomol Struct Dyn 2023; 41:705-721. [PMID: 34861797 DOI: 10.1080/07391102.2021.2011416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hepatitis E Virus (HEV) infection is an emergent zoonotic disease, where chronic hepatitis E associated to solid organ transplant (SOT) recipients, related to genotype 3, is the clinical manifestation of major concern. In this setting, ribavirin (RBV) treatment is the only available therapy, though drug-resistant variants could emerge leading to a therapeutic failure. Crystallographic structures have not been reported for most of the HEV proteins, including the RNA-polymerase (RdRp). Therefore, the mechanism of action of RBV against HEV and the molecular interactions between this drug and RdRp are largely unknown. In this work, we aimed to model in silico the 3 D structure of a novel HEV3 RdRp (HEV_C1_Uy) from a chronically HEV infected-SOT recipient treated with RBV and to perform a molecular docking simulation between RBV triphosphate (RBVT), 7-methyl-guanosine-5'-triphosphate and the modelled protein. The models were generated using I-TASSER server and validated with multiple bioinformatics tools. The docking analysis were carried out with AutoDock Vina and LeDock software. We obtained a suitable model for HEV_C1_Uy (C-Score=-1.33, RMSD = 10.4 ± 4.6 Å). RBVT displayed a binding affinity of -7.6 ± 0.2 Kcal/mol by molecular docking, mediated by 6 hydrogen-bonds (Q195-O14, S198-O11, E257-O13, S260-O2, O3, S311-O11) between the finger's-palm-domains and a free binding energy of 31.26 ± 16.81 kcal/mol by molecular dynamics simulations. We identified the possible HEV RdRp interacting region for incoming nucleotides or analogs and provide novel insights that will contribute to better understand the molecular interactions of RBV and the enzyme and the mechanism of action of this antiviral drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Florencia Cancela
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Rendon-Marin
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, sede Bucaramanga, Bucaramanga, Colombia
| | - Carolina Quintero-Gil
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, sede Bucaramanga, Bucaramanga, Colombia
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Edinburgh, UK
| | - Gediminas Gumbis
- Institute of Quantitative Biology, Biochemistry and Biotechnology, The University of Edinburgh, Edinburgh, UK
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Mirazo
- Sección Virología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.,Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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14
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Malet H, Williams HM, Cusack S, Rosenthal M. The mechanism of genome replication and transcription in bunyaviruses. PLoS Pathog 2023; 19:e1011060. [PMID: 36634042 PMCID: PMC9836281 DOI: 10.1371/journal.ppat.1011060] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bunyaviruses are negative sense, single-strand RNA viruses that infect a wide range of vertebrate, invertebrate and plant hosts. WHO lists three bunyavirus diseases as priority diseases requiring urgent development of medical countermeasures highlighting their high epidemic potential. While the viral large (L) protein containing the RNA-dependent RNA polymerase is a key enzyme in the viral replication cycle and therefore a suitable drug target, our knowledge on the structure and activities of this multifunctional protein has, until recently, been very limited. However, in the last few years, facilitated by the technical advances in the field of cryogenic electron microscopy, many structures of bunyavirus L proteins have been solved. These structures significantly enhance our mechanistic understanding of bunyavirus genome replication and transcription processes and highlight differences and commonalities between the L proteins of different bunyavirus families. Here, we provide a review of our current understanding of genome replication and transcription in bunyaviruses with a focus on the viral L protein. Further, we compare within bunyaviruses and with the related influenza virus polymerase complex and highlight open questions.
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Affiliation(s)
- Hélène Malet
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
- Institut Universitaire de France (IUF), Paris, France
| | - Harry M. Williams
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
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15
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Aljuaid A, Salam A, Almehmadi M, Baammi S, Alshabrmi FM, Allahyani M, Al-Zaydi KM, Izmirly AM, Almaghrabi S, Baothman BK, Shahab M. Structural Homology-Based Drug Repurposing Approach for Targeting NSP12 SARS-CoV-2. Molecules 2022; 27:7732. [PMID: 36431833 PMCID: PMC9694939 DOI: 10.3390/molecules27227732] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2, also known as SARS-CoV-2, is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 has a highly conserved non-structural protein 12 (NSP-12) involved in RNA-dependent RNA polymerase (RdRp) activity. For the identification of potential inhibitors for NSP-12, computational approaches such as the identification of homologous proteins that have been previously targeted by FDA-approved antivirals can be employed. Herein, homologous proteins of NSP-12 were retrieved from Protein DataBank (PDB) and the evolutionary conserved sequence and structure similarity of the active site of the RdRp domain of NSP-12 was characterized. The identified homologous structures of NSP-12 belonged to four viral families: Coronaviridae, Flaviviridae, Picornaviridae, and Caliciviridae, and shared evolutionary conserved relationships. The multiple sequences and structural alignment of homologous structures showed highly conserved amino acid residues that were located at the active site of the RdRp domain of NSP-12. The conserved active site of the RdRp domain of NSP-12 was evaluated for binding affinity with the FDA-approved antivirals, i.e., Sofosbuvir and Dasabuvir in a molecular docking study. The molecular docking of Sofosbuvir and Dasabuvir with the active site that contains conserved motifs (motif A-G) of the RdRp domain of NSP-12 revealed significant binding affinity. Furthermore, MD simulation also inferred the potency of Sofosbuvir and Dasabuvir. In conclusion, targeting the active site of the RdRp domain of NSP-12 with Dasabuvir and Sofosbuvir might reduce viral replication and pathogenicity and could be further studied for the treatment of SARS-CoV-2.
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Affiliation(s)
- Abdulelah Aljuaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Abdus Salam
- Precision Medicine Lab, Laboratory Building, Rehman Medical Institute, Phase-V, Hayatabad, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - Fahad M. Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Mamdouh Allahyani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khadijah M. Al-Zaydi
- Department of Chemistry, College of Science, University of Jeddah, Jeddah 23738, Saudi Arabia
| | - Abdullah M. Izmirly
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center and Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Sarah Almaghrabi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
- Center of Innovations in Personalized Medicine (CIPM), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Bandar K. Baothman
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences in Rabigh, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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16
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Cressey TN, Shareef AM, Kleiner VA, Noton SL, Byrne PO, McLellan JS, Mühlberger E, Fearns R. Distinctive features of the respiratory syncytial virus priming loop compared to other non-segmented negative strand RNA viruses. PLoS Pathog 2022; 18:e1010451. [PMID: 35731802 PMCID: PMC9255747 DOI: 10.1371/journal.ppat.1010451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/05/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
De novo initiation by viral RNA-dependent RNA polymerases often requires a polymerase priming residue, located within a priming loop, to stabilize the initiating NTPs. Polymerase structures from three different non-segmented negative strand RNA virus (nsNSV) families revealed putative priming loops in different conformations, and an aromatic priming residue has been identified in the rhabdovirus polymerase. In a previous study of the respiratory syncytial virus (RSV) polymerase, we found that Tyr1276, the L protein aromatic amino acid residue that most closely aligns with the rhabdovirus priming residue, is not required for RNA synthesis but two nearby residues, Pro1261 and Trp1262, were required. In this study, we examined the roles of Pro1261 and Trp1262 in RNA synthesis initiation. Biochemical studies showed that substitution of Pro1261 inhibited RNA synthesis initiation without inhibiting back-priming, indicating a defect in initiation. Biochemical and minigenome experiments showed that the initiation defect incurred by a P1261A substitution could be rescued by factors that would be expected to increase the stability of the initiation complex, specifically increased NTP concentration, manganese, and a more efficient promoter sequence. These findings indicate that Pro1261 of the RSV L protein plays a role in initiation, most likely in stabilizing the initiation complex. However, we found that substitution of the corresponding proline residue in a filovirus polymerase had no effect on RNA synthesis initiation or elongation. These results indicate that despite similarities between the nsNSV polymerases, there are differences in the features required for RNA synthesis initiation. RSV has a significant impact on human health. It is the major cause of respiratory disease in infants and exerts a significant toll on the elderly and immunocompromised. RSV is a member of the Mononegavirales, the non-segmented, negative strand RNA viruses (nsNSVs). Like other viruses in this order, RSV encodes an RNA dependent RNA polymerase, which is responsible for transcribing and replicating the viral genome. Due to its essential role during the viral replication cycle, the polymerase is a promising candidate target for antiviral inhibitors and so a greater understanding of the mechanistic basis of its activities could aid antiviral drug development. In this study, we identified an amino acid residue within the RSV polymerase that appears to stabilize the RNA synthesis initiation complex and showed that it plays a role in both transcription and RNA replication. However, the corresponding residue in a different nsNSV polymerase does not appear to play a similar role. This work reveals a key feature of the RSV polymerase but identifies differences with the polymerases of other related viruses.
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Affiliation(s)
- Tessa N. Cressey
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Afzaal M. Shareef
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Victoria A. Kleiner
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Sarah L. Noton
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Patrick O. Byrne
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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17
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Alam A, Agrawal GP, Khan S, Khalilullah H, Saifullah MK, Arshad MF. Towards the discovery of potential RdRp inhibitors for the treatment of COVID-19: structure guided virtual screening, computational ADME and molecular dynamics study. Struct Chem 2022; 33:1569-1583. [PMID: 35669792 PMCID: PMC9161180 DOI: 10.1007/s11224-022-01976-2] [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: 12/09/2021] [Accepted: 05/25/2022] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) has become a major challenge affecting almost every corner of the world, with more than five million deaths worldwide. Despite several efforts, no drug or vaccine has shown the potential to check the ever-mutating SARS-COV-2. The emergence of novel variants is a major concern increasing the need for the discovery of novel therapeutics for the management of this pandemic. Out of several potential drug targets such as S protein, human ACE2, TMPRSS2 (transmembrane protease serine 2), 3CLpro, RdRp, and PLpro (papain-like protease), RNA-dependent RNA polymerase (RdRP) is a vital enzyme for viral RNA replication in the mammalian host cell and is one of the legitimate targets for the development of therapeutics against this disease. In this study, we have performed structure-based virtual screening to identify potential hit compounds against RdRp using molecular docking of a commercially available small molecule library of structurally diverse and drug-like molecules. Since non-optimal ADME properties create hurdles in the clinical development of drugs, we performed detailed in silico ADMET prediction to facilitate the selection of compounds for further studies. The results from the ADMET study indicated that most of the hit compounds had optimal properties. Moreover, to explore the conformational dynamics of protein-ligand interaction, we have performed an atomistic molecular dynamics simulation which indicated a stable interaction throughout the simulation period. We believe that the current findings may assist in the discovery of drug candidates against SARS-CoV-2.
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Affiliation(s)
- Aftab Alam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj, 11942 Kingdom of Saudi Arabia
| | | | - Shamshir Khan
- College of Dentistry and Pharmacy, Buraydah Private Colleges, Al-Qassim, Kingdom of Saudi Arabia
| | - Habibullah Khalilullah
- Department of Pharmaceutical Chemistry and Pharmacognosy Unaizah College of Pharmacy, Qassim University, Buraydah, Kingdom of Saudi Arabia
| | - Muhammed Khalid Saifullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, Umm-Al Qura University Makkah, Mecca, Kingdom of Saudi Arabia
| | - Mohammed Faiz Arshad
- Department of Research and Scientific Communications, Isthmus Research and Publishing House, U-13, Near Badi Masjid, Pulpehlad Pur, New Delhi, 110044 India
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18
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Li AWH, Zabrady K, Bainbridge LJ, Zabrady M, Naseem-Khan S, Berger MB, Kolesar P, Cisneros GA, Doherty AJ. Molecular basis for the initiation of DNA primer synthesis. Nature 2022; 605:767-773. [PMID: 35508653 PMCID: PMC9149119 DOI: 10.1038/s41586-022-04695-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/28/2022] [Indexed: 11/08/2022]
Abstract
During the initiation of DNA replication, oligonucleotide primers are synthesized de novo by primases and are subsequently extended by replicative polymerases to complete genome duplication. The primase-polymerase (Prim-Pol) superfamily is a diverse grouping of primases, which includes replicative primases and CRISPR-associated primase-polymerases (CAPPs) involved in adaptive immunity1-3. Although much is known about the activities of these enzymes, the precise mechanism used by primases to initiate primer synthesis has not been elucidated. Here we identify the molecular bases for the initiation of primer synthesis by CAPP and show that this mechanism is also conserved in replicative primases. The crystal structure of a primer initiation complex reveals how the incoming nucleotides are positioned within the active site, adjacent to metal cofactors and paired to the templating single-stranded DNA strand, before synthesis of the first phosphodiester bond. Furthermore, the structure of a Prim-Pol complex with double-stranded DNA shows how the enzyme subsequently extends primers in a processive polymerase mode. The structural and mechanistic studies presented here establish how Prim-Pol proteins instigate primer synthesis, revealing the requisite molecular determinants for primer synthesis within the catalytic domain. This work also establishes that the catalytic domain of Prim-Pol enzymes, including replicative primases, is sufficient to catalyse primer formation.
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Affiliation(s)
- Arthur W H Li
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Lewis J Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Matej Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Sehr Naseem-Khan
- Department of Chemistry, University of North Texas, Denton, TX, USA
| | - Madison B Berger
- Department of Chemistry, University of North Texas, Denton, TX, USA
- Department of Physics and Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Peter Kolesar
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX, USA
- Department of Physics and Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
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19
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IL-26 inhibits hepatitis C virus replication in hepatocytes. J Hepatol 2022; 76:822-831. [PMID: 34952035 DOI: 10.1016/j.jhep.2021.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/15/2021] [Accepted: 12/07/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Interleukin-26 (IL-26) is a proinflammatory cytokine that has properties atypical for a cytokine, such as direct antibacterial activity and DNA-binding capacity. We previously observed an accumulation of IL-26 in fibrotic and inflammatory lesions in the livers of patients with chronic HCV infection and showed that infiltrating CD3+ lymphocytes were the principal source of IL-26. Surprisingly, IL-26 was also detected in the cytoplasm of hepatocytes from HCV-infected patients, even though these cells do not produce IL-26, even when infected with HCV. Based on this observation and possible interactions between IL-26 and nucleic acids, we investigated the possibility that IL-26 controlled HCV infection independently of the immune system. METHODS We evaluated the ability of IL-26 to interfere with HCV replication in hepatocytes and investigated the mechanisms by which IL-26 exerts its antiviral activity. RESULTS We showed that IL-26 penetrated HCV-infected hepatocytes, where it interacted directly with HCV double-stranded RNA replication intermediates, thereby inhibiting viral replication. IL-26 interfered with viral RNA-dependent RNA polymerase activity, preventing the de novo synthesis of viral genomic single-stranded RNA. CONCLUSIONS These findings reveal a new role for IL-26 in direct protection against HCV infection, independently of the immune system, and increase our understanding of the antiviral defense mechanisms controlling HCV infection. Future studies should evaluate the possible use of IL-26 for treating other chronic disorders caused by RNA viruses, for which few treatments are currently available, or emerging RNA viruses. LAY SUMMARY This study sheds new light on the body's arsenal for controlling hepatitis C virus (HCV) infection and identifies interleukin-26 (IL-26) as an antiviral molecule capable of blocking HCV replication. IL-26, which has unique biochemical and structural characteristics, penetrates infected hepatocytes and interacts directly with viral RNA, thereby blocking viral replication. IL-26 is, therefore, a new player in antiviral defenses, operating independently of the immune system. It is of considerable potential interest for treating HCV infection and other chronic disorders caused by RNA viruses for which few treatments are currently available, and for combating emerging RNA viruses.
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Ogino M, Green TJ, Ogino T. GDP polyribonucleotidyltransferase domain of vesicular stomatitis virus polymerase regulates leader-promoter escape and polyadenylation-coupled termination during stop-start transcription. PLoS Pathog 2022; 18:e1010287. [PMID: 35108335 PMCID: PMC8843114 DOI: 10.1371/journal.ppat.1010287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/14/2022] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
The unconventional mRNA capping enzyme (GDP polyribonucleotidyltransferase, PRNTase) domain of the vesicular stomatitis virus (VSV) L protein possesses a dual-functional "priming-capping loop" that governs terminal de novo initiation for leader RNA synthesis and capping of monocistronic mRNAs during the unique stop-start transcription cycle. Here, we investigated the roles of basic amino acid residues on a helix structure directly connected to the priming-capping loop in viral RNA synthesis and identified single point mutations that cause previously unreported defective phenotypes at different steps of stop-start transcription. Mutations of residue R1183 (R1183A and R1183K) dramatically reduced the leader RNA synthesis activity by hampering early elongation, but not terminal de novo initiation or productive elongation, suggesting that the mutations negatively affect escape from the leader promoter. On the other hand, mutations of residue R1178 (R1178A and R1178K) decreased the efficiency of polyadenylation-coupled termination of mRNA synthesis at the gene junctions, but not termination of leader RNA synthesis at the leader-to-N-gene junction, resulting in the generation of larger amounts of aberrant polycistronic mRNAs. In contrast, both the R1183 and R1178 residues are not essential for cap-forming activities. The R1183K mutation was lethal to VSV, whereas the R1178K mutation attenuated VSV and triggered the production of the polycistronic mRNAs in infected cells. These observations suggest that the PRNTase domain plays multiple roles in conducting accurate stop-start transcription beyond its known role in pre-mRNA capping. Vesicular stomatitis virus (VSV), an animal rhabdovirus closely related to rabies virus, has served as a paradigm for understanding the basic molecular mechanisms of transcription and replication by rhabdoviruses (e.g., rabies) and other non-segmented negative strand (NNS) RNA viruses, such as measles and Ebola. NNS RNA viral polymerases sequentially synthesize the non-coding leader RNA and monocistronic mRNAs from the 3′-terminal leader region and internal genes, respectively, on their genomes by the stop-start transcription mechanism. A hallmark of NNS RNA viral polymerases is the presence of a unique enzymatic domain, called GDP polyribonucleotidyltransferase (PRNTase), which catalyzes pre-mRNA 5′-capping, one of the essential mRNA modifications. Our recent study revealed that the VSV PRNTase domain directs transcription initiation at the 3′-end of the genome as well as pre-mRNA capping with the dual functional priming-capping loop during stop-start transcription. Here, we further show that a helix structure flanked by the priming-capping loop regulates not only transcription elongation at an early phase of leader RNA synthesis but also polyadenylation-coupled transcription termination at gene junctions. These findings indicate that the PRNTase domain acts as a key regulatory domain for stop-start transcription as well as a catalytic domain for pre-mRNA capping.
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Affiliation(s)
- Minako Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, United States of America
| | - Todd J. Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tomoaki Ogino
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, United States of America
- * E-mail:
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21
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Gong P. Within and Beyond the Nucleotide Addition Cycle of Viral RNA-dependent RNA Polymerases. Front Mol Biosci 2022; 8:822218. [PMID: 35083282 PMCID: PMC8784604 DOI: 10.3389/fmolb.2021.822218] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
Abstract
Nucleotide addition cycle (NAC) is a fundamental process utilized by nucleic acid polymerases when carrying out nucleic acid biosynthesis. An induced-fit mechanism is usually taken by these polymerases upon NTP/dNTP substrate binding, leading to active site closure and formation of a phosphodiester bond. In viral RNA-dependent RNA polymerases, the post-chemistry translocation is stringently controlled by a structurally conserved motif, resulting in asymmetric movement of the template-product duplex. This perspective focuses on viral RdRP NAC and related mechanisms that have not been structurally clarified to date. Firstly, RdRP movement along the template strand in the absence of catalytic events may be relevant to catalytic complex dissociation or proofreading. Secondly, pyrophosphate or non-cognate NTP-mediated cleavage of the product strand 3′-nucleotide can also play a role in reactivating paused or arrested catalytic complexes. Furthermore, non-cognate NTP substrates, including NTP analog inhibitors, can not only alter NAC when being misincorporated, but also impact on subsequent NACs. Complications and challenges related to these topics are also discussed.
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Affiliation(s)
- Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China
- *Correspondence: Peng Gong,
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22
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Comparison of RNA synthesis initiation properties of non-segmented negative strand RNA virus polymerases. PLoS Pathog 2021; 17:e1010151. [PMID: 34914795 PMCID: PMC8717993 DOI: 10.1371/journal.ppat.1010151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/30/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
It is generally thought that the promoters of non-segmented, negative strand RNA viruses (nsNSVs) direct the polymerase to initiate RNA synthesis exclusively opposite the 3´ terminal nucleotide of the genome RNA by a de novo (primer independent) initiation mechanism. However, recent studies have revealed that there is diversity between different nsNSVs with pneumovirus promoters directing the polymerase to initiate at positions 1 and 3 of the genome, and ebolavirus polymerases being able to initiate at position 2 on the template. Studies with other RNA viruses have shown that polymerases that engage in de novo initiation opposite position 1 typically have structural features to stabilize the initiation complex and ensure efficient and accurate initiation. This raised the question of whether different nsNSV polymerases have evolved fundamentally different structural properties to facilitate initiation at different sites on their promoters. Here we examined the functional properties of polymerases of respiratory syncytial virus (RSV), a pneumovirus, human parainfluenza virus type 3 (PIV-3), a paramyxovirus, and Marburg virus (MARV), a filovirus, both on their cognate promoters and on promoters of other viruses. We found that in contrast to the RSV polymerase, which initiated at positions 1 and 3 of its promoter, the PIV-3 and MARV polymerases initiated exclusively at position 1 on their cognate promoters. However, all three polymerases could recognize and initiate from heterologous promoters, with the promoter sequence playing a key role in determining initiation site selection. In addition to examining de novo initiation, we also compared the ability of the RSV and PIV-3 polymerases to engage in back-priming, an activity in which the promoter template is folded into a secondary structure and nucleotides are added to the template 3´ end. This analysis showed that whereas the RSV polymerase was promiscuous in back-priming activity, the PIV-3 polymerase generated barely detectable levels of back-primed product, irrespective of promoter template sequence. Overall, this study shows that the polymerases from these three nsNSV families are fundamentally similar in their initiation properties, but have differences in their abilities to engage in back-priming.
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23
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Pyle JD, Whelan SPJ, Bloyet LM. Structure and function of negative-strand RNA virus polymerase complexes. Enzymes 2021; 50:21-78. [PMID: 34861938 DOI: 10.1016/bs.enz.2021.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Viruses with negative-strand RNA genomes (NSVs) include many highly pathogenic and economically devastating disease-causing agents of humans, livestock, and plants-highlighted by recent Ebola and measles virus epidemics, and continuously circulating influenza virus. Because of their protein-coding orientation, NSVs face unique challenges for efficient gene expression and genome replication. To overcome these barriers, NSVs deliver a large and multifunctional RNA-dependent RNA polymerase into infected host cells. NSV-encoded polymerases contain all the enzymatic activities required for transcription and replication of their genome-including RNA synthesis and mRNA capping. Here, we review the structures and functions of NSV polymerases with a focus on key domains responsible for viral replication and gene expression. We highlight shared and unique features among polymerases of NSVs from the Mononegavirales, Bunyavirales, and Articulavirales orders.
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Affiliation(s)
- Jesse D Pyle
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States; Ph.D. Program in Virology, Harvard Medical School, Boston, MA, United States
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States.
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Abstract
The RNA-dependent RNA polymerase (RdRp) of all known double-stranded RNA viruses is located within the viral particle and is responsible for the transcription and replication of the viral genome. Through an RT-PCR assay, we determined that purified virions, in vitro translated RdRp proteins, and purified recombinant RdRp proteins of partitiviruses also have reverse transcriptase (RT) function. We show that partitivirus RdRps 1) synthesized DNA from homologous and heterologous dsRNA templates; 2) are active using both ssRNA and dsRNA templates; and 3) are active at lower temperatures compared to an optimal reaction temperature of commercial RT enzymes. This finding poses an intriguing question: why do partitiviruses, with dsRNA genomes, have a polymerase with RT functions? In comparison, 3Dpol, the RdRp of poliovirus, did not show any RT activity. Our findings lead us to propose a new evolutionary model for RNA viruses where the RdRp of dsRNA viruses could be the ancestor of RdRps.
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Affiliation(s)
- Mahtab Peyambari
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
| | | | - Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
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25
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Levanova AA, Vainio EJ, Hantula J, Poranen MM. RNA-Dependent RNA Polymerase from Heterobasidion RNA Virus 6 Is an Active Replicase In Vitro. Viruses 2021; 13:v13091738. [PMID: 34578320 PMCID: PMC8473416 DOI: 10.3390/v13091738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/16/2022] Open
Abstract
Heterobasidion RNA virus 6 (HetRV6) is a double-stranded (ds)RNA mycovirus and a member of the recently established genus Orthocurvulavirus within the family Orthocurvulaviridae. The purpose of the study was to determine the biochemical requirements for RNA synthesis catalyzed by HetRV6 RNA-dependent RNA polymerase (RdRp). HetRV6 RdRp was expressed in Escherichia coli and isolated to near homogeneity using liquid chromatography. The enzyme activities were studied in vitro using radiolabeled UTP. The HetRV6 RdRp was able to initiate RNA synthesis in a primer-independent manner using both virus-related and heterologous single-stranded (ss)RNA templates, with a polymerization rate of about 46 nt/min under optimal NTP concentration and temperature. NTPs with 2'-fluoro modifications were also accepted as substrates in the HetRV6 RdRp-catalyzed RNA polymerization reaction. HetRV6 RdRp transcribed viral RNA genome via semi-conservative mechanism. Furthermore, the enzyme demonstrated terminal nucleotidyl transferase (TNTase) activity. Presence of Mn2+ was required for the HetRV6 RdRp catalyzed enzymatic activities. In summary, our study shows that HetRV6 RdRp is an active replicase in vitro that can be potentially used in biotechnological applications, molecular biology, and biomedicine.
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Affiliation(s)
- Alesia A. Levanova
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (A.A.L.); (M.M.P.)
| | - Eeva J. Vainio
- Natural Resources Institute Finland, 00790 Helsinki, Finland; (E.J.V.); (J.H.)
| | - Jarkko Hantula
- Natural Resources Institute Finland, 00790 Helsinki, Finland; (E.J.V.); (J.H.)
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland
- Correspondence: (A.A.L.); (M.M.P.)
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26
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Xu X, Zhang L, Chu JTS, Wang Y, Chin AWH, Chong TH, Dai Z, Poon LLM, Cheung PPH, Huang X. A novel mechanism of enhanced transcription activity and fidelity for influenza A viral RNA-dependent RNA polymerase. Nucleic Acids Res 2021; 49:8796-8810. [PMID: 34379778 PMCID: PMC8421151 DOI: 10.1093/nar/gkab660] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/13/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
During RNA elongation, the influenza A viral (IAV) RNA-dependent RNA polymerase (RdRp) residues in the active site interact with the triphosphate moiety of nucleoside triphosphate (NTP) for catalysis. The molecular mechanisms by which they control the rate and fidelity of NTP incorporation remain elusive. Here, we demonstrated through enzymology, virology and computational approaches that the R239 and K235 in the PB1 subunit of RdRp are critical to controlling the activity and fidelity of transcription. Contrary to common beliefs that high-fidelity RdRp variants exert a slower incorporation rate, we discovered a first-of-its-kind, single lysine-to-arginine mutation on K235 exhibited enhanced fidelity and activity compared with wild-type. In particular, we employed a single-turnover NTP incorporation assay for the first time on IAV RdRp to show that K235R mutant RdRp possessed a 1.9-fold increase in the transcription activity of the cognate NTP and a 4.6-fold increase in fidelity compared to wild-type. Our all-atom molecular dynamics simulations further elucidated that the higher activity is attributed to the shorter distance between K235R and the triphosphate moiety of NTP compared with wild-type. These results provide novel insights into NTP incorporation and fidelity control mechanisms, which lay the foundation for the rational design of IAV vaccine and antiviral targets.
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Affiliation(s)
- Xinzhou Xu
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julie Tung Sem Chu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuqing Wang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Bioengineering Graduate Program, Department of Biological and Chemical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alex Wing Hong Chin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Tin Hang Chong
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Zixi Dai
- Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Leo Lit Man Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Immunity and Infection, Hong Kong Science Park, Hong Kong, China
| | - Peter Pak-Hang Cheung
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, China.,Li Ka Shing Institute of Health Sciences, Li Ka Shing Medical Sciences Building, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Xuhui Huang
- The Hong Kong University of Science and Technology-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen 518057, China.,Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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27
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Zhang BY, Liu W, Jia H, Lu G, Gong P. An induced-fit de novo initiation mechanism suggested by a pestivirus RNA-dependent RNA polymerase. Nucleic Acids Res 2021; 49:8811-8821. [PMID: 34365500 PMCID: PMC8421227 DOI: 10.1093/nar/gkab666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/15/2021] [Accepted: 08/06/2021] [Indexed: 01/09/2023] Open
Abstract
Viral RNA-dependent RNA polymerases (RdRPs) play central roles in the genome replication and transcription processes of RNA viruses. RdRPs initiate RNA synthesis either in primer-dependent or de novo mechanism, with the latter often assisted by a 'priming element' (PE) within the RdRP thumb domain. However, RdRP PEs exhibit high-level structural diversity, making it difficult to reconcile their conserved function in de novo initiation. Here we determined a 3.1-Å crystal structure of the Flaviviridae classical swine fever virus (CSFV) RdRP with a relative complete PE. Structure-based mutagenesis in combination with enzymology data further highlights the importance of a glycine residue (G671) and the participation of residues 665-680 in RdRP initiation. When compared with other representative Flaviviridae RdRPs, CSFV RdRP PE is structurally distinct but consistent in terminal initiation preference. Taken together, our work suggests that a conformational change in CSFV RdRP PE is necessary to fulfill de novo initiation, and similar 'induced-fit' mechanisms may be commonly taken by PE-containing de novo viral RdRPs.
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Affiliation(s)
| | - Weichi Liu
- Correspondence may also be addressed to Weichi Liu.
| | - Hengxia Jia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, Hubei 430071, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, No.44 Xiao Hong Shan, Wuhan, Hubei 430071, China
| | - Peng Gong
- To whom correspondence should be addressed. Tel: +86 27 87197578; Fax: +86 27 87197578;
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28
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Proline to Threonine Mutation at Position 162 of NS5B of Classical Swine Fever Virus Vaccine C Strain Promoted Genome Replication and Infectious Virus Production by Facilitating Initiation of RNA Synthesis. Viruses 2021; 13:v13081523. [PMID: 34452387 PMCID: PMC8402891 DOI: 10.3390/v13081523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/11/2022] Open
Abstract
The 3′untranslated region (3′UTR) and NS5B of classical swine fever virus (CSFV) play vital roles in viral genome replication. In this study, two chimeric viruses, vC/SM3′UTR and vC/b3′UTR, with 3′UTR substitution of CSFV Shimen strain or bovine viral diarrhea virus (BVDV) NADL strain, were constructed based on the infectious cDNA clone of CSFV vaccine C strain, respectively. After virus rescue, each recombinant chimeric virus was subjected to continuous passages in PK-15 cells. The representative passaged viruses were characterized and sequenced. Serial passages resulted in generation of mutations and the passaged viruses exhibited significantly increased genomic replication efficiency and infectious virus production compared to parent viruses. A proline to threonine mutation at position 162 of NS5B was identified in both passaged vC/SM3′UTR and vC/b3′UTR. We generated P162T mutants of two chimeras using the reverse genetics system, separately. The single P162T mutation in NS5B of vC/SM3′UTR or vC/b3′UTR played a key role in increased viral genome replication and infectious virus production. The P162T mutation increased vC/SM3′UTRP162T replication in rabbits. From RNA-dependent RNA polymerase (RdRp) assays in vitro, the NS5B containing P162T mutation (NS5BP162T) exhibited enhanced RdRp activity for different RNA templates. We further identified that the enhanced RdRp activity originated from increased initiation efficiency of RNA synthesis. These findings revealed a novel function for the NS5B residue 162 in modulating pestivirus replication.
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29
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Bhatia S, Narayanan N, Nagpal S, Nair DT. Antiviral therapeutics directed against RNA dependent RNA polymerases from positive-sense viruses. Mol Aspects Med 2021; 81:101005. [PMID: 34311994 DOI: 10.1016/j.mam.2021.101005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 01/18/2023]
Abstract
Viruses with positive-sense single stranded RNA (+ssRNA) genomes are responsible for different diseases and represent a global health problem. In addition to developing new vaccines that protect against severe illness on infection, it is imperative to identify new antiviral molecules to treat infected patients. The genome of these RNA viruses generally codes for an enzyme with RNA dependent RNA polymerase (RdRP) activity. This molecule is centrally involved in the duplication of the RNA genome. Inhibition of this enzyme by small molecules will prevent duplication of the RNA genome and thus reduce the viral titer. An overview of the different therapeutic strategies used to inhibit RdRPs from +ssRNA viruses is provided, along with an analysis of these enzymes to highlight new binding sites for inhibitors.
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Affiliation(s)
- Sonam Bhatia
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Naveen Narayanan
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India
| | - Shilpi Nagpal
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, India.
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30
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Winston DS, Boehr DD. Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity. Enzymes 2021; 49:149-193. [PMID: 34696831 DOI: 10.1016/bs.enz.2021.06.001] [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] [Indexed: 06/13/2023]
Abstract
All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.
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Affiliation(s)
- Dennis S Winston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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31
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Gong P. Structural basis of viral RNA-dependent RNA polymerase nucleotide addition cycle in picornaviruses. Enzymes 2021; 49:215-233. [PMID: 34696833 DOI: 10.1016/bs.enz.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of processive nucleic acid polymerases, carrying out DNA-independent replication/transcription processes. Although viral RdRPs have versatile global structures, they do share a structurally highly conserved active site comprising catalytic motifs A-G. In spite of different initiation modes, the nucleotide addition cycle (NAC) in the RdRP elongation phase probably follows consistent mechanisms. In this chapter, representative structures of picornavirus RdRP elongation complexes are used to illustrate RdRP NAC mechanisms. In the pre-chemistry part of the NAC, RdRPs utilize a unique palm domain-based active site closure that can be further decomposed into two sequential steps. In the post-chemistry part of the NAC, the translocation process is stringently controlled by the RdRP-specific motif G, resulting in asymmetric movements of the template-product RNA. Future efforts to elucidate regulation/intervention mechanisms by mismatched NTPs or nucleotide analog antivirals are necessary to achieve comprehensive understandings of viral RdRP NAC.
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Affiliation(s)
- Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China; Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China.
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32
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Domanska A, Guryanov S, Butcher SJ. A comparative analysis of parechovirus protein structures with other picornaviruses. Open Biol 2021; 11:210008. [PMID: 34315275 PMCID: PMC8316810 DOI: 10.1098/rsob.210008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/01/2021] [Indexed: 12/26/2022] Open
Abstract
Parechoviruses belong to the genus Parechovirus within the family Picornaviridae and are non-enveloped icosahedral viruses with a single-stranded RNA genome. Parechoviruses include human and animal pathogens classified into six species. Those that infect humans belong to the Parechovirus A species and can cause infections ranging from mild gastrointestinal or respiratory illness to severe neonatal sepsis. There are no approved antivirals available to treat parechovirus (nor any other picornavirus) infections. In this parechovirus review, we focus on the cleaved protein products resulting from the polyprotein processing after translation comparing and contrasting their known or predicted structures and functions to those of other picornaviruses. The review also includes our original analysis from sequence and structure prediction. This review highlights significant structural differences between parechoviral and other picornaviral proteins, suggesting that parechovirus drug development should specifically be directed to parechoviral targets.
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Affiliation(s)
- Aušra Domanska
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, and Helsinki Institute of Life Sciences–Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Sergey Guryanov
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, and Helsinki Institute of Life Sciences–Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Sarah J. Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, and Helsinki Institute of Life Sciences–Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
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Ferrero DS, Falqui M, Verdaguer N. Snapshots of a Non-Canonical RdRP in Action. Viruses 2021; 13:v13071260. [PMID: 34203380 PMCID: PMC8310298 DOI: 10.3390/v13071260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
RNA viruses typically encode their own RNA-dependent RNA polymerase (RdRP) to ensure genome replication and transcription. The closed “right hand” architecture of RdRPs encircles seven conserved structural motifs (A to G) that regulate the polymerization activity. The four palm motifs, arranged in the sequential order A to D, are common to all known template dependent polynucleotide polymerases, with motifs A and C containing the catalytic aspartic acid residues. Exceptions to this design have been reported in members of the Permutotetraviridae and Birnaviridae families of positive single stranded (+ss) and double-stranded (ds) RNA viruses, respectively. In these enzymes, motif C is located upstream of motif A, displaying a permuted C–A–B–D connectivity. Here we study the details of the replication elongation process in the non-canonical RdRP of the Thosea asigna virus (TaV), an insect virus from the Permutatetraviridae family. We report the X-ray structures of three replicative complexes of the TaV polymerase obtained with an RNA template-primer in the absence and in the presence of incoming rNTPs. The structures captured different replication events and allowed to define the critical interactions involved in: (i) the positioning of the acceptor base of the template strand, (ii) the positioning of the 3’-OH group of the primer nucleotide during RNA replication and (iii) the recognition and positioning of the incoming nucleotide. Structural comparisons unveiled a closure of the active site on the RNA template-primer binding, before rNTP entry. This conformational rearrangement that also includes the repositioning of the motif A aspartate for the catalytic reaction to take place is maintained on rNTP and metal ion binding and after nucleotide incorporation, before translocation.
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34
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Musarra-Pizzo M, Pennisi R, Ben-Amor I, Mandalari G, Sciortino MT. Antiviral Activity Exerted by Natural Products against Human Viruses. Viruses 2021; 13:v13050828. [PMID: 34064347 PMCID: PMC8147851 DOI: 10.3390/v13050828] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/01/2021] [Indexed: 12/13/2022] Open
Abstract
Viral infections are responsible for several chronic and acute diseases in both humans and animals. Despite the incredible progress in human medicine, several viral diseases, such as acquired immunodeficiency syndrome, respiratory syndromes, and hepatitis, are still associated with high morbidity and mortality rates in humans. Natural products from plants or other organisms are a rich source of structurally novel chemical compounds including antivirals. Indeed, in traditional medicine, many pathological conditions have been treated using plant-derived medicines. Thus, the identification of novel alternative antiviral agents is of critical importance. In this review, we summarize novel phytochemicals with antiviral activity against human viruses and their potential application in treating or preventing viral disease.
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Affiliation(s)
- Maria Musarra-Pizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale SS. Annunziata, 98168 Messina, Italy; (M.M.-P.); (R.P.); (I.B.-A.)
| | - Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale SS. Annunziata, 98168 Messina, Italy; (M.M.-P.); (R.P.); (I.B.-A.)
- Shenzhen International Institute for Biomedical Research, 1301 Guanguang Rd. 3F Building 1-B, Silver Star Hi-Tech Park Longhua District, Shenzhen 518116, China
| | - Ichrak Ben-Amor
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale SS. Annunziata, 98168 Messina, Italy; (M.M.-P.); (R.P.); (I.B.-A.)
- Unit of Biotechnology and Pathologies, Higher Institute of Biotechnology of Sfax, University of Sfax, Sfax 3029, Tunisia
| | - Giuseppina Mandalari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale SS. Annunziata, 98168 Messina, Italy; (M.M.-P.); (R.P.); (I.B.-A.)
- Correspondence: (G.M.); (M.T.S.); Tel.: +39-090-6767-5217 (G.M. & M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale SS. Annunziata, 98168 Messina, Italy; (M.M.-P.); (R.P.); (I.B.-A.)
- Correspondence: (G.M.); (M.T.S.); Tel.: +39-090-6767-5217 (G.M. & M.T.S.)
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35
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Guedes IA, Costa LSC, Dos Santos KB, Karl ALM, Rocha GK, Teixeira IM, Galheigo MM, Medeiros V, Krempser E, Custódio FL, Barbosa HJC, Nicolás MF, Dardenne LE. Drug design and repurposing with DockThor-VS web server focusing on SARS-CoV-2 therapeutic targets and their non-synonym variants. Sci Rep 2021; 11:5543. [PMID: 33692377 PMCID: PMC7946942 DOI: 10.1038/s41598-021-84700-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/16/2021] [Indexed: 02/07/2023] Open
Abstract
The COVID-19 caused by the SARS-CoV-2 virus was declared a pandemic disease in March 2020 by the World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and drug repurposing to find effective treatments against this disease. In this work, we present the developments implemented in the DockThor-VS web server to provide a virtual screening (VS) platform with curated structures of potential therapeutic targets from SARS-CoV-2 incorporating genetic information regarding relevant non-synonymous variations. The web server facilitates repurposing VS experiments providing curated libraries of currently available drugs on the market. At present, DockThor-VS provides ready-for-docking 3D structures for wild type and selected mutations for Nsp3 (papain-like, PLpro domain), Nsp5 (Mpro, 3CLpro), Nsp12 (RdRp), Nsp15 (NendoU), N protein, and Spike. We performed VS experiments of FDA-approved drugs considering the therapeutic targets available at the web server to assess the impact of considering different structures and mutations to identify possible new treatments of SARS-CoV-2 infections. The DockThor-VS is freely available at www.dockthor.lncc.br .
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Affiliation(s)
- Isabella A Guedes
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Leon S C Costa
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Karina B Dos Santos
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Ana L M Karl
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | | | - Iury M Teixeira
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Marcelo M Galheigo
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Vivian Medeiros
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | | | - Fábio L Custódio
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Helio J C Barbosa
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil
| | - Marisa F Nicolás
- Laboratório de Bioinformática (Labinfo), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil.
| | - Laurent E Dardenne
- Grupo de Modelagem Molecular em Sistemas Biológicos (GMMSB), National Laboratory for Scientific Computing - LNCC, Petrópolis, RJ, Brazil.
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36
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Structure Unveils Relationships between RNA Virus Polymerases. Viruses 2021; 13:v13020313. [PMID: 33671332 PMCID: PMC7922027 DOI: 10.3390/v13020313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022] Open
Abstract
RNA viruses are the fastest evolving known biological entities. Consequently, the sequence similarity between homologous viral proteins disappears quickly, limiting the usability of traditional sequence-based phylogenetic methods in the reconstruction of relationships and evolutionary history among RNA viruses. Protein structures, however, typically evolve more slowly than sequences, and structural similarity can still be evident, when no sequence similarity can be detected. Here, we used an automated structural comparison method, homologous structure finder, for comprehensive comparisons of viral RNA-dependent RNA polymerases (RdRps). We identified a common structural core of 231 residues for all the structurally characterized viral RdRps, covering segmented and non-segmented negative-sense, positive-sense, and double-stranded RNA viruses infecting both prokaryotic and eukaryotic hosts. The grouping and branching of the viral RdRps in the structure-based phylogenetic tree follow their functional differentiation. The RdRps using protein primer, RNA primer, or self-priming mechanisms have evolved independently of each other, and the RdRps cluster into two large branches based on the used transcription mechanism. The structure-based distance tree presented here follows the recently established RdRp-based RNA virus classification at genus, subfamily, family, order, class and subphylum ranks. However, the topology of our phylogenetic tree suggests an alternative phylum level organization.
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37
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Picarazzi F, Vicenti I, Saladini F, Zazzi M, Mori M. Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge. Molecules 2020; 25:E5695. [PMID: 33287144 PMCID: PMC7730706 DOI: 10.3390/molecules25235695] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
The RNA-dependent RNA polymerase (RdRp) is an essential enzyme for the viral replication process, catalyzing the viral RNA synthesis using a metal ion-dependent mechanism. In recent years, RdRp has emerged as an optimal target for the development of antiviral drugs, as demonstrated by recent approvals of sofosbuvir and remdesivir against Hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively. In this work, we overview the main sequence and structural features of the RdRp of emerging RNA viruses such as Coronaviruses, Flaviviruses, and HCV, as well as inhibition strategies implemented so far. While analyzing the structural information available on the RdRp of emerging RNA viruses, we provide examples of success stories such as for HCV and SARS-CoV-2. In contrast, Flaviviruses' story has raised attention about how the lack of structural details on catalytically-competent or ligand-bound RdRp strongly hampers the application of structure-based drug design, either in repurposing and conventional approaches.
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Affiliation(s)
- Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.S.); (M.Z.)
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018–2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy;
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38
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Noreen, Ali R, Badshah SL, Faheem M, Abbasi SW, Ullah R, Bari A, Jamal SB, Mahmood HM, Haider A, Haider S. Identification of potential inhibitors of Zika virus NS5 RNA-dependent RNA polymerase through virtual screening and molecular dynamic simulations. Saudi Pharm J 2020; 28:1580-1591. [PMID: 33424251 PMCID: PMC7783101 DOI: 10.1016/j.jsps.2020.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
Zika virus (ZIKV) is one of the mosquito borne flavivirus with several outbreaks in past few years in tropical and subtropical regions. The non-structural proteins of flaviviruses are suitable active targets for inhibitory drugs due to their role in pathogenicity. In ZIKV, the non-structural protein 5 (NS5) RNA-Dependent RNA polymerase replicates its genome. Here we have performed virtual screening to identify suitable ligands that can potentially halt the ZIKV NS5 RNA dependent RNA polymerase (RdRp). During this process, we searched and screened a library of ligands against ZIKV NS5 RdRp. The selected ligands with significant binding energy and ligand-receptor interactions were further processed. Among the selected docked conformations, top five was further optimized at atomic level using molecular dynamic simulations followed by binding free energy calculations. The interactions of ligands with the target structure of ZIKV RdRp revealed that they form strong bonds within the active sites of the receptor molecule. The efficacy of these drugs against ZIKV can be further analyzed through in-vitro and in-vivo studies.
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Affiliation(s)
- Noreen
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Roshan Ali
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University, Peshawar, Pakistan
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy (MAPPRC), College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmacuitcal Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Hafiz Majid Mahmood
- Department of Pharmacology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Adnan Haider
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sajjad Haider
- Department of Chemical Engineering, College of Engineering, King Saud University, Riyadh, Saudi Arabia
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39
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Two RNA Tunnel Inhibitors Bind in Highly Conserved Sites in Dengue Virus NS5 Polymerase: Structural and Functional Studies. J Virol 2020; 94:JVI.01130-20. [PMID: 32907977 DOI: 10.1128/jvi.01130-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/29/2020] [Indexed: 11/20/2022] Open
Abstract
Dengue virus (DENV) NS5 RNA-dependent RNA polymerase (RdRp), an important drug target, synthesizes viral RNA and is essential for viral replication. While a number of allosteric inhibitors have been reported for hepatitis C virus RdRp, few have been described for DENV RdRp. Following a diverse compound screening campaign and a rigorous hit-to-lead flowchart combining biochemical and biophysical approaches, two DENV RdRp nonnucleoside inhibitors were identified and characterized. These inhibitors show low- to high-micromolar inhibition in DENV RNA polymerization and cell-based assays. X-ray crystallography reveals that they bind in the enzyme RNA template tunnel. One compound (NITD-434) induced an allosteric pocket at the junction of the fingers and palm subdomains by displacing residue V603 in motif B. Binding of another compound (NITD-640) ordered the fingers loop preceding the F motif, close to the RNA template entrance. Most of the amino acid residues that interacted with these compounds are highly conserved in flaviviruses. Both sites are important for polymerase de novo initiation and elongation activities and essential for viral replication. This work provides evidence that the RNA tunnel in DENV RdRp offers interesting target sites for inhibition.IMPORTANCE Dengue virus (DENV), an important arthropod-transmitted human pathogen that causes a spectrum of diseases, has spread dramatically worldwide in recent years. Despite extensive efforts, the only commercial vaccine does not provide adequate protection to naive individuals. DENV NS5 polymerase is a promising drug target, as exemplified by the development of successful commercial drugs against hepatitis C virus (HCV) polymerase and HIV-1 reverse transcriptase. High-throughput screening of compound libraries against this enzyme enabled the discovery of inhibitors that induced binding sites in the RNA template channel. Characterizations by biochemical, biophysical, and reverse genetics approaches provide a better understanding of the biological relevance of these allosteric sites and the way forward to design more-potent inhibitors.
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40
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Non-nucleoside Inhibitors of Zika Virus RNA-Dependent RNA Polymerase. J Virol 2020; 94:JVI.00794-20. [PMID: 32796069 DOI: 10.1128/jvi.00794-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/02/2020] [Indexed: 02/08/2023] Open
Abstract
Zika virus (ZIKV) remains a potentially significant public health concern because it can cause teratogenic effects, such as microcephaly in newborns and neurological disease, like Guillain-Barré syndrome. Together with efforts to develop a vaccine, the discovery of antiviral molecules is important to control ZIKV infections and to prevent its most severe symptoms. Here, we report the development of small nonnucleoside inhibitors (NNIs) of ZIKV RNA-dependent RNA polymerase (RdRp) activity. These NNIs target an allosteric pocket (N pocket) located next to a putative hinge region between the thumb and the palm subdomains that was originally described for dengue virus (DENV) RdRp. We first tested the activity of DENV RdRp N-pocket inhibitors against ZIKV RdRp, introduced chemical modifications into these molecules, and assessed their potency using both enzymatic and cell-based assays. The most potent compound had a 50% inhibitory concentration value of 7.3 μM and inhibited ZIKV replication in a cell-based assay with a 50% effective concentration value of 24.3 μM. Importantly, we report four high-resolution crystal structures detailing how these NNIs insert into the N pocket of ZIKV RdRp. Our observations point to subtle differences in the size, shape, chemical environment, and hydration of the N pocket from ZIKV RdRp from those of the N pocket from DENV RdRp that are crucial for the design of improved antiviral inhibitors with activity against ZIKV.IMPORTANCE Zika virus belongs to the Flavivirus genus, which comprises several important human pathogens. There is currently neither an approved vaccine nor antiviral drugs available to prevent infection by ZIKV. The nonstructural protein 5 (NS5) polymerase, which is responsible for replicating the viral RNA genome, represents one of the most promising targets for antiviral drug development. Starting from compounds recently developed against dengue virus NS5, we designed and synthesized inhibitors targeting Zika virus NS5. We show that these novel compounds inhibit viral replication by targeting the polymerase activity. High-resolution X-ray crystallographic structures of protein-inhibitor complexes demonstrated specific binding to an allosteric site within the polymerase, called the N pocket. This work paves the way for the future structure-based design of potent compounds specifically targeting ZIKV RNA polymerase activity.
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41
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Coggins SA, Mahboubi B, Schinazi RF, Kim B. Mechanistic cross-talk between DNA/RNA polymerase enzyme kinetics and nucleotide substrate availability in cells: Implications for polymerase inhibitor discovery. J Biol Chem 2020; 295:13432-13443. [PMID: 32737197 PMCID: PMC7521635 DOI: 10.1074/jbc.rev120.013746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/31/2020] [Indexed: 01/01/2023] Open
Abstract
Enzyme kinetic analysis reveals a dynamic relationship between enzymes and their substrates. Overall enzyme activity can be controlled by both protein expression and various cellular regulatory systems. Interestingly, the availability and concentrations of intracellular substrates can constantly change, depending on conditions and cell types. Here, we review previously reported enzyme kinetic parameters of cellular and viral DNA and RNA polymerases with respect to cellular levels of their nucleotide substrates. This broad perspective exposes a remarkable co-evolution scenario of DNA polymerase enzyme kinetics with dNTP levels that can vastly change, depending on cell proliferation profiles. Similarly, RNA polymerases display much higher Km values than DNA polymerases, possibly due to millimolar range rNTP concentrations found in cells (compared with micromolar range dNTP levels). Polymerases are commonly targeted by nucleotide analog inhibitors for the treatments of various human diseases, such as cancers and viral pathogens. Because these inhibitors compete against natural cellular nucleotides, the efficacy of each inhibitor can be affected by varying cellular nucleotide levels in their target cells. Overall, both kinetic discrepancy between DNA and RNA polymerases and cellular concentration discrepancy between dNTPs and rNTPs present pharmacological and mechanistic considerations for therapeutic discovery.
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Affiliation(s)
- Si'Ana A Coggins
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Bijan Mahboubi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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42
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Tunghirun C, Narkthong V, Chaicumpa W, Chimnaronk S. Interference of dengue replication by blocking the access of 3' SL RNA to the viral RNA-dependent RNA polymerase. Antiviral Res 2020; 182:104921. [PMID: 32835694 DOI: 10.1016/j.antiviral.2020.104921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/25/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023]
Abstract
The four circulating serotypes of dengue virus (DENV) occasionally cause potentially fetal symptoms of severe dengue, which there is currently no specific treatment available. Extensive efforts have been made to inhibit viral replication processes by impeding the activity of an exclusive RNA-dependent RNA polymerase (RdRp) in the viral non-structural protein 5 (NS5). In our earlier work, we identified the characteristic, specific interaction between the C-terminal thumb subdomain of RdRp and an apical loop in the 3' stem-loop (SL) element in the DENV RNA genome, which is fundamental for viral replication. Here, we demonstrated a new approach for interfering viral replication via blocking of 3' SL RNA binding to RdRp by the single-chain variable fragments (scFvs). We isolated and cloned 3 different human scFvs that bound to RdRp from DENV serotype 2 and interfered with 3' SL-binding, utilizing a combination of phage-display panning and Alpha methods. When tagged with a cell penetrating peptide, a selected scFv clone, 2E3, entered cells and partially colocalized with NS5 in the cytoplasm of infected HuH-7 cells. 2E3 significantly inhibited DENV RNA replication with sub-nanomolar EC50 values and significantly reduced the production of infectious particles. The molecular docking models suggested that 2E3 recognized both palm and thumb subdomains of RdRp, and interacted with Lys841, a key residue involved in RNA binding. Our results provide a new potential therapeutic molecule specific for flaviviral infection.
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Affiliation(s)
- Chairat Tunghirun
- The Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand
| | - Veerakorn Narkthong
- Siriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Sarin Chimnaronk
- The Laboratory of RNA Biology, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakhon Pathom, 73170, Thailand; Siriraj Center of Research Excellence for Systems Pharmacology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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43
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Pagadala NS, Bhat R, Kumar D J, Landi A. Discovery of anti-influenza nucleoside triphosphates targeting the catalytic site of A/PR/8/34/H1N1 polymerase. Med Chem Res 2020; 29:1463-1477. [PMID: 32837136 PMCID: PMC7246003 DOI: 10.1007/s00044-020-02561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/12/2020] [Indexed: 11/28/2022]
Abstract
In an effort to develop potent anti-influenza drugs that inhibit the activity of influenza virus RNA-dependent RNA polymerase (IAV RdRp), a database of nucleoside triphosphates with ~800 molecules were docked with the homology model of IAV RdRp from A/PR/8/34/H1N1 strain. Out of top 12 molecules that bind with higher affinities to the catalytic site of IAV RdRp above and below the PB1 priming loop, only seven molecules decreased the transcriptional activity of the viral RNA polymerase with an IC50 in the range of 0.09–3.58 µM. Molecular docking combining with experimental study indicated that the molecules with linear chain are more effective in inhibiting IAV RdRp replication than the molecules with V-shaped and are cyclic in nature. A correlation between ΔG and LogIC50 for these seven compounds resulted an R2 value of 0.73. Overall, these newly developed seven nucleoside triphosphates lay a strong foundation for the future development of a new therapeutics that can satisfy the Lipinski’s rule of five exhibiting high specificity to the catalytic site of influenza-A viruses.
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Affiliation(s)
- Nataraj Sekhar Pagadala
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
| | - Rakesh Bhat
- Precision Bio Laboratories, Edmonton, AB Canada
| | - Jagadeesh Kumar D
- Department of Biotechnology, Sir M. Visvesvaraya Institute of Technology, Bangalore, India
| | - Abdolamir Landi
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1 Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB Canada
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44
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Ahmad M, Dwivedy A, Mariadasse R, Tiwari S, Kar D, Jeyakanthan J, Biswal BK. Prediction of Small Molecule Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus-2 RNA-dependent RNA Polymerase. ACS OMEGA 2020; 5:18356-18366. [PMID: 32743211 PMCID: PMC7391942 DOI: 10.1021/acsomega.0c02096] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 05/08/2023]
Abstract
The current COVID-19 outbreak warrants the design and development of novel anti-COVID therapeutics. Using a combination of bioinformatics and computational tools, we modelled the 3D structure of the RdRp (RNA-dependent RNA polymerase) of SARS-CoV2 (severe acute respiratory syndrome coronavirus-2) and predicted its probable GTP binding pocket in the active site. GTP is crucial for the formation of the initiation complex during RNA replication. This site was computationally targeted using a number of small molecule inhibitors of the hepatitis C RNA polymerase reported previously. Further optimizations suggested a lead molecule that may prove fruitful in the development of potent inhibitors against the RdRp of SARS-CoV2.
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Affiliation(s)
- Mohammed Ahmad
- National
Institute of Immunology, New Delhi 110067, India
| | | | - Richard Mariadasse
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
| | - Satish Tiwari
- National
Institute of Immunology, New Delhi 110067, India
| | - Deepsikha Kar
- National
Institute of Immunology, New Delhi 110067, India
| | - Jeyaraman Jeyakanthan
- Department
of Bioinformatics, Alagappa University, karaikudi 630004, Tamil Nadu, India
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45
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Wang Y, Anirudhan V, Du R, Cui Q, Rong L. RNA-dependent RNA polymerase of SARS-CoV-2 as a therapeutic target. J Med Virol 2020; 93:300-310. [PMID: 32633831 DOI: 10.1002/jmv.26264] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/23/2022]
Abstract
The global pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), named coronavirus disease 2019, has infected more than 8.9 million people worldwide. This calls for urgent effective therapeutic measures. RNA-dependent RNA polymerase (RdRp) activity in viral transcription and replication has been recognized as an attractive target to design novel antiviral strategies. Although SARS-CoV-2 shares less genetic similarity with SARS-CoV (~79%) and Middle East respiratory syndrome coronavirus (~50%), the respective RdRps of the three coronaviruses are highly conserved, suggesting that RdRp is a good broad-spectrum antiviral target for coronaviruses. In this review, we discuss the antiviral potential of RdRp inhibitors (mainly nucleoside analogs) with an aim to provide a comprehensive account of drug discovery on SARS-CoV-2.
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Affiliation(s)
- Yanyan Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Varada Anirudhan
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois
| | - Ruikun Du
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Collaborative Innovation Center for Antiviral Traditional Chinese Medicine, Jinan, China.,Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
| | - Qinghua Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China.,Shandong Provincial Collaborative Innovation Center for Antiviral Traditional Chinese Medicine, Jinan, China.,Qingdao Academy of Chinese Medicinal Sciences, Shandong University of Traditional Chinese Medicine, Qingdao, China
| | - Lijun Rong
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois
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46
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Aftab SO, Ghouri MZ, Masood MU, Haider Z, Khan Z, Ahmad A, Munawar N. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. J Transl Med 2020; 18:275. [PMID: 32635935 PMCID: PMC7339606 DOI: 10.1186/s12967-020-02439-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/25/2020] [Indexed: 02/13/2023] Open
Abstract
Background The Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) outbreak originating in Wuhan, China, has raised global health concerns and the pandemic has now been reported on all inhabited continents. Hitherto, no antiviral drug is available to combat this viral outbreak. Methods Keeping in mind the urgency of the situation, the current study was designed to devise new strategies for drug discovery and/or repositioning against SARS-CoV-2. In the current study, RNA-dependent RNA polymerase (RdRp), which regulates viral replication, is proposed as a potential therapeutic target to inhibit viral infection. Results Evolutionary studies of whole-genome sequences of SARS-CoV-2 represent high similarity (> 90%) with other SARS viruses. Targeting the RdRp active sites, ASP760 and ASP761, by antiviral drugs could be a potential therapeutic option for inhibition of coronavirus RdRp, and thus viral replication. Target-based virtual screening and molecular docking results show that the antiviral Galidesivir and its structurally similar compounds have shown promise against SARS-CoV-2. Conclusions The anti-polymerase drugs predicted here—CID123624208 and CID11687749—may be considered for in vitro and in vivo clinical trials.
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Affiliation(s)
- Syed Ovais Aftab
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan.,Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zubair Ghouri
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan. .,Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Umer Masood
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Zeshan Haider
- Center of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Aftab Ahmad
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan. .,Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan.
| | - Nayla Munawar
- Department of Chemistry, United Arab Emirates University, Al-Ain, UAE
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47
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Aftab SO, Ghouri MZ, Masood MU, Haider Z, Khan Z, Ahmad A, Munawar N. Analysis of SARS-CoV-2 RNA-dependent RNA polymerase as a potential therapeutic drug target using a computational approach. J Transl Med 2020. [DOI: https://doi.org/10.1186/s12967-020-02439-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Zhang WF, Stephen P, Thériault JF, Wang R, Lin SX. Novel Coronavirus Polymerase and Nucleotidyl-Transferase Structures: Potential to Target New Outbreaks. J Phys Chem Lett 2020; 11:4430-4435. [PMID: 32392072 PMCID: PMC7243427 DOI: 10.1021/acs.jpclett.0c00571] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/11/2020] [Indexed: 05/30/2023]
Abstract
The pandemic outbreak of a new coronavirus (CoV), SARS-CoV-2, has captured the world's attention, demonstrating that CoVs represent a continuous global threat. As this is a highly contagious virus, it is imperative to understand RNA-dependent-RNA-polymerase (RdRp), the key component in virus replication. Although the SARS-CoV-2 genome shares 80% sequence identity with severe acute respiratory syndrome SARS-CoV, their RdRps and nucleotidyl-transferases (NiRAN) share 98.1% and 93.2% identity, respectively. Sequence alignment of six coronaviruses demonstrated higher identity among their RdRps (60.9%-98.1%) and lower identity among their Spike proteins (27%-77%). Thus, a 3D structural model of RdRp, NiRAN, non-structural protein 7 (nsp7), and nsp8 of SARS-CoV-2 was generated by modeling starting from the SARS counterpart structures. Furthermore, we demonstrate the binding poses of three viral RdRp inhibitors (Galidesivir, Favipiravir, and Penciclovir), which were recently reported to have clinical significance for SARS-CoV-2. The network of interactions established by these drug molecules affirms their efficacy to inhibit viral RNA replication and provides an insight into their structure-based rational optimization for SARS-CoV-2 inhibition.
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Affiliation(s)
- Wen-Fa Zhang
- Axe Molecular Endocrinology and Nephrology,
CHU Research Center and Laval University, Québec City,
Québec G1 V 4G2, Canada
| | - Preyesh Stephen
- Axe Molecular Endocrinology and Nephrology,
CHU Research Center and Laval University, Québec City,
Québec G1 V 4G2, Canada
- Department of Biomedical and Molecular Sciences,
Queen’s University, Kingston, Ontario K7L 3N6,
Canada
| | - Jean-François Thériault
- Axe Molecular Endocrinology and Nephrology,
CHU Research Center and Laval University, Québec City,
Québec G1 V 4G2, Canada
| | - Ruixuan Wang
- Axe Molecular Endocrinology and Nephrology,
CHU Research Center and Laval University, Québec City,
Québec G1 V 4G2, Canada
| | - Sheng-Xiang Lin
- Axe Molecular Endocrinology and Nephrology,
CHU Research Center and Laval University, Québec City,
Québec G1 V 4G2, Canada
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49
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Seifert M, van Nies P, Papini FS, Arnold JJ, Poranen MM, Cameron CE, Depken M, Dulin D. Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases. Nucleic Acids Res 2020; 48:5591-5602. [PMID: 32286652 PMCID: PMC7261197 DOI: 10.1093/nar/gkaa233] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/30/2020] [Indexed: 01/05/2023] Open
Abstract
RNA virus survival depends on efficient viral genome replication, which is performed by the viral RNA dependent RNA polymerase (RdRp). The recent development of high throughput magnetic tweezers has enabled the simultaneous observation of dozens of viral RdRp elongation traces on kilobases long templates, and this has shown that RdRp nucleotide addition kinetics is stochastically interrupted by rare pauses of 1-1000 s duration, of which the short-lived ones (1-10 s) are the temporal signature of a low fidelity catalytic pathway. We present a simple and precise temperature controlled system for magnetic tweezers to characterize the replication kinetics temperature dependence between 25°C and 45°C of RdRps from three RNA viruses, i.e. the double-stranded RNA bacteriophage Φ6, and the positive-sense single-stranded RNA poliovirus (PV) and human rhinovirus C (HRV-C). We found that Φ6 RdRp is largely temperature insensitive, while PV and HRV-C RdRps replication kinetics are activated by temperature. Furthermore, the activation energies we measured for PV RdRp catalytic state corroborate previous estimations from ensemble pre-steady state kinetic studies, further confirming the catalytic origin of the short pauses and their link to temperature independent RdRp fidelity. This work will enable future temperature controlled study of biomolecular complex at the single molecule level.
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Affiliation(s)
- Mona Seifert
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Pauline van Nies
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Flávia S Papini
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Jamie J Arnold
- Department of Microbiology and Immunology, School of Medicine, The University of North Carolina Chapel Hill, 6012 Marsico Hall, CB 7290 Mason Farm Road, NC 27599, USA
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikki Biocenter 1, P.O. Box 56 (Viikinkaari 9), 00014 Helsinki, Finland
| | - Craig E Cameron
- Department of Microbiology and Immunology, School of Medicine, The University of North Carolina Chapel Hill, 6012 Marsico Hall, CB 7290 Mason Farm Road, NC 27599, USA
| | - Martin Depken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands,Correspondence may also be addressed to Martin Depken. Tel: +31 15 27 81305;
| | - David Dulin
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany,To whom correspondence should be addressed. Tel: +49 9131 85 70347; Fax: +49 9131 85 35903;
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50
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Abstract
Chronic hepatitis C virus (HCV) infection is a significant public health problem, with a worldwide prevalence of approximately 170 million. Current therapy for HCV infection includes the prolonged administration of a combination of ribavirin and PEGylated interferon-α, for over a decade. This regimen is expensive and often associated with a poor antiviral response and unwanted side effects. A highly effective combination treatment is likely required for the future management of HCV infections and entry inhibitors could play an important role. Currently, no entry inhibitor has been licensed for the prophylactic treatment of hepatitis C. Therefore, additional agents that combat HCV infection are urgently needed and must be developed. Many phytochemical constituents have been identified that display considerable inhibition of HCV at some stage of the life cycle. This review will summarise the current state of knowledge on natural products and their possible activities in the context of HCV infection.
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Affiliation(s)
| | - Abeer Temraz
- Pharmacognosy Department College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
- Pharmacognosy Department Faculty of Pharmacy For Girls, Al-Azhar University, Nasr City, Cairo, Egypt
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