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Nie Z, Zhai F, Zhang H, Zheng H, Pei J. The multiple roles of viral 3D pol protein in picornavirus infections. Virulence 2024; 15:2333562. [PMID: 38622757 PMCID: PMC11020597 DOI: 10.1080/21505594.2024.2333562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
The Picornaviridae are a large group of positive-sense, single-stranded RNA viruses, and most research has focused on the Enterovirus genus, given they present a severe health risk to humans. Other picornaviruses, such as foot-and-mouth disease virus (FMDV) and senecavirus A (SVA), affect agricultural production with high animal mortality to cause huge economic losses. The 3Dpol protein of picornaviruses is widely known to be used for genome replication; however, a growing number of studies have demonstrated its non-polymerase roles, including modulation of host cell biological processes, viral replication complex assembly and localization, autophagy, and innate immune responses. Currently, there is no effective vaccine to control picornavirus diseases widely, and clinical therapeutic strategies have limited efficiency in combating infections. Many efforts have been made to develop different types of drugs to prohibit virus survival; the most important target for drug development is the virus polymerase, a necessary element for virus replication. For picornaviruses, there are also active efforts in targeted 3Dpol drug development. This paper reviews the interaction of 3Dpol proteins with the host and the progress of drug development targeting 3Dpol.
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Affiliation(s)
- Zhenyu Nie
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
| | - Fengge Zhai
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Han Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jingjing Pei
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
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Kuzikov M, Reinshagen J, Wycisk K, Corona A, Esposito F, Malune P, Manelfi C, Iaconis D, Beccari A, Tramontano E, Nowotny M, Windshügel B, Gribbon P, Zaliani A. Drug repurposing screen to identify inhibitors of the RNA polymerase (nsp12) and helicase (nsp13) from SARS-CoV-2 replication and transcription complex. Virus Res 2024; 343:199356. [PMID: 38490582 PMCID: PMC10958470 DOI: 10.1016/j.virusres.2024.199356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Coronaviruses contain one of the largest genomes among the RNA viruses, coding for 14-16 non-structural proteins (nsp) that are involved in proteolytic processing, genome replication and transcription, and four structural proteins that build the core of the mature virion. Due to conservation across coronaviruses, nsps form a group of promising drug targets as their inhibition directly affects viral replication and, therefore, progression of infection. A minimal but fully functional replication and transcription complex was shown to be formed by one RNA-dependent RNA polymerase (nsp12), one nsp7, two nsp8 accessory subunits, and two helicase (nsp13) enzymes. Our approach involved, targeting nsp12 and nsp13 to allow multiple starting point to interfere with virus infection progression. Here we report a combined in-vitro repurposing screening approach, identifying new and confirming reported SARS-CoV-2 nsp12 and nsp13 inhibitors.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany.
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Krzysztof Wycisk
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Paolo Malune
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Daniela Iaconis
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Andrea Beccari
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Marcin Nowotny
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
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Poudel B, Mullins J, Fiedler JD, Zhong S. Genome-Wide Association Study of Fungicide Sensitivity in a Fusarium graminearum Population Collected from North Dakota. Phytopathology 2024:PHYTO05230180KC. [PMID: 38079375 DOI: 10.1094/phyto-05-23-0180-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Fusarium head blight is a destructive disease of small grains. The disease is predominantly caused by the haploid ascomycete fungus Fusarium graminearum in North America. To understand the genetics of quantitative traits for sensitivity to fungicides in this fungal pathogen, we conducted a genome-wide association study of sensitivity to two demethylation inhibition class fungicides, tebuconazole and prothioconazole, using an F. graminearum population of 183 isolates collected between 1981 and 2013 from North Dakota. Baseline sensitivity to tebuconazole and prothioconazole was established using 21 isolates collected between 1981 and 1994. Most fungal isolates were sensitive to both tebuconazole and prothioconazole; however, five isolates showed significantly reduced sensitivity to prothioconazole. The genome-wide association study identified one significant marker-trait association on chromosome 3 for tebuconazole resistance, whereas six significant marker-trait associations, one on chromosome 1, three on chromosome 2, and two on chromosome 4, were detected for prothioconazole resistance. Functional annotation of the marker-trait association for tebuconazole revealed a candidate gene encoding a basic helix-loop-helix domain-containing protein that reinforces sterol in the fungal membrane. Putative genes for prothioconazole resistance were also identified, which are involved in RNA interference, the detoxification by ubiquitin-proteasome pathway, and membrane integrity reinforcement. Considering the potential of the pathogen toward overcoming chemical control, continued monitoring of fungal sensitivities to commercially applied fungicides, especially those containing prothioconazole, is warranted to reduce risks of fungicide resistance in the pathogen populations.
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Affiliation(s)
- Bikash Poudel
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Joseph Mullins
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Jason D Fiedler
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Fargo, ND 58102
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Zhao Y, Zhang X, Mu T, Wu X. Complete genome sequence of a novel partitivirus with a dsRNA3 segment, isolated from Fusarium commune strain CP-SX-3 causing strawberry root rot. Arch Virol 2024; 169:60. [PMID: 38430446 DOI: 10.1007/s00705-024-06004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/24/2024] [Indexed: 03/03/2024]
Abstract
A novel partitivirus, Fusarium commune partitivirus 1 (FcoPV1), was identified in Fusarium commune strain CP-SX-3 isolated from diseased roots of strawberry with symptoms of root rot. The complete genome of FcoPV1 comprises three double-stranded RNAs (dsRNAs): dsRNA1 (1,825 nt), dsRNA2 (1,592 nt), and dsRNA3 (1,421 nt). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), and dsRNA2 contains a single ORF (ORF2) encoding a coat protein (CP). dsRNA3 is a possible satellite RNA that does not appear to encode a known protein. BLASTp analysis revealed that RdRp (86.59%) and CP (74.13%) encoded by the two ORFs (ORF1 and ORF2) had the highest sequence similarity to their counterparts in Fusarium equiseti partitivirus 1 (FePV1). Phylogenetic analysis based on the complete amino acid sequence of RdRp suggested that FcoPV1 should be considered a member of a new species in the proposed genus "Zetapartitivirus" within the family Partitiviridae. To the best of our knowledge, this is the first report of a zetapartitivirus infecting phytopathogenic F. commune.
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Affiliation(s)
- Yumeng Zhao
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
- Liaoning Institute of Pomology, Yingkou City, Liaoning, 115009, People's Republic of China
| | - Xinyi Zhang
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Tongyu Mu
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
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Pastore B, Hertz HL, Tang W. Pre-piRNA trimming safeguards piRNAs against erroneous targeting by RNA-dependent RNA polymerase. Cell Rep 2024; 43:113692. [PMID: 38244197 PMCID: PMC10949418 DOI: 10.1016/j.celrep.2024.113692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
The Piwi/Piwi-interacting RNA (piRNA) pathway protects genome integrity in animal germ lines. Maturation of piRNAs involves nucleolytic processing at both 5' and 3' ends. The ribonuclease PARN-1 and its orthologs mediate piRNA 3' trimming in worms, insects, and mammals. However, the significance of this evolutionarily conserved processing step is not fully understood. Employing C. elegans as a model, we recently discovered that 3' trimming protects piRNAs against non-templated nucleotide additions and degradation. Here, we find that worms lacking PARN-1 accumulate an uncharacterized RNA species termed anti-piRNAs, which are antisense to piRNAs. Anti-piRNAs associate with Piwi proteins, are 17-19 nucleotides long, and begin with 5' guanine or adenine. Untrimmed pre-piRNAs are misdirected by the terminal nucleotidyltransferase RDE-3 and RNA-dependent RNA polymerase EGO-1, leading to the formation of anti-piRNAs. This work identifies a class of small RNAs in parn-1 mutants and provides insight into the activities of RDE-3, EGO-1, and Piwi proteins.
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Affiliation(s)
- Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Hannah L Hertz
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
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Kurosawa M, Kato F, Hishiki T, Ito S, Fujisawa H, Yamaguchi T, Moriguchi M, Hosokawa K, Watanabe T, Saito-Tarashima N, Minakawa N, Fujimuro M. Sofosbuvir Suppresses the Genome Replication of DENV1 in Human Hepatic Huh7 Cells. Int J Mol Sci 2024; 25:2022. [PMID: 38396699 PMCID: PMC10889370 DOI: 10.3390/ijms25042022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Dengue virus (DENV) causes dengue fever and dengue hemorrhagic fever, and DENV infection kills 20,000 people annually worldwide. Therefore, the development of anti-DENV drugs is urgently needed. Sofosbuvir (SOF) is an effective drug for HCV-related diseases, and its triphosphorylated metabolite inhibits viral RNA synthesis by the RNA-dependent RNA polymerase (RdRp) of HCV. (2'R)-2'-Deoxy-2'-fluoro-2'-methyluridine (FMeU) is the dephosphorylated metabolite produced from SOF. The effects of SOF and FMeU on DENV1 replication were analyzed using two DENV1 replicon-based methods that we previously established. First, a replicon-harboring cell assay showed that DENV1 replicon replication in human hepatic Huh7 cells was decreased by SOF but not by FMeU. Second, a transient replicon assay showed that DENV1 replicon replication in Huh7 cells was decreased by SOF; however, in hamster kidney BHK-21 cells, it was not suppressed by SOF. Additionally, the replicon replication in Huh7 and BHK-21 cells was not affected by FMeU. Moreover, we assessed the effects of SOF on infectious DENV1 production. SOF suppressed infectious DENV1 production in Huh7 cells but not in monkey kidney Vero cells. To examine the substrate recognition of the HCV and DENV1 RdRps, the complex conformation of SOF-containing DENV1 RdRp or HCV RdRp was predicted using AlphaFold 2. These results indicate that SOF may be used as a treatment for DENV1 infection.
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Affiliation(s)
- Madoka Kurosawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Fumihiro Kato
- Department of Virology III, National Institute of Infectious Diseases, Tokyo 208-0011, Japan;
| | - Takayuki Hishiki
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
| | - Saori Ito
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Hiroki Fujisawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Tatsuo Yamaguchi
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Misato Moriguchi
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Kohei Hosokawa
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
| | - Tadashi Watanabe
- Department of Virology, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan;
| | - Noriko Saito-Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima 770-8505, Japan; (N.S.-T.); (N.M.)
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Tokushima 770-8505, Japan; (N.S.-T.); (N.M.)
| | - Masahiro Fujimuro
- Department of Cell Biology, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan; (M.K.); (S.I.); (H.F.); (T.Y.); (M.M.); (K.H.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wang T, Zheng G, Chen Z, Wang Y, Zhao C, Li Y, Yuan Y, Duan H, Zhu H, Yang X, Li W, Du W, Li Y, Li D. Drug repurposing screens identify Tubercidin as a potent antiviral agent against porcine nidovirus infections. Virus Res 2024; 339:199275. [PMID: 38008220 PMCID: PMC10730850 DOI: 10.1016/j.virusres.2023.199275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/18/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
The emergence of new coronaviruses poses a significant threat to animal husbandry and human health. Porcine epidemic diarrhea virus (PEDV) is considered a re-emerging porcine enteric coronavirus, which causes fatal watery diarrhea in piglets. Currently, there are no effective drugs to combat PEDV. Drug repurposing screens have emerged as an attractive strategy to accelerate antiviral drug discovery and development. Here, we screened 206 natural products for antiviral activity using live PEDV infection in Vero cells and identified ten candidate antiviral agents. Among them, Tubercidin, a nucleoside analog derived from Streptomyces tubercidicus, showed promising antiviral activity against PEDV infection. Furthermore, we demonstrated that Tubercidin exhibited significant antiviral activity against both classical and variant PEDV. Time of addition assay showed that Tubercidin displayed a significant inhibitory effect on viral post-entry events but not during other periods. Molecular docking analysis indicated that Tubercidin had better docking efficiency and formed hydrophobic interactions with the active pocket of RNA-dependent RNA polymerase (RdRp) of PEDV and other nidoviruses. Additionally, Tubercidin can effectively suppress other porcine nidoviruses, such as SADS-CoV and PRRSV, demonstrating its broad-spectrum antiviral properties. In summary, our findings provide valuable evidence for the antiviral activity of Tubercidin and offer insights into the development of new strategies for the prevention and treatment of coronavirus infections.
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Affiliation(s)
- Tianliang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Guanmin Zheng
- School of Medicine, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Zilu Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yue Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Chenxu Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yaqin Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yixin Yuan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Hong Duan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China
| | - Hongsen Zhu
- School of Medicine, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China
| | - Wentao Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wenjuan Du
- Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CL, the Netherlands
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China.
| | - Dongliang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Agricultural University, Zhengzhou, Henan 450046, China.
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Shen L, Zhang Z, Wang R, Wu S, Wang Y, Fu S. Metatranscriptomic data mining together with microfluidic card uncovered the potential pathogens and seasonal RNA viral ecology in a drinking water source. J Appl Microbiol 2024; 135:lxad310. [PMID: 38130237 DOI: 10.1093/jambio/lxad310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
AIMS Despite metatranscriptomics becoming an emerging tool for pathogen surveillance, very little is known about the feasibility of this approach for understanding the fate of human-derived pathogens in drinking water sources. METHODS AND RESULTS We conducted multiplexed microfluidic cards and metatranscriptomic sequencing of the drinking water source in a border city of North Korea in four seasons. Microfluidic card detected norovirus, hepatitis B virus (HBV), enterovirus, and Vibrio cholerae in the water. Phylogenetic analyses showed that environmental-derived sequences from norovirus GII.17, genotype C of HBV, and coxsackievirus A6 (CA6) were genetically related to the local clinical isolates. Meanwhile, metatranscriptomic assembly suggested that several bacterial pathogens, including Acinetobacter johnsonii and V. cholerae might be prevalent in the studied region. Metatranscriptomic analysis recovered 349 species-level groups with substantial viral diversity without detection of norovirus, HBV, and CA6. Seasonally distinct virus communities were also found. Specifically, 126, 73, 126, and 457 types of viruses were identified in spring, summer, autumn, and winter, respectively. The viromes were dominated by the Pisuviricota phylum, including members from Marnaviridae, Dicistroviridae, Luteoviridae, Potyviridae, Picornaviridae, Astroviridae, and Picobirnaviridae families. Further phylogenetic analyses of RNA (Ribonucleic Acid)-dependent RNA polymerase (RdRp) sequences showed a diverse set of picorna-like viruses associated with shellfish, of which several novel picorna-like viruses were also identified. Additionally, potential animal pathogens, including infectious bronchitis virus, Bat dicibavirus, Bat nodavirus, Bat picornavirus 2, infectious bursal disease virus, and Macrobrachium rosenbergii nodavirus were also identified. CONCLUSIONS Our data illustrate the divergence between microfluidic cards and metatranscriptomics, highlighting that the combination of both methods facilitates the source tracking of human viruses in challenging settings without sufficient clinical surveillance.
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Affiliation(s)
- Lixin Shen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ziqiang Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Rui Wang
- College of Marine Science and Environment, Dalian Ocean University, Dalian 116023, China
| | - Shuang Wu
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yongjie Wang
- College of Food Technology and Sciences, Shanghai Ocean University, Shanghai 200093, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai 200093, China
| | - Songzhe Fu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Department of Microbiology, College of Life Sciences, Northwest University, Xi'an 710069, China
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11
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Zhang Y, Chai M, Cheng X, Xu K. Transiently Induce RNA Silencing in Plants Using a Tobacco Necrosis Virus A (TNV-A)-Based dsRNA Production System. Methods Mol Biol 2024; 2771:83-89. [PMID: 38285394 DOI: 10.1007/978-1-0716-3702-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Transgenic expression of hairpin RNA or artificial microRNA is widely used for genetic studies in plant science. However, induction of RNA silencing by transgenic method may have a problem when studying essential genes. Here, we provide an in planta transient double-stranded RNA (dsRNA) producing system using a tobacco necrosis virus A (TNV-A)-based replicon for efficiently inducing RNA silencing in plants. In this system, the target sequence is placed between the cauliflower mosaic virus 35S promoter and the 3'-terminal part of viral genomic RNA, while the C-terminal part of TNV-A RNA-dependent RNA polymerase (p82C) is expressed by a different promoter. The endogenous RNA polymerase-synthesized target sequence is recruited by p82C to produce dsRNA to induce RNA silencing.
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Affiliation(s)
- Yuanming Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Mengzhu Chai
- College of Plant Protection/Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaofei Cheng
- College of Plant Protection/Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Kai Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Microbiology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
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12
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Cox RM, Plemper RK. Design and Execution of In Vitro Polymerase Assays for Measles Virus and Related Mononegaviruses. Methods Mol Biol 2024; 2808:19-33. [PMID: 38743360 DOI: 10.1007/978-1-0716-3870-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Morbilliviruses such as measles virus (MeV) are responsible for major morbidity and mortality worldwide, despite the availability of an effective vaccine and global vaccination campaigns. MeV belongs to the mononegavirus order of viral pathogens that store their genetic information in non-segmented negative polarity RNA genomes. Genome replication and viral gene expression are carried out by a virus-encoded RNA-dependent RNA polymerase (RdRP) complex that has no immediate host cell analog. To better understand the organization and regulation of the viral RdRP and mechanistically characterize antiviral candidates, biochemical RdRP assays have been developed that employ purified recombinant polymerase complexes and synthetic RNA templates to monitor the initiation of RNA synthesis and RNA elongation in vitro. In this article, we will discuss strategies for the efficient expression and preparation of mononegavirus polymerase complexes, provide detailed protocols for the execution and optimization of RdRP assays, evaluate alternative options for the choice of template and detection system, and describe the application of the assay for the characterization of inhibitor candidates. Although MeV RdRP assays are the focus of this article, the general strategies and experimental approaches are readily transferable to related viruses in the mononegavirus order.
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Affiliation(s)
- Robert M Cox
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Richard K Plemper
- Center for Translational Antiviral Research, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA.
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13
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Samir A, Elshemey W, Elfiky A. Can de-phosphorylation of serine-5 in the C-terminal domain of human polymerase II affect its interaction with the PA C-terminal domain of bat Flu A polymerase? J Biomol Struct Dyn 2024; 42:1-10. [PMID: 36455997 DOI: 10.1080/07391102.2022.2152872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Influenza viruses depend on the host transcription machinery to create their new progeny viral mRNA. They need the host transcription machinery to hijack the 5'-capped RNA from the host RNAs in order to utilize them to activate their viral transcription. In this study, we computationally regenerated the interaction between 3 heptad repeats, phosphorylated at the fifth serine residue in each repeat, from human polymerase and the CT D of the PA subunit of viral RNA polymerase (Holo 3SEP). We also studied the effect of the de-phosphorylation of the Serine-5 in the middle heptad repeat on the stability of the interaction (Holo 2SEP). The dynamics of the protein association and the heptad repeat in both cases are studied using appropriate in silico tools. This is followed by applying the MM-GBSA method based on relative binding estimation to show the effect of the de-phosphorylation of the middle Serine-5. Results indicate a clear change in total relative binding energy in Holo 2SEP, compared to Holo 3SEP, with no shift in occupied amino acids involved in the interaction in both cases. Knowing that de-phosphorylation of one serine-5 has no significant contribution to the investigated interactions opens the door for further studies to understand the role of the middle heptad serine-5 in these interactions, as its dephosphorylation caused a decrease by ≈13% in the binding affinity values obtained using MM-GBSA. The current in silico study represents a one-step-ahead insight into the RNA-dependent RNA polymerase (RdRP) mechanism that is yet to be verified in the lab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ahmed Samir
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Wael Elshemey
- Department of Physics, Faculty of Science, Islamic University of Madinah, Madinah, Saudi Arabia
| | - Abdo Elfiky
- Biophysics Department, Faculty of Sciences, Cairo University, Giza, Egypt
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14
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Yang L, Zeng XT, Luo RH, Ren SX, Liang LL, Huang QX, Tang Y, Fan H, Ren HY, Zhang WJ, Zheng YT, Cheng W. SARS-CoV-2 NSP12 utilizes various host splicing factors for replication and splicing regulation. J Med Virol 2024; 96:e29396. [PMID: 38235848 DOI: 10.1002/jmv.29396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/19/2023] [Accepted: 01/01/2024] [Indexed: 01/19/2024]
Abstract
The RNA-dependent RNA polymerase (RdRp) is a crucial element in the replication and transcription of RNA viruses. Although the RdRps of lethal human coronaviruses severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) have been extensively studied, the molecular mechanism of the catalytic subunit NSP12, which is involved in pathogenesis, remains unclear. In this study, the biochemical and cell biological results demonstrate the interactions between SARS-CoV-2 NSP12 and seven host proteins, including three splicing factors (SLU7, PPIL3, and AKAP8). The entry efficacy of SARS-CoV-2 considerably decreased when SLU7 or PPIL3 was knocked out, indicating that abnormal splicing of the host genome was responsible for this occurrence. Furthermore, the polymerase activity and stability of SARS-CoV-2 RdRp were affected by the three splicing factors to varying degrees. In addition, NSP12 and its homologues from SARS-CoV and MERS-CoV suppressed the alternative splicing of cellular genes, which were influenced by the three splicing factors. Overall, our research illustrates that SARS-CoV-2 NSP12 can engage with various splicing factors, thereby impacting virus entry, replication, and gene splicing. This not only improves our understanding of how viruses cause diseases but also lays the foundation for the development of antiviral therapies.
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Affiliation(s)
- Li Yang
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xiao-Tao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Rong-Hua Luo
- Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Si-Xue Ren
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Lin-Lin Liang
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Qiu-Xia Huang
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Ying Tang
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Hong Fan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Hai-Yan Ren
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wan-Jiang Zhang
- Department of Pathophysiology, Shihezi University School of Medicine, the Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Shihezi, Xinjiang, China
| | - Yong-Tang Zheng
- Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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15
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Brunel J, Urzua É, Gerlier D, Bloyet LM. A Semiquantitative Protein-Fragment Complementation Assay to Study Protein-Protein Interactions of the Polymerase Complex in Cellula. Methods Mol Biol 2024; 2808:9-17. [PMID: 38743359 DOI: 10.1007/978-1-0716-3870-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Protein-fragment complementation assays (PCAs) are powerful tools to investigate protein-protein interactions in a cellular context. These are especially useful to study unstable proteins and weak interactions that may not resist protein isolation or purification. The PCA based on the reconstitution of the Gaussia princeps luciferase (split-luc) is a sensitive approach allowing the mapping of protein-protein interactions and the semiquantitative measurement of binding affinity. Here, we describe the split-luc protocol we used to map the viral interactome of measles virus polymerase complex.
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Affiliation(s)
- Joanna Brunel
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS UMR5308, Université Claude Bernard Lyon1, ENS Lyon, Lyon, France
| | - Érica Urzua
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS UMR5308, Université Claude Bernard Lyon1, ENS Lyon, Lyon, France
| | - Denis Gerlier
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS UMR5308, Université Claude Bernard Lyon1, ENS Lyon, Lyon, France
| | - Louis-Marie Bloyet
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS UMR5308, Université Claude Bernard Lyon1, ENS Lyon, Lyon, France.
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16
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Liu Y, Gao Y, Cheng X, Bai Y. Production of Double-Stranded RNA in Planta by a Potato Mop-Top Virus (PMTV)-Based Vector for Inducing Gene Silencing. Methods Mol Biol 2024; 2771:119-126. [PMID: 38285398 DOI: 10.1007/978-1-0716-3702-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
RNA silencing (also known as gene silencing) is an evolutionary conserved mechanism that is involved in regulating gene expression, suppressing mobile elements, and defensing virus infection. RNA silencing is triggered by double-stranded RNA via Dicer or Dicer-like riboendonucleases. DsRNAs are also the replication intermediates of all RNA viruses; as a result, plant RNA viruses are ideal candidates to induce RNA silencing. A large body of plant viruses have been modified into vectors for RNA silencing in varied plant species. Here, we described a simple, time-saving, and operable system for gene function and genetic breeding study of potato and Nicotiana benthamiana using a potato mop-top (MPTV)-based vector.
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Affiliation(s)
- Ye Liu
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China
- Potato Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yanlin Gao
- Potato Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Xiaofei Cheng
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China.
| | - Yanju Bai
- Potato Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
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17
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Arisaka F. Isolation and grouping of RNA phages by Itaru Watanabe et al. (1967). Proc Jpn Acad Ser B Phys Biol Sci 2024; 100:253-263. [PMID: 38599846 DOI: 10.2183/pjab.100.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
I. Watanabe et al. isolated approximately 30 strains of RNA phages from various parts of Japan. To isolate RNA phages, they assessed the infection specificity of male Escherichia coli and RNase sensitivity. They found that the isolated strains of RNA phages could be serologically separated into three groups. Furthermore, most of them were serologically related, and the antiphage rabbit serum prepared by one of these phages neutralized most of the other phages. The only serologically unrelated phage was the RNA phage Qβ, which was isolated at the Institute for Virus Research, Kyoto University, in 1961.
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18
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Reuscher CM, Barth S, Gockel F, Netsch A, Seitz K, Rümenapf T, Lamp B. Processing of the 3C/D Region of the Deformed Wing Virus (DWV). Viruses 2023; 15:2344. [PMID: 38140585 PMCID: PMC10748302 DOI: 10.3390/v15122344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
The deformed wing virus (DWV) belongs to the genus Iflavirus and the family Iflaviridae within the order Picornavirales. It is an important pathogen of the Western honey bee, Apis mellifera, causing major losses among honey bee colonies in association with the ectoparasitic mite Varroa destructor. Although DWV is one of the best-studied insect viruses, the mechanisms of viral replication and polyprotein processing have been poorly studied in the past. We investigated the processing of the protease-polymerase region at the C-terminus of the polyprotein in more detail using recombinant expression, novel serological reagents, and virus clone mutagenesis. Edman degradation of purified maturated polypeptides uncovered the C- and N-termini of the mature 3C-like (3CL) protease and RNA-dependent RNA polymerase (3DL, RdRp), respectively. Autocatalytic processing of the recombinant DWV 3CL protease occurred at P1 Q2118 and P1' G2119 (KPQ/GST) as well as P1 Q2393 and P1' S2394 (HAQ/SPS) cleavage sites. New monoclonal antibodies (Mab) detected the mature 3CL protease with an apparent molecular mass of 32 kDa, mature 3DL with an apparent molecular mass of 55 kDa as well as a dominant 3CDL precursor of 90 kDa in DWV infected honey bee pupae. The observed pattern corresponds well to data obtained via recombinant expression and N-terminal sequencing. Finally, we were able to show that 3CL protease activity and availability of the specific protease cleavage sites are essential for viral replication, protein synthesis, and establishment of infection using our molecular clone of DWV-A.
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Affiliation(s)
- Carina Maria Reuscher
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany
| | - Sandra Barth
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany
| | - Fiona Gockel
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany
- Institute of Medical Virology, Justus Liebig University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany
| | - Anette Netsch
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany
| | - Kerstin Seitz
- Department for Pathobiology, Institute of Virology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Till Rümenapf
- Department for Pathobiology, Institute of Virology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Benjamin Lamp
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Biomedical Research Center (BFS), Schubertstrasse 81, 35392 Giessen, Germany
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20
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Jiang Y, Liu X, Tian X, Zhou J, Wang Q, Wang B, Yu W, Jiang Y, Hsiang T, Qi X. RNA interference of Aspergillus flavus in response to Aspergillus flavus partitivirus 1 infection. Front Microbiol 2023; 14:1252294. [PMID: 38033556 PMCID: PMC10682719 DOI: 10.3389/fmicb.2023.1252294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/19/2023] [Indexed: 12/02/2023] Open
Abstract
RNA interference (RNAi) is one of the important defense responses against viral infection, but its mechanism and impact remain unclear in mycovirus infections. In our study, reverse genetics and virus-derived small RNA sequencing were used to show the antiviral responses of RNAi components in Aspergillus flavus infected with Aspergillus flavus partitivirus 1 (AfPV1). qRT-PCR revealed that AfPV1 infection induced the expression of the RNAi components in A. flavus compared with noninfected A. flavus. Knock mutants of each RNAi component were generated, but the mutants did not exhibit any obvious phenotypic changes compared with the A. flavus parental strain. However, after AfPV1 inoculation, production of AfPV1 was significantly less than in the parental strain. Furthermore, sporulation was greater in each AfPV1-infected mutant compared with the AfPV1-infected parental A. flavus. We also investigated the sensitivity of virus-free and AfPV1-infected RNAi mutants and the parental strain to cell wall stress, osmotic stress, genotoxic stress, and oxidative stress. The mutants of DCLs and AGOs infected by AfPV1 displayed more changes than RDRP mutants in response to the first three stresses. Small RNA sequencing analysis suggested that AfPV1 infection reduced the number of unique reads of sRNA in A. flavus, although there were many vsiRNA derived from the AfPV1 genome. GO term and KEGG pathway analyses revealed that the functions of sRNA affected by AfPV1 infection were closely related to vacuole production. These results provide a better understanding of the functional role of RNAi in the impact of AfPV1 on the hypovirulence of A. flavus.
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Affiliation(s)
- Yinhui Jiang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Xiang Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Xun Tian
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Jianhong Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Bi Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yanping Jiang
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology of Guizhou Province, Guizhou Medical University, Guiyang, China
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Edgar R. Known phyla dominate the Tara Oceans RNA virome. Virus Evol 2023; 9:vead063. [PMID: 38028147 PMCID: PMC10649353 DOI: 10.1093/ve/vead063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/03/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
A recent study proposed five new RNA virus phyla, two of which, 'Taraviricota' and 'Arctiviricota', were stated to be 'dominant in the oceans'. However, the study's assignments classify 28,353 putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five proposed new phyla combined. I re-mapped the reads to the contigs, finding that known phyla also account for a large majority (93.8%) of reads according to the study's classifications, and that contigs originally assigned to 'Arctiviricota' accounted for only a tiny fraction (0.01%) of reads from Arctic Ocean samples. Performing my own virus identification and classifications, I found that 99.95 per cent of reads could be assigned to known phyla. The most abundant species was Beihai picorna-like virus 34 (15% of reads), and the most abundant order-like cluster was classified as Picornavirales (45% of reads). Sequences in the claimed new phylum 'Pomiviricota' were placed inside a phylogenetic tree for established order Durnavirales with 100 per cent confidence. Moreover, two contigs assigned to the proposed phylum 'Taraviricota' were found to have high-identity alignments to dinoflagellate proteins, tentatively identifying this group of RdRp-like sequences as deriving from non-viral transcripts. Together, these results comprehensively contradict the claim that new phyla dominate the data.
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22
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Liu X, Xu Z, Liang J, Xu T, Zou W, Zhu L, Wu Y, Dong C, Lan K, Wu S, Zhou HB. Rational design and optimization of acylthioureas as novel potent influenza virus non-nucleoside polymerase inhibitors. Eur J Med Chem 2023; 259:115678. [PMID: 37531746 DOI: 10.1016/j.ejmech.2023.115678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/12/2023] [Accepted: 07/23/2023] [Indexed: 08/04/2023]
Abstract
Evidence suggests that rapidly evolving virus subvariants risk rendering current vaccines and anti-influenza drugs ineffective. Hence, exploring novel scaffolds or new targets of anti-influenza drugs is of great urgency. Herein, we report the discovery of a series of acylthiourea derivatives produced via a scaffold-hopping strategy as potent antiviral agents against influenza A and B subtypes. The most effective compound 10m displayed subnanomolar activity against H1N1 proliferation (EC50 = 0.8 nM) and exhibited inhibitory activity toward other influenza strains, including influenza B virus and H1N1 variant (H1N1, H274Y). Additionally, druggability evaluation revealed that 10m exhibited favorable pharmacokinetic properties and was metabolically stable in liver microsome preparations from three different species as well as in human plasma. In vitro and in vivo toxicity studies confirmed that 10m demonstrated a high safety profile. Furthermore, 10m exhibited satisfactory antiviral activity in a lethal influenza virus mouse model. Moreover, mechanistic studies indicated that these acylthiourea derivatives inhibited influenza virus proliferation by targeting influenza virus RNA-dependent RNA polymerase. Thus, 10m is a potential lead compound for the further exploration of treatment options for influenza.
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Affiliation(s)
- Xinjin Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhichao Xu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jinsen Liang
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ting Xu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenting Zou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lijun Zhu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yihe Wu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Chune Dong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Shuwen Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Hai-Bing Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Provincial Key Laboratory of Developmentally Originated Disease, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (MOE) and Hubei Province Engineering and Technology Research Center for Fluorinated Pharmaceuticals, Wuhan University, Wuhan, 430071, China.
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23
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Hedskog C, Rodriguez L, Roychoudhury P, Huang ML, Jerome KR, Hao L, Ireton RC, Li J, Perry JK, Han D, Camus G, Greninger AL, Gale M, Porter DP. Viral Resistance Analyses From the Remdesivir Phase 3 Adaptive COVID-19 Treatment Trial-1 (ACTT-1). J Infect Dis 2023; 228:1263-1273. [PMID: 37466213 PMCID: PMC10629708 DOI: 10.1093/infdis/jiad270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Remdesivir is approved for treatment of coronavirus disease 2019 (COVID-19) in nonhospitalized and hospitalized adult and pediatric patients. Here we present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) resistance analyses from the phase 3 ACTT-1 randomized placebo-controlled trial conducted in adult participants hospitalized with COVID-19. METHODS Swab samples were collected at baseline and longitudinally through day 29. SARS-CoV-2 genomes were sequenced using next-generation sequencing. Phenotypic analysis was conducted directly on participant virus isolates and/or using SARS-CoV-2 subgenomic replicons expressing mutations identified in the Nsp12 target gene. RESULTS Among participants with both baseline and postbaseline sequencing data, emergent Nsp12 substitutions were observed in 12 of 31 (38.7%) and 12 of 30 (40.0%) participants in the remdesivir and placebo arms, respectively. No emergent Nsp12 substitutions in the remdesivir arm were observed in more than 1 participant. Phenotyping showed low to no change in susceptibility to remdesivir relative to wild-type Nsp12 reference for the substitutions tested: A16V (0.8-fold change in EC50), P323L + V792I (2.2-fold), C799F (2.5-fold), K59N (1.0-fold), and K59N + V792I (3.4-fold). CONCLUSIONS The similar rate of emerging Nsp12 substitutions in the remdesivir and placebo arms and the minimal change in remdesivir susceptibility among tested substitutions support a high barrier to remdesivir resistance development in COVID-19 patients. Clinical Trials Registration. NCT04280705.
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Affiliation(s)
| | | | - Pavitra Roychoudhury
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Meei-Li Huang
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Linhui Hao
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Renee C Ireton
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Jiani Li
- Gilead Sciences, Inc, Foster City, California, USA
| | | | - Dong Han
- Gilead Sciences, Inc, Foster City, California, USA
| | | | - Alexander L Greninger
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington, Seattle, Washington, USA
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24
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Uemura K, Nobori H, Sato A, Toba S, Kusakabe S, Sasaki M, Tabata K, Matsuno K, Maeda N, Ito S, Tanaka M, Anraku Y, Kita S, Ishii M, Kanamitsu K, Orba Y, Matsuura Y, Hall WW, Sawa H, Kida H, Matsuda A, Maenaka K. 2-thiouridine is a broad-spectrum antiviral nucleoside analogue against positive-strand RNA viruses. Proc Natl Acad Sci U S A 2023; 120:e2304139120. [PMID: 37831739 PMCID: PMC10589713 DOI: 10.1073/pnas.2304139120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/23/2023] [Indexed: 10/15/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are causing significant morbidity and mortality worldwide. Furthermore, over 1 million cases of newly emerging or re-emerging viral infections, specifically dengue virus (DENV), are known to occur annually. Because no virus-specific and fully effective treatments against these or many other viruses have been approved, there is an urgent need for novel, effective therapeutic agents. Here, we identified 2-thiouridine (s2U) as a broad-spectrum antiviral ribonucleoside analogue that exhibited antiviral activity against several positive-sense single-stranded RNA (ssRNA+) viruses, such as DENV, SARS-CoV-2, and its variants of concern, including the currently circulating Omicron subvariants. s2U inhibits RNA synthesis catalyzed by viral RNA-dependent RNA polymerase, thereby reducing viral RNA replication, which improved the survival rate of mice infected with DENV2 or SARS-CoV-2 in our animal models. Our findings demonstrate that s2U is a potential broad-spectrum antiviral agent not only against DENV and SARS-CoV-2 but other ssRNA+ viruses.
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Affiliation(s)
- Kentaro Uemura
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka565-0871, Japan
| | - Haruaki Nobori
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
| | - Akihiko Sato
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
| | - Shinsuke Toba
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Shinji Kusakabe
- Drug Discovery and Disease Research Laboratory, Shionogi & Co. Ltd., Osaka561-0825, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Koshiro Tabata
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Keita Matsuno
- Unit of Risk Analysis and Management, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- One Health Research Center, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Naoyoshi Maeda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Shiori Ito
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Mayu Tanaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Mayumi Ishii
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, Tokyo113-0033, Japan
| | - Kayoko Kanamitsu
- Lead Exploration Unit, Drug Discovery Initiative, The University of Tokyo, Tokyo113-0033, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Osaka565-0871, Japan
| | - William W. Hall
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- National Virus Reference Laboratory, School of Medicine, University College of Dublin, DublinD04, Ireland
- Global Virus Network, Baltimore, MD21201
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
- One Health Research Center, Hokkaido University, Sapporo001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
- Global Virus Network, Baltimore, MD21201
| | - Hiroshi Kida
- Laboratory for Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo001-0020, Japan
| | - Akira Matsuda
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo001-0021, Japan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo060-0812, Japan
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25
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Felix da Silva Gomes G, Goes Camargo P, de Santiago-Silva KM, Suzukawa HT, Sotero da Silva Ribeiro AP, Orsato A, Nakazato G, Yamada-Ogatta SF, Faccin-Galhardi LC, da Silva Lima CH, de Lima Ferreira Bispo M, Perez CC. In silico approaches and in vitro assays identify a coumarin derivative as antiviral potential against SARS-CoV-2. J Biomol Struct Dyn 2023; 41:8978-8991. [PMID: 36326347 DOI: 10.1080/07391102.2022.2140203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
COVID-19, a disease caused by SARS-CoV-2, was declared a pandemic in 2020 and created a global crisis in health systems, with more than 545 million confirmed cases and 6.33 million deaths. In this sense, this work aims to identify possible inhibitors of the SARS-CoV-2 RdRp enzyme using in silico approaches. RdRp is a crucial enzyme in the replication and assembly cycle of new viral particles and a critical pharmacological target in the treatment of COVID-19. We performed a virtual screening based on molecular docking from our in-house chemical library, which contains a diversity of 313 structures from different chemical classes. Nine compounds were selected since they showed important interactions with the active site from RdRp. Next, the ADME-Tox in silico predictions served as a filter and selected the three most promising compounds: a coumarin LMed-052, a hydantoin LMed-087, and a guanidine LMed-250. Molecular dynamics simulations revealed details such as changes in the positions of ligands and catalytic residues during the simulations compared to the complex from molecular docking studies. Binding free energy analysis was performed using the MMGBSA method, demonstrating that LMed-052 and LMed-087 have better affinities for the RdRp by energetic contributions to the stability of the complexes when compared to LMed-250. Furthermore, LMed-052 showed significant in vitro inhibition against MHV-3, decreasing 99% of viral titers. Finally, these findings are useful to guide structural modifications aiming to improve the potential of these compounds to act as inhibitors of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gabriel Felix da Silva Gomes
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Priscila Goes Camargo
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Kaio Maciel de Santiago-Silva
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Helena Tiemi Suzukawa
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | | | - Alexandre Orsato
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Gerson Nakazato
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Sueli Fumie Yamada-Ogatta
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Ligia Carla Faccin-Galhardi
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Camilo Henrique da Silva Lima
- Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelle de Lima Ferreira Bispo
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
| | - Carla Cristina Perez
- Laboratório de Síntese de Moléculas Medicinais (LaSMMed), Departamento de Química, Centro de Ciências Exatas, Universidade Estadual de Londrina, Londrina, Brazil
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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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27
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Kim SM, Kim EH, Casel MAB, Kim YI, Sun R, Kwak MJ, Yoo JS, Yu M, Yu KM, Jang SG, Rollon R, Choi JH, Gil J, Eun K, Kim H, Ensser A, Hwang J, Song MS, Kim MH, Jung JU, Choi YK. SARS-CoV-2 variants with NSP12 P323L/G671S mutations display enhanced virus replication in ferret upper airways and higher transmissibility. Cell Rep 2023; 42:113077. [PMID: 37676771 DOI: 10.1016/j.celrep.2023.113077] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/02/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023] Open
Abstract
With the emergence of multiple predominant SARS-CoV-2 variants, it becomes important to have a comprehensive assessment of their viral fitness and transmissibility. Here, we demonstrate that natural temperature differences between the upper (33°C) and lower (37°C) respiratory tract have profound effects on SARS-CoV-2 replication and transmissibility. Specifically, SARS-CoV-2 variants containing the NSP12 mutations P323L or P323L/G671S exhibit enhanced RNA-dependent RNA polymerase (RdRp) activity at 33°C compared with 37°C and high transmissibility. Molecular dynamics simulations and microscale thermophoresis demonstrate that the NSP12 P323L and P323L/G671S mutations stabilize the NSP12-NSP7-NSP8 complex through hydrophobic effects, leading to increased viral RdRp activity. Furthermore, competitive transmissibility assay reveals that reverse genetic (RG)-P323L or RG-P323L/G671S NSP12 outcompetes RG-WT (wild-type) NSP12 for replication in the upper respiratory tract, allowing markedly rapid transmissibility. This suggests that NSP12 P323L or P323L/G671S mutation of SARS-CoV-2 is associated with increased RdRp complex stability and enzymatic activity, promoting efficient transmissibility.
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Affiliation(s)
- Se-Mi Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Eun-Ha Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Mark Anthony B Casel
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Young-Il Kim
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Rong Sun
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mi-Jeong Kwak
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ji-Seung Yoo
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Mina Yu
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea
| | - Kwang-Min Yu
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Seung-Gyu Jang
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Rare Rollon
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Jeong Ho Choi
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Juryeon Gil
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kiyoung Eun
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hyunggee Kim
- Institute of Animal Molecular Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea; Department of Biotechnology, School of Life Sciences and Biotechnology, Korea University, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Armin Ensser
- Institute for Clinical and Molecular Virology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Jungwon Hwang
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Min-Suk Song
- College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogens and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Young Ki Choi
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science (IBS), Daejeon 34126, Republic of Korea; College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Republic of Korea.
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28
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Zhang X, Shi H, Li J, Wu X. Complete genome sequence of a novel virus isolated from the phytopathogenic fungus Ceratobasidium sp. AG-A strain SHX-YJLC-1. Arch Virol 2023; 168:241. [PMID: 37668772 DOI: 10.1007/s00705-023-05868-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/30/2023] [Indexed: 09/06/2023]
Abstract
A novel mycovirus, Ceratobasidium bipartite virus 1 (CBV1), was identified in Ceratobasidium sp. AG-A strain SHX-YJLC-1 isolated from diseased potato stems. The complete genome of CBV1 consists of two double-stranded RNA (dsRNA) segments: dsRNA1 (2311 bp) and dsRNA2 (1761 bp). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), while dsRNA2 contains a single ORF (ORF2) encoding a hypothetical protein (HP) with unknown function. BLASTp analysis revealed that RdRp (75.04%) and HP (61.86%) encoded by the two ORFs have the highest sequence similarity to their counterparts in Rhizoctonia solani dsRNA virus 11 (RsRV11). The genome organization and phylogenetic analysis indicated that the closest relatives to CBV1 are members of the proposed family "Bipartitiviridae". Based on the collective results, CBV1 is inferred to be a new member of the proposed family "Bipartitiviridae". This is the first report on the complete genome sequence of the novel bipartitivirus CBV1, which infects Ceratobasidium sp. AG-A strain SHX-YJLC-1.
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Affiliation(s)
- Xinyi Zhang
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China
| | - Hao Shi
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China
| | - Jinting Li
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China.
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29
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Xu T, Zhang L. Current understanding of nucleoside analogs inhibiting the SARS-CoV-2 RNA-dependent RNA polymerase. Comput Struct Biotechnol J 2023; 21:4385-4394. [PMID: 37711189 PMCID: PMC10498173 DOI: 10.1016/j.csbj.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Since the outbreak of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has become a main target for antiviral therapeutics due to its essential role in viral replication and transcription. Thus, nucleoside analogs structurally resemble the natural RdRp substrate and hold great potential as inhibitors. Until now, extensive experimental investigations have been performed to explore nucleoside analogs to inhibit the RdRp, and concerted efforts have been made to elucidate the underlying molecular mechanisms further. This review begins by discussing the nucleoside analogs that have demonstrated inhibition in the experiments. Second, we examine the current understanding of the molecular mechanisms underlying the action of nucleoside analogs on the SARS-CoV-2 RdRp. Recent findings in structural biology and computational research are presented through the classification of inhibitory mechanisms. This review summarizes previous experimental findings and mechanistic investigations of nucleoside analogs inhibiting SARS-CoV-2 RdRp. It would guide the rational design of antiviral medications and research into viral transcriptional mechanisms.
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Affiliation(s)
- Tiantian Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fujian 361005, China
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30
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Jeon K, Ro HJ, Kang JG, Jeong DE, Kim J, Lee Y, Yoon GY, Kang JI, Bae JY, Kim JI, Park MS, Lee KH, Cho HS, Kim Y, Cho NH. A natural variation in the RNA polymerase of severe fever with thrombocytopenia syndrome virus enhances viral replication and in vivo virulence. J Med Virol 2023; 95:e29099. [PMID: 37702580 DOI: 10.1002/jmv.29099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/07/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023]
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease with high mortality in Eastern Asia. The disease is caused by the SFTS virus (SFTSV), also known as Dabie bandavirus, which has a segmented RNA genome consisting of L, M, and S segments. Previous studies have suggested differential viral virulence depending on the genotypes of SFTSV; however, the critical viral factor involved in the differential viral virulence is unknown. Here, we found a significant difference in viral replication in vitro and virulence in vivo between two Korean isolates belonging to the F and B genotypes, respectively. By generating viral reassortants using the two viral strains, we demonstrated that the L segment, which encodes viral RNA-dependent RNA polymerase (RdRp), is responsible for the enhanced viral replication and virulence. Comparison of amino acid sequences and viral replication rates revealed a point variation, E251K, on the surface of RdRp to be the most significant determinant for the enhanced viral replication rate and in vivo virulence. The effect of the variation was further confirmed using recombinant SFTSV generated by reverse genetic engineering. Therefore, our results indicate that natural variations affecting the viral replicase activity could significantly contribute to the viral virulence of SFTSV.
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Affiliation(s)
- Kyeongseok Jeon
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyo-Jin Ro
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jun-Gu Kang
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Da-Eun Jeong
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Joowan Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yebeen Lee
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ga-Yeon Yoon
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Ju-Il Kang
- Institute of Endemic Disease, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, Vaccine Innovation Center, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Vaccine Innovation Center, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Vaccine Innovation Center, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea
| | - Keun Hwa Lee
- Department of Microbiology and Environmental Biology & Medical Parasitology, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Yuri Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Disease, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Endemic Disease, Seoul National University Medical Research Center, Seoul, Republic of Korea
- Seoul National University Bundang Hospital, Seongnam, Gyeonggi-do, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Gangwon-do, Republic of Korea
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31
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Ma Y, Wang J, Pan X, Zhang J, Shan Y. Identification of potential targets against SARS-CoV-2 of antiviral drugs based on photoaffinity probes. Drug Dev Res 2023; 84:1142-1158. [PMID: 37165797 DOI: 10.1002/ddr.22075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/14/2023] [Accepted: 04/08/2023] [Indexed: 05/12/2023]
Abstract
Facing the sudden outbreak of coronavirus disease 2019 (COVID-19), it is extremely urgent to develop effective antiviral drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Drug repurposing is a promising strategy for the treatment of COVID-19. To identify the precise target protein of marketed medicines, we initiate a chemical biological program to identify precise target of potential antivirus drugs. In this study, two types of recombinant human coronavirus SARS-CoV-2 RdRp protein capturing probes with various photoaffinity labeling units were designed and synthesized based on the structure of FDA-approved drugs stavudine, remdesivir, acyclovir, and aladenosine. Fortunately, it was found that one novel photoaffinity probe, RD-1, could diaplayed good affinity with SARS-CoV-2 RdRp around the residue ARG_553. In addition, RD-1 probe also exhibited potent inhibitory activity against 3CLpro protease. Taken together, our findings will elucidate the structural basis for the efficacy of marketed drugs, and explore a rapid and efficient strategy of drug repurposing based on the identification of new targets. Moreover, these results could also provide a scientific basis for the clinical application of marketed drugs.
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Affiliation(s)
- Yuexiang Ma
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Emergency, Xijing Hospital, Air Force Medical University, Xi'an, China
| | - Jin Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yuanyuan Shan
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Gupta N, Ogino M, Watkins DE, Yu T, Green TJ, Ogino T. Discontinuous L-binding motifs in the transactivation domain of the vesicular stomatitis virus P protein are required for terminal de novo transcription initiation by the L protein. J Virol 2023; 97:e0024623. [PMID: 37578231 PMCID: PMC10506490 DOI: 10.1128/jvi.00246-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/18/2023] [Indexed: 08/15/2023] Open
Abstract
The phospho- (P) protein, the co-factor of the RNA polymerase large (L) protein, of vesicular stomatitis virus (VSV, a prototype of nonsegmented negative-strand RNA viruses) plays pivotal roles in transcription and replication. However, the precise mechanism underlying the transcriptional transactivation by the P protein has remained elusive. Here, using an in vitro transcription system and a series of deletion mutants of the P protein, we mapped a region encompassing residues 51-104 as a transactivation domain (TAD) that is critical for terminal de novo initiation, the initial step of synthesis of the leader RNA and anti-genome/genome, with the L protein. Site-directed mutagenesis revealed that conserved amino acid residues in three discontinuous L-binding sites within the TAD are essential for the transactivation activity of the P protein or important for maintaining its full activity. Importantly, relative inhibitory effects of TAD point mutations on synthesis of the full-length leader RNA and mRNAs from the 3'-terminal leader region and internal genes, respectively, of the genome were similar to those on terminal de novo initiation. Furthermore, any of the examined TAD mutations did not alter the gradient pattern of mRNAs synthesized from internal genes, nor did they induce the production of readthrough transcripts. These results suggest that these TAD mutations impact mainly terminal de novo initiation but rarely other steps (e.g., elongation, termination, internal initiation) of single-entry stop-start transcription. Consistently, the mutations of the essential or important amino acid residues within the P TAD were lethal or deleterious to VSV replication in host cells. IMPORTANCE RNA-dependent RNA polymerase L proteins of nonsegmented negative-strand RNA viruses belonging to the Mononegavirales order require their cognate co-factor P proteins or their counterparts for genome transcription and replication. However, exact roles of these co-factor proteins in modulating functions of L proteins during transcription and replication remain unknown. In this study, we revealed that three discrete L-binding motifs within a transactivation domain of the P protein of vesicular stomatitis virus, a prototypic nonsegmented negative-strand RNA virus, are required for terminal de novo initiation mediated by the L protein, which is the first step of synthesis of the leader RNA as well as genome/anti-genome.
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Affiliation(s)
- Nirmala Gupta
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Minako Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Dean E. Watkins
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Tiffany Yu
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Todd J. Green
- Department of Microbiology, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tomoaki Ogino
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medical Microbiology and Immunology, College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
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Le Lay C, Hamm JN, Williams TJ, Shi M, Cavicchioli R, Holmes EC. Viral community composition of hypersaline lakes. Virus Evol 2023; 9:vead057. [PMID: 37692898 PMCID: PMC10492444 DOI: 10.1093/ve/vead057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/03/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023] Open
Abstract
Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments.
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Affiliation(s)
- Callum Le Lay
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mang Shi
- State Key Laboratory for Biocontrol, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, P.O. Box 59, Den Burg NL-1790 AB, The Netherlands
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Rashmi SH, Disha KS, Sudheesh N, Karunakaran J, Joseph A, Jagadesh A, Mudgal PP. Repurposing of approved antivirals against dengue virus serotypes: an in silico and in vitro mechanistic study. Mol Divers 2023:10.1007/s11030-023-10716-5. [PMID: 37632595 DOI: 10.1007/s11030-023-10716-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Dengue is an emerging, mosquito-borne viral disease of international public health concern. Dengue is endemic in more than 100 countries across the world. However, there are no clinically approved antivirals for its cure. Drug repurposing proves to be an efficient alternative to conventional drug discovery approaches in this regard, as approved drugs with an established safety profile are tested for new indications, which circumvents several time-consuming experiments. In the present study, eight approved RNA-dependent RNA polymerase inhibitors of Hepatitis C virus were virtually screened against the Dengue virus polymerase protein, and their antiviral activity was assessed in vitro. Schrödinger software was used for in silico screening, where the compounds were passed through several hierarchical filters. Among the eight compounds, dasabuvir was finally selected for in vitro cytotoxicity and antiviral screening. Cytotoxicity profiling of dasabuvir in Vero cells revealed changes in cellular morphology, cell aggregation, and detachment at 50 μM. Based on these results, four noncytotoxic concentrations of dasabuvir (0.1, 0.25, 0.5, and 1 µM) were selected for antiviral screening against DENV-2 under three experimental conditions: pre-infection, co-infection, and post-infection treatment, by plaque reduction assay. Viral plaques were reduced significantly (p < 0.05) in the co-infection and post-infection treatment regimens; however, no reduction was observed in the pretreatment group. This indicated a possible interference of dasabuvir with NS5 RdRp, as seen from in silico interaction studies, translating into a reduction in virus plaques. Such studies reiterate the usefulness of drug repurposing as a viable strategy in antiviral drug discovery. In this drug repurposing study, dasabuvir, a known anti-hepatitis C drug, was selected through virtual screening and assessed for its anti-dengue activity.
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Affiliation(s)
- S H Rashmi
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - K Sai Disha
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - N Sudheesh
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Joseph Karunakaran
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Anitha Jagadesh
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India
| | - P P Mudgal
- Manipal Institute of Virology, Manipal Academy of Higher Education, Manipal, India.
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35
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Zhu KW. Efficacy and safety evaluation of Azvudine in the prospective treatment of COVID-19 based on four phase III clinical trials. Front Pharmacol 2023; 14:1228548. [PMID: 37693894 PMCID: PMC10484631 DOI: 10.3389/fphar.2023.1228548] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/04/2023] [Indexed: 09/12/2023] Open
Abstract
Azvudine (FNC) is a synthetic nucleoside analog used to treat adult patients living with human immunodeficiency virus-1 (HIV-1) infection with high viral load. After phosphorylation, Azvudine inhibits RNA-dependent RNA polymerase, leading to the discontinuation of RNA chain synthesis in viruses. In addition, Azvudine is the first dual-target nucleoside oral drug worldwide to simultaneously target reverse transcriptase and viral infectivity factors in the treatment of HIV infection. On 9 August 2022, Azvudine was incorporated into the Guidelines for the Diagnosis and Treatment of Coronavirus Disease 2019 (version ninth) issued by the National Health Commission and the National Administration of Traditional Chinese Medicine. The recommended oral dose of Azvudine for the treatment of moderate coronavirus disease 2019 (COVID-19) is 5 mg once daily, and the duration of Azvudine treatment should not exceed 14 days. Four phase III clinical trials were performed during 2020-2022 to evaluate the efficacy and safety of Azvudine in the treatment of COVID-19. The results revealed that Azvudine could reduce nucleic acid-negative conversion time, viral load, and time to improvement in clinical conditions in patients with moderate COVID-19. In addition, Azvudine exhibited good safety and tolerance. Thereafter, Azvudine was incorporated into the Chinese guidelines and expert consensus for the treatment of COVID-19 and was highly approbated. Furthermore, Azvudine was also included in the Chinese guidelines for HIV infection.
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Gratteri C, Ambrosio FA, Lupia A, Moraca F, Catalanotti B, Costa G, Bellocchi M, Carioti L, Salpini R, Ceccherini-Silberstein F, Frazia SL, Malagnino V, Sarmati L, Svicher V, Bryant S, Artese A, Alcaro S. Molecular and Structural Aspects of Clinically Relevant Mutations of SARS-CoV-2 RNA-Dependent RNA Polymerase in Remdesivir-Treated Patients. Pharmaceuticals (Basel) 2023; 16:1143. [PMID: 37631058 PMCID: PMC10459223 DOI: 10.3390/ph16081143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
(1) Background: SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is a promising therapeutic target to fight COVID-19, and many RdRp inhibitors nucleotide/nucleoside analogs, such as remdesivir, have been identified or are in clinical studies. However, the appearance of resistant mutations could reduce their efficacy. In the present work, we structurally evaluated the impact of RdRp mutations found at baseline in 39 patients treated with remdesivir and associated with a different degree of antiviral response in vivo. (2) Methods: A refined bioinformatics approach was applied to assign SARS-CoV-2 clade and lineage, and to define RdRp mutational profiles. In line with such a method, the same mutations were built and analyzed by combining docking and thermodynamics evaluations with both molecular dynamics and representative pharmacophore models. (3) Results: Clinical studies revealed that patients bearing the most prevalent triple mutant P323L+671S+M899I, which was present in 41% of patients, or the more complex mutational profile P323L+G671S+L838I+D738Y+K91E, which was found with a prevalence of 2.6%, showed a delayed reduced response to remdesivir, as confirmed by the increase in SARS-CoV-2 viral load and by a reduced theoretical binding affinity versus RdRp (ΔGbindWT = -122.70 kcal/mol; ΔGbindP323L+671S+M899I = -84.78 kcal/mol; ΔGbindP323L+G671S+L838I+D738Y+K91E = -96.74 kcal/mol). Combined computational approaches helped to rationalize such clinical observations, offering a mechanistic understanding of the allosteric effects of mutants on the global motions of the viral RNA synthesis machine and in the changes of the interactions patterns of remdesivir during its binding.
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Affiliation(s)
- Carmen Gratteri
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy;
| | - Antonio Lupia
- Dipartimento di Scienze della vita e dell’ambiente, Università degli Studi di Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy;
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Federica Moraca
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Bruno Catalanotti
- Dipartimento di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Maria Bellocchi
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Luca Carioti
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Francesca Ceccherini-Silberstein
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (M.B.); (L.C.); (R.S.); (F.C.-S.)
| | - Simone La Frazia
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Vincenzo Malagnino
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Loredana Sarmati
- Dipartimento di Medicina dei Sistemi, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy; (V.M.); (L.S.)
| | - Valentina Svicher
- Dipartimento di Biologia, Università Tor Vergata di Roma, Via della Ricerca Scientifica, 1, 00133 Roma, Italy; (S.L.F.); (V.S.)
| | - Sharon Bryant
- Inte:Ligand GmbH, Mariahilferstrasse 74B/11, 1070 Vienna, Austria;
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (C.G.); (G.C.); (S.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, 88100 Catanzaro, Italy
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Deshpande S, Huo W, Shrestha R, Sparrow K, Wood JM, Evans GB, Harris LD, Kingston RL, Bulloch EMM. Galidesivir Triphosphate Promotes Stalling of Dengue-2 Virus Polymerase Immediately Prior to Incorporation. ACS Infect Dis 2023; 9:1658-1673. [PMID: 37488090 PMCID: PMC10739630 DOI: 10.1021/acsinfecdis.3c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 07/26/2023]
Abstract
Millions of people are infected by the dengue and Zika viruses each year, resulting in significant morbidity and mortality. Galidesivir is an adenosine nucleoside analog that can attenuate flavivirus replication in cell-based assays and animal models of infection. Galidesivir is converted to the triphosphorylated form by host kinases and subsequently incorporated into viral RNA by viral RNA polymerases. This has been proposed to lead to the delayed termination of RNA synthesis. Here, we report direct in vitro testing of the effects of Galidesivir triphosphate on dengue-2 and Zika virus polymerase activity. Galidesivir triphosphate was chemically synthesized, and inhibition of RNA synthesis followed using a dinucleotide-primed assay with a homopolymeric poly(U) template. Galidesivir triphosphate was equipotent against dengue-2 and Zika polymerases, with IC50 values of 42 ± 12 μM and 47 ± 5 μM, respectively, at an ATP concentration of 20 μM. RNA primer extension assays show that the dengue-2 polymerase stalls while attempting to add a Galidesivir nucleotide to the nascent RNA chain, evidenced by the accumulation of RNA products truncated immediately upstream of Galidesivir incorporation sites. Nevertheless, Galidesivir is incorporated at isolated sites with low efficiency, leading to the subsequent synthesis of full-length RNA with no evidence of delayed chain termination. The incorporation of Galidesivir at consecutive sites is strongly disfavored, highlighting the potential for modulation of inhibitory effects of nucleoside analogs by the template sequence. Our results suggest that attenuation of dengue replication by Galidesivir may not derive from the early termination of RNA synthesis following Galidesivir incorporation.
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Affiliation(s)
- Sandesh Deshpande
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Wenjuan Huo
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Rinu Shrestha
- Ferrier
Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Kevin Sparrow
- Ferrier
Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
| | - James M. Wood
- Ferrier
Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Gary B. Evans
- Ferrier
Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Lawrence D. Harris
- Ferrier
Research Institute, Victoria University of Wellington, 69 Gracefield Rd, Lower Hutt 5010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Richard L. Kingston
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
| | - Esther M. M. Bulloch
- School
of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand
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de Jesús López Medina Y, Tamayo-Molina YS, Valdés-López JF, Urcuqui-Inchima S. Protective Effects of Caffeine on Chikungunya and Zika Virus Infections: An in Vitro and in Silico Study. Chem Biodivers 2023; 20:e202300192. [PMID: 37489706 DOI: 10.1002/cbdv.202300192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Infection by viruses Chikungunya (CHIKV) and Zika (ZIKV) continue to be serious problems in tropical and subtropical areas of the world. Here, we evaluated the antiviral and virucidal activity of caffeine against CHIKV and ZIKV in Vero, A549, and Huh-7 cell lines. Results showed that caffeine displays antiviral properties against both viruses. By pre-and post-infection treatment, caffeine significantly inhibited CHIKV and ZIKV replication in a dose-dependent manner. Furthermore, caffeine showed a virucidal effect against ZIKV. Molecular docking suggests the possible binding of caffeine with envelope protein and RNA-dependent RNA polymerase of CHIKV and ZIKV. This is the first study that showed an antiviral effect of caffeine against CHIKV and ZIKV. Although further studies are needed to better understand the mechanism of caffeine-mediated repression of viral replication, caffeine appears to be a promising compound that could be used for in vivo studies, perhaps in synergy with other compounds present in daily beverages.
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Affiliation(s)
| | | | - Juan Felipe Valdés-López
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Silvio Urcuqui-Inchima
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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Lanrewaju AA, Enitan-Folami AM, Nyaga MM, Sabiu S, Swalaha FM. Metabolites profiling and cheminformatics bioprospection of selected medicinal plants against the main protease and RNA-dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2023:1-21. [PMID: 37464870 DOI: 10.1080/07391102.2023.2236718] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Despite the existence of some vaccines, SARS-CoV-2 (S-2) infections persist for various reasons relating to vaccine reluctance, rapid mutation rate, and an absence of specific treatments targeted to the infection. Due to their availability, low cost and low toxicity, research into potentially repurposing phytometabolites as therapeutic alternatives has gained attention. Therefore, this study explored the antiviral potential of metabolites of some medicinal plants [Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum (Sesame plant)] identified using liquid chromatography-mass spectrometry (LCMS) as possible inhibitory agents against the S-2 main protease (S-2 MP) and RNA-dependent RNA polymerase (RP) using computational approaches. Molecular docking was used to identify the compounds with the best affinities for the selected therapeutics targets. Afterwards, compounds with poor physicochemical characteristics, pharmacokinetics, and drug-likeness were screened out. The top-ranked compounds were further subjected to a 120-ns molecular dynamics (MD) simulation. Only quercetin 3-O-rhamnoside (-48.77 kcal/mol) had higher binding free energy than the reference standard (zafirlukast) (-44.99 kcal/mol) against S-2 MP. Conversely, all the top-ranked compounds (ellagic acid hexoside, spiraeoside, apigenin-4'-glucoside and chrysoeriol 7-glucuronide) except gnetin L (-24.24 kcal/mol) had higher binding free energy (-55.19 kcal/mol, -52.75 kcal/mol, -47.22 kcal/mol and -43.35 kcal/mol) respectively, against S-2 RP relative to the reference standard (-34.79 kcal/mol). The MD simulations study further revealed that the investigated inhibitors are thermodynamically stable and form structurally compatible complexes that impede the regular operation of the respective S-2 therapeutic targets. Although, these S-2 therapeutic candidates are promising, further in vitro and in vivo evaluation is required and highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | | | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | - Feroz Mahomed Swalaha
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
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Alandijany TA, El-Daly MM, Tolah AM, Bajrai LH, Khateb AM, Alsaady IM, Altwaim SA, Dubey A, Dwivedi VD, Azhar EI. Investigating the Mechanism of Action of Anti-Dengue Compounds as Potential Binders of Zika Virus RNA-Dependent RNA Polymerase. Viruses 2023; 15:1501. [PMID: 37515188 PMCID: PMC10384299 DOI: 10.3390/v15071501] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
The World Health Organization (WHO) has designated the Zika virus (ZIKV) as a significant risk to the general public's health. Currently, there are no vaccinations or medications available to treat or prevent infection with the Zika virus. Thus, it is urgently required to develop a highly efficient therapeutic molecule. In the presented study, a computationally intensive search was carried out to identify potent compounds that have the potential to bind and block the activity of ZIKV NS5 RNA-dependent RNA polymerase (RdRp). The anti-dengue chemical library was subjected to high-throughput virtual screening and MM/GBSA analysis in order to rate the potential candidates. The top three compounds were then chosen. According to the MM/GBSA analysis, compound 127042987 from the database had the highest binding affinity to the protein with a minimum binding free energy of -77.16 kcal/mole. Compound 127042987 had the most stable RMSD trend and the greatest number of hydrogen bond interactions when these chemical complexes were evaluated further under a 100 ns molecular dynamics simulation. Compound 127042987 displayed the best binding free energy (GBind) of -96.50 kcal/mol, surpassing the native ligand binding energy (-66.17 kcal/mole). Thereafter, an MM/GBSA binding free energy study was conducted to validate the stability of selected chemical complexes. Overall, this study illustrated that compound 127042987 showed preferred binding free energies, suggesting a possible inhibitory mechanism against ZIKV-RdRp. As per this study, it was proposed that compound 127042987 could be used as a therapeutic option to prevent Zika virus infection. These compounds need to be tested in experiments for further validation.
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Affiliation(s)
- Thamir A Alandijany
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Mai M El-Daly
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Ahmed M Tolah
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabig 25732, Saudi Arabia
| | - Leena H Bajrai
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Aiah M Khateb
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Madinah 42353, Saudi Arabia
| | - Isra M Alsaady
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Sarah A Altwaim
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 20136, Saudi Arabia
| | - Amit Dubey
- Computational Chemistry & Drug Discovery Division, Quanta Calculus, Greater Noida 201310, India
| | - Vivek Dhar Dwivedi
- Bioinformatics Research Division, Quanta Calculus, Greater Noida 201310, India
| | - Esam I Azhar
- Special Infectious Agents Unit-BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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Arcos S, Han AX, te Velthuis AJW, Russell CA, Lauring AS. Mutual information networks reveal evolutionary relationships within the influenza A virus polymerase. Virus Evol 2023; 9:vead037. [PMID: 37325086 PMCID: PMC10263469 DOI: 10.1093/ve/vead037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/27/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
The influenza A virus (IAV) RNA polymerase is an essential driver of IAV evolution. Mutations that the polymerase introduces into viral genome segments during replication are the ultimate source of genetic variation, including within the three subunits of the IAV polymerase (polymerase basic protein 2, polymerase basic protein 1, and polymerase acidic protein). Evolutionary analysis of the IAV polymerase is complicated, because changes in mutation rate, replication speed, and drug resistance involve epistatic interactions among its subunits. In order to study the evolution of the human seasonal H3N2 polymerase since the 1968 pandemic, we identified pairwise evolutionary relationships among ∼7000 H3N2 polymerase sequences using mutual information (MI), which measures the information gained about the identity of one residue when a second residue is known. To account for uneven sampling of viral sequences over time, we developed a weighted MI (wMI) metric and demonstrate that wMI outperforms raw MI through simulations using a well-sampled severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dataset. We then constructed wMI networks of the H3N2 polymerase to extend the inherently pairwise wMI statistic to encompass relationships among larger groups of residues. We included hemagglutinin (HA) in the wMI network to distinguish between functional wMI relationships within the polymerase and those potentially due to hitch-hiking on antigenic changes in HA. The wMI networks reveal coevolutionary relationships among residues with roles in replication and encapsidation. Inclusion of HA highlighted polymerase-only subgraphs containing residues with roles in the enzymatic functions of the polymerase and host adaptability. This work provides insight into the factors that drive and constrain the rapid evolution of influenza viruses.
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Zhang H, Zhao C, Zhang X, Li J, Gong P, Wang X, Li X, Wang X, Zhang X, Cheng S, Yue T, Zhang N. A potential role for Giardia chaperone protein GdDnaJ in regulating Giardia proliferation and Giardiavirus replication. Parasit Vectors 2023; 16:168. [PMID: 37226181 DOI: 10.1186/s13071-023-05787-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Giardia duodenalis (referred to as Giardia) is a flagellated binucleate protozoan parasite, which causes one of the most common diarrheal diseases, giardiasis, worldwide. Giardia can be infected by Giardiavirus (GLV), a small endosymbiotic dsRNA virus belongs to the Totiviridae family. However, the regulation of GLV and a positive correlation between GLV and Giardia virulence is yet to be elucidated. METHODS To identify potential regulators of GLV, we performed a yeast two-hybrid (Y2H) screen to search for interacting proteins of RdRp. GST pull-down, co-immunoprecipitation and bimolecular fluorescence complementation (BiFC) assay were used to verify the direct physical interaction between GLV RdRp and its new binding partner. In addition, their in vivo interaction and colocalization in Giardia trophozoites were examined by using Duolink proximal ligation assay (Duolink PLA). RESULTS From Y2H screen, the Giardia chaperone protein, Giardia DnaJ (GdDnaJ), was identified as a new binding partner for GLV RdRp. The direct interaction between GdDnaJ and GLV RdRp was verified via GST pull-down, co-immunoprecipitation and BiFC. In addition, colocalization and in vivo interaction between GdDnaJ and RdRp in Giardia trophozoites were confirmed by Duolink PLA. Further analysis revealed that KNK437, the inhibitor of GdDnaJ, can significantly reduce the replication of GLVs and the proliferation of Giardia. CONCLUSION Taken together, our results suggested a potential role of GdDnaJ in regulating Giardia proliferation and GLV replication through interaction with GLV RdRp.
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Affiliation(s)
- Hongbo Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Chunyan Zhao
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xichen Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Jianhua Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Pengtao Gong
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xiaocen Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xin Li
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xin Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Xu Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Shuqin Cheng
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Taotao Yue
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Nan Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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Sun SR, Wang ZQ, Liang QG, Qin Y, Chen JL, Wang G, Chang H, Wang Q, Gao SJ. First report of Capsicum chlorosis virus naturally infecting Ageratum conyzoides in China. Plant Dis 2023. [PMID: 37227437 DOI: 10.1094/pdis-01-23-0025-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Capsicum chlorosis virus (CaCV; family Tospoviridae, genus Orthotospovirus) was first reported to infect capsicum (Capsicum annuum) and tomato (Solanum lycopersicum) in Australia in 2002 (McMichael et al., 2002). Subsequently, its infection was detected in different plants including waxflower (Hoya calycina Schlecter) in the United States (Melzer et al. 2014), peanut (Arachis hypogaea) in India (Vijayalakshmi et al. 2016), and spider lily (Hymenocallis americana) (Huang et al. 2017), Chilli pepper (Capsicum annuum) (Zheng et al. 2020), and Feiji cao (Chromolaena odorata) (Chen et al. 2022) in China. Ageratum conyzoides L. (commonly known as goat weed, family Asteraceae) is a natural weed in crop fields distributed in subtropical and tropical areas and a reservoir host of numerous plant pathogens (She et al. 2013). In April 2022, we observed that 90% of plants of A. conyzoides in maize fields in Sanya, Hainan province, China, exhibited typical virus-like symptoms of vein yellowing, leaf chlorosis, and distortion (Fig. S1 A-C). Total RNA was extracted from one symptomatic leaf of A. conyzoides. Small RNA libraries were constructed using the small RNA Sample Pre Kit (Illumina, San Diego, USA) for sequencing with an Illumina Novaseq 6000 platform (Biomarker Technologies Corporation, Beijing, China). A total 15,848,189 clean reads were obtained after removing low-quality reads. Quality-controlled qualified reads were assembled into contigs using Velvet 1.0.5 software with a k-mer value of 17. One hundred contigs shared nucleotide identity ranging from 85.7% to 100% with the CaCV using BLASTn searches online (https://blast.ncbi.nlm.nih.gov/Blast.cgi?). Numerous contigs (45, 34, and 21) obtained in this study were mapped to the L, M, and S RNA segments of the CaCV-Hainan isolate (GenBank accession no. KX078565- KX078567) from spider lily (Hymenocallis americana) in Hainan province, China, respectively. The full-length of L, M, and S RNA segments of CaCV-AC were determined to be 8,913, 4,841, and 3,629 bp, respectively (GenBank accession no. OQ597167- OQ597169). Furthermore, five symptomatic leaf samples were tested to be positive for CaCV using a CaCV enzyme-linked immunosorbent assay (ELISA) kit (MEIMIAN, Jiangsu, China) (Fig. S1-D). Total RNA from these leaves was amplified by RT-PCR with two sets of primer pairs. Primers CaCV-F (5'-ACTTTCCATCAACCTCTGT-3') and CaCV-R (5'-GTTATGGCCATATTTCCCT-3') were used for the amplification of 828 bp fragment from nucleocapsid protein (NP) on CaCV S RNA. While another, primers gL3637 (5'-CCTTTAACAGTDGAAACAT-3') and gL4435c (5'-CATDGCRCAAGARTGRTARACAGA-3') were used for the amplification of 816 bp fragment from RNA-dependent RNA polymerase (RdRP) on CaCV L RNA (Fig. S1-E and -F) (Basavaraj et al. 2020). These amplicons were cloned into the pCE2 TA/Blunt-Zero vector (Vazyme, Nanjing, China) and three independent positive colonies of Escherichia coli DH5α carrying each viral amplicon were sequenced. These sequences were deposited in the GenBank database under accession nos. OP616700-OP616709. Pairwise sequence comparison revealed that nucleotide sequences of NP and RdRP genes of the five CaCV isolates shared 99.5% (812 bp out of 828 bp) and 99.4% (799 bp out of 816 bp) nucleotide identities, respectively. They showed 86.2-99.2% and 86.5-99.1% nucleotide identities with corresponding nucleotide sequences of other CaCV isolates derived from GenBank database, respectively. The highest nucleotide sequence identity (99%) of the CaCV isolates obtained in the study was observed with the CaCV-Hainan isolate. Phylogenetic analysis based on NP amino acid demonstrated that six CaCV isolates (this study = 5 and NCBI database = 1) clustered into one distinct clade (Fig. S2). Our data confirmed for the first time the presence of CaCV naturally infecting A. conyzoides plant in China, which enriches information on the host range and will be helpful for disease management.
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Affiliation(s)
- Sheng-Ren Sun
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - Zhu-Qing Wang
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - Qing-Gan Liang
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - Yuanxia Qin
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - Jun-Lü Chen
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - Gang Wang
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - Hailong Chang
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - Qinnan Wang
- Guangdong Academy of Sciences, 514144, Institute of Nanfan & Seed Industry, Guangzhou, Guangdong, China
- Ministry of Agriculture of Guangdong Sugarcane Germplasm Resources and Utilization of Scientific Observation Test Station, Sanya, Hainan, China;
| | - San-Ji Gao
- Fujian Agriculture and Forestry University, 12449, National Engineering Research Center for Sugarcane, 15 Shangxiadian Rd, Fuzhou, China, 350002;
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Nakagawa S, Sakaguchi S, Ogura A, Mineta K, Endo T, Suzuki Y, Gojobori T. Current trends in RNA virus detection through metatranscriptome sequencing data. FEBS Open Bio 2023. [PMID: 37163224 DOI: 10.1002/2211-5463.13626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.
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Affiliation(s)
- So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, 259-1193, Japan
- Division of Genome Sciences, Institute of Medical Sciences, Tokai University, Kanagawa, 259-1193, Japan
- Division of Interdisciplinary Merging of Health Research, Micro/Nano Technology Center, Tokai University, Kanagawa, 259-1292, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Atsushi Ogura
- Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Toshinori Endo
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, 060-0814, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Science, Nagoya City University, Nagoya, 467-8501, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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45
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Moury B, Michon T, Simon V, Palloix A. A Single Nonsynonymous Substitution in the RNA-Dependent RNA Polymerase of Potato virus Y Allows the Simultaneous Breakdown of Two Different Forms of Antiviral Resistance in Capsicum annuum. Viruses 2023; 15:v15051081. [PMID: 37243167 DOI: 10.3390/v15051081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The dominant Pvr4 gene in pepper (Capsicum annuum) confers resistance to members of six potyvirus species, all of which belong to the Potato virus Y (PVY) phylogenetic group. The corresponding avirulence factor in the PVY genome is the NIb cistron (i.e., RNA-dependent RNA polymerase). Here, we describe a new source of potyvirus resistance in the Guatemalan accession C. annuum cv. PM949. PM949 is resistant to members of at least three potyvirus species, a subset of those controlled by Pvr4. The F1 progeny between PM949 and the susceptible cultivar Yolo Wonder was susceptible to PVY, indicating that the resistance is recessive. The segregation ratio between resistant and susceptible plants observed in the F2 progeny matched preferably with resistance being determined by two unlinked recessive genes independently conferring resistance to PVY. Inoculations by grafting resulted in the selection of PVY mutants breaking PM949 resistance and, less efficiently, Pvr4-mediated resistance. The codon substitution E472K in the NIb cistron of PVY, which was shown previously to be sufficient to break Pvr4 resistance, was also sufficient to break PM949 resistance, a rare example of cross-pathogenicity effect. In contrast, the other selected NIb mutants showed specific infectivity in PM949 or Pvr4 plants. Comparison of Pvr4 and PM949 resistance, which share the same target in PVY, provides interesting insights into the determinants of resistance durability.
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Affiliation(s)
- Benoît Moury
- INRAE, Pathologie Végétale, 84140 Montfavet, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, CS 20032, 33882 Villenave d'Ornon, France
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46
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Sayan M, Arikan A, Sanlidag E. Molecular Epidemiology of SARS-CoV-2 Omicron Sub-Lineages Isolated from Turkish Patients Infected with COVID-19. Viruses 2023; 15:v15051066. [PMID: 37243152 DOI: 10.3390/v15051066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral resistance of RdRp and 3CLpro inhibitors. The Stanford University Coronavirus Antiviral & Resistance Database online tool was used for variant analyses of the strains uploaded to GISAID as Omicron (n = 20.959) between January 2021 and February,2023. Out of 288 different Omicron subvariants, B.1, BA.1, BA.2, BA.4, BE.1, BF.1, BM.1, BN.1, BQ.1, CK.1, CL.1, and XBB.1 were the main determined subvariants, and BA.1 (34.7%), BA.2 (30.8%), and BA.5 (23.6%) were reported most frequently. RdRp and 3CLPro-related resistance mutations were determined in n = 150, 0.72% sequences, while the rates of resistance against RdRp and 3CLpro inhibitors were reported at 0.1% and 0.6%, respectively. Mutations that were previously associated with a reduced susceptibility to remdesivir, nirmatrelvir/r, and ensitrelvir were most frequently detected in BA.2 (51.3%). The mutations detected at the highest rate were A449A/D/G/V (10.5%), T21I (10%), and L50L/F/I/V (6%). Our findings suggest that continuous monitoring of variants, due to the diversity of Omicron lineages, is necessary for global risk assessment. Although drug-resistant mutations do not pose a threat, the tracking of drug mutations will be necessary due to variant heterogenicity.
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Affiliation(s)
- Murat Sayan
- PCR Unit, Research, and Education Hospital, Faculty of Medicine, Kocaeli University, Kocaeli 41380, Turkey
- DESAM Research Institute, Near East University, Nicosia 99138, Cyprus
| | - Ayse Arikan
- DESAM Research Institute, Near East University, Nicosia 99138, Cyprus
- Department of Medical Microbiology and Clinical Microbiology, Near East University, Nicosia 99138, Cyprus
- Department of Medical Microbiology and Clinical Microbiology, Kyrenia University, Kyrenia 99320, Cyprus
| | - Erdal Sanlidag
- DESAM Research Institute, Near East University, Nicosia 99138, Cyprus
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47
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Roy BG, DeBlasio S, Yang Y, Thannhauser T, Heck M, Fuchs M. Profiling Plant Proteome and Transcriptome Changes during Grapevine Fanleaf Virus Infection. J Proteome Res 2023. [PMID: 37099450 DOI: 10.1021/acs.jproteome.3c00069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Viruses can elicit varying types and severities of symptoms during plant host infection. We investigated changes in the proteome and transcriptome of Nicotiana benthamiana plants infected by grapevine fanleaf virus (GFLV) with an emphasis on vein clearing symptom development. Comparative, time-course liquid chromatography tandem mass spectrometry and 3' ribonucleic acid sequencing analyses of plants infected by two wildtype GFLV strains, one symptomatic and one asymptomatic, and their asymptomatic mutant strains carrying a single amino acid change in the RNA-dependent RNA polymerase (RdRP) were conducted to identify host biochemical pathways involved in viral symptom development. During peak vein clearing symptom display at 7 days post-inoculation (dpi), protein and gene ontologies related to immune response, gene regulation, and secondary metabolite production were overrepresented when contrasting wildtype GFLV strain GHu and mutant GHu-1EK802GPol. Prior to the onset of symptom development at 4 dpi and when symptoms faded away at 12 dpi, protein and gene ontologies related to chitinase activity, hypersensitive response, and transcriptional regulation were identified. This systems biology approach highlighted how a single amino acid of a plant viral RdRP mediates changes to the host proteome (∼1%) and transcriptome (∼8.5%) related to transient vein clearing symptoms and the network of pathways involved in the virus-host arms race.
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Affiliation(s)
- Brandon G Roy
- Plant Pathology and Plant-Microbe Biology Section, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, New York 14456, United States
| | - Stacy DeBlasio
- Emerging Pests and Pathogens Research Unit, United States Department of Agriculture─Agricultural Research Service, Ithaca, New York 14853, United States
| | - Yong Yang
- Emerging Pests and Pathogens Research Unit, United States Department of Agriculture─Agricultural Research Service, Ithaca, New York 14853, United States
| | - Theodore Thannhauser
- Emerging Pests and Pathogens Research Unit, United States Department of Agriculture─Agricultural Research Service, Ithaca, New York 14853, United States
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, United States Department of Agriculture─Agricultural Research Service, Ithaca, New York 14853, United States
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, United States
| | - Marc Fuchs
- Plant Pathology and Plant-Microbe Biology Section, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, New York 14456, United States
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48
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Apostle A, Yin Y, Chillar K, Eriyagama AMDN, Arneson R, Burke E, Fang S, Yuan Y. Effects of Epitranscriptomic RNA Modifications on the Catalytic Activity of the SARS-CoV-2 Replication Complex. Chembiochem 2023; 24:e202300095. [PMID: 36752976 PMCID: PMC10121919 DOI: 10.1002/cbic.202300095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 causes individualized symptoms. Many reasons have been given. We propose that an individual's epitranscriptomic system could be responsible as well. The viral RNA genome can be subject to epitranscriptomic modifications, which can be different for different individuals, and thus epitranscriptomics can affect many events including RNA replication differently. In this context, we studied the effects of modifications including pseudouridine (Ψ), 5-methylcytosine (m5 C), N6-methyladenosine (m6 A), N1-methyladenosine (m1 A) and N3-methylcytosine (m3 C) on the activity of SARS-CoV-2 replication complex (SC2RC). We found that Ψ, m5 C, m6 A and m3 C had little effect, whereas m1 A inhibited the enzyme. Both m1 A and m3 C disrupt canonical base pairing, but they had different effects. The fact that m1 A inhibits SC2RC implies that the modification can be difficult to detect. This fact also implies that individuals with upregulated m1 A including cancer, obesity and diabetes patients might have milder symptoms. However, this contradicts clinical observations. Relevant discussions are provided.
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Affiliation(s)
- Alexander Apostle
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Yipeng Yin
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Komal Chillar
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Adikari M D N Eriyagama
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Reed Arneson
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Emma Burke
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Shiyue Fang
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Yinan Yuan
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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49
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Metwally K, Abo-Dya NE, Alahmdi MI, Albalawi MZ, Yahya G, Aljoundi A, Salifu EY, Elamin G, Ibrahim MAA, Sayed Y, Fanucchi S, Soliman MES. The Unusual Architecture of RNA-Dependent RNA Polymerase (RdRp)'s Catalytic Chamber Provides a Potential Strategy for Combination Therapy against COVID-19. Molecules 2023; 28:molecules28062806. [PMID: 36985777 PMCID: PMC10057333 DOI: 10.3390/molecules28062806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The unusual and interesting architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) was recently explored using Cryogenic Electron Microscopy (Cryo-EM), which revealed the presence of two distinctive binding cavities within the catalytic chamber. In this report, first, we mapped out and fully characterized the variations between the two binding sites, BS1 and BS2, for significant differences in their amino acid architecture, size, volume, and hydrophobicity. This was followed by investigating the preferential binding of eight antiviral agents to each of the two binding sites, BS1 and BS2, to understand the fundamental factors that govern the preferential binding of each drug to each binding site. Results showed that, in general, hydrophobic drugs, such as remdesivir and sofosbuvir, bind better to both binding sites than relatively less hydrophobic drugs, such as alovudine, molnupiravir, zidovudine, favilavir, and ribavirin. However, suramin, which is a highly hydrophobic drug, unexpectedly showed overall weaker binding affinities in both binding sites when compared to other drugs. This unexpected observation may be attributed to its high binding solvation energy, which disfavors overall binding of suramin in both binding sites. On the other hand, hydrophobic drugs displayed higher binding affinities towards BS1 due to its higher hydrophobic architecture when compared to BS2, while less hydrophobic drugs did not show a significant difference in binding affinities in both binding sites. Analysis of binding energy contributions revealed that the most favorable components are the ΔEele, ΔEvdw, and ΔGgas, whereas ΔGsol was unfavorable. The ΔEele and ΔGgas for hydrophobic drugs were enough to balance the unfavorable ΔGsol, leaving the ΔEvdw to be the most determining factor of the total binding energy. The information presented in this report will provide guidelines for tailoring SARS-CoV-2 inhibitors with enhanced binding profiles.
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Affiliation(s)
- Kamel Metwally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Nader E Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Mohammed Issa Alahmdi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Maha Z Albalawi
- Pharm D Program, Faculty of Pharmacy, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Aimen Aljoundi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Elliasu Y Salifu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Ghazi Elamin
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud A A Ibrahim
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
- CompChem Lab, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Sylvia Fanucchi
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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50
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McCollum C, Courtney CM, O’Connor NJ, Aunins TR, Jordan TX, Rogers KL, Brindley S, Brown JM, Nagpal P, Chatterjee A. Safety and Biodistribution of Nanoligomers Targeting the SARS-CoV-2 Genome for the Treatment of COVID-19. ACS Biomater Sci Eng 2023; 9:1656-1671. [PMID: 36853144 PMCID: PMC10000012 DOI: 10.1021/acsbiomaterials.2c00669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023]
Abstract
As the world braces to enter its fourth year of the coronavirus disease 2019 (COVID-19) pandemic, the need for accessible and effective antiviral therapeutics continues to be felt globally. The recent surge of Omicron variant cases has demonstrated that vaccination and prevention alone cannot quell the spread of highly transmissible variants. A safe and nontoxic therapeutic with an adaptable design to respond to the emergence of new variants is critical for transitioning to the treatment of COVID-19 as an endemic disease. Here, we present a novel compound, called SBCoV202, that specifically and tightly binds the translation initiation site of RNA-dependent RNA polymerase within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome, inhibiting viral replication. SBCoV202 is a Nanoligomer, a molecule that includes peptide nucleic acid sequences capable of binding viral RNA with single-base-pair specificity to accurately target the viral genome. The compound has been shown to be safe and nontoxic in mice, with favorable biodistribution, and has shown efficacy against SARS-CoV-2 in vitro. Safety and biodistribution were assessed using three separate administration methods, namely, intranasal, intravenous, and intraperitoneal. Safety studies showed the Nanoligomer caused no outward distress, immunogenicity, or organ tissue damage, measured through observation of behavior and body weight, serum levels of cytokines, and histopathology of fixed tissue, respectively. SBCoV202 was evenly biodistributed throughout the body, with most tissues measuring Nanoligomer concentrations well above the compound KD of 3.37 nM. In addition to favorable availability to organs such as the lungs, lymph nodes, liver, and spleen, the compound circulated through the blood and was rapidly cleared through the renal and urinary systems. The favorable biodistribution and lack of immunogenicity and toxicity set Nanoligomers apart from other antisense therapies, while the adaptability of the nucleic acid sequence of Nanoligomers provides a defense against future emergence of drug resistance, making these molecules an attractive potential treatment for COVID-19.
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Affiliation(s)
- Colleen
R. McCollum
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Colleen M. Courtney
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Sachi Bio, Colorado Technology Center, Louisville, Colorado 80027, United States
| | - Nolan J. O’Connor
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Thomas R. Aunins
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Tristan X. Jordan
- Department
of Microbiology, New York University Langone, New York, New York 10016, United States
| | - Keegan L. Rogers
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Stephen Brindley
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Jared M. Brown
- Department
of Pharmaceutical Sciences, University of
Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Prashant Nagpal
- Sachi Bio, Colorado Technology Center, Louisville, Colorado 80027, United States
- Antimicrobial
Regeneration Consortium Labs, Louisville, Colorado 80027, United States
| | - Anushree Chatterjee
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
- Sachi Bio, Colorado Technology Center, Louisville, Colorado 80027, United States
- Antimicrobial
Regeneration Consortium Labs, Louisville, Colorado 80027, United States
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