1
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Tsukamoto Y, Igarashi M, Kato H. Targeting cap1 RNA methyltransferases as an antiviral strategy. Cell Chem Biol 2024; 31:86-99. [PMID: 38091983 DOI: 10.1016/j.chembiol.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/30/2023] [Accepted: 11/20/2023] [Indexed: 01/21/2024]
Abstract
Methylation is one of the critical modifications that regulates numerous biological processes. Guanine capping and methylation at the 7th position (m7G) have been shown to mature mRNA for increased RNA stability and translational efficiency. The m7G capped cap0 RNA remains immature and requires additional methylation at the first nucleotide (N1-2'-O-Me), designated as cap1, to achieve full maturation. This cap1 RNA with N1-2'-O-Me prevents its recognition by innate immune sensors as non-self. Viruses have also evolved various strategies to produce self-like capped RNAs with the N1-2'-O-Me that potentially evades the antiviral response and establishes an efficient replication. In this review, we focus on the importance of the presence of N1-2'-O-Me in viral RNAs and discuss the potential for drug development by targeting host and viral N1-2'-O-methyltransferases.
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Affiliation(s)
- Yuta Tsukamoto
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany.
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2
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Derewenda ZS. C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids. Int J Mol Sci 2023; 24:13165. [PMID: 37685972 PMCID: PMC10488043 DOI: 10.3390/ijms241713165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
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Affiliation(s)
- Zygmunt Stanislaw Derewenda
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903-2628, USA
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3
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Wu J, Ye HQ, Zhang QY, Lu G, Zhang B, Gong P. A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase. PLoS Pathog 2020; 16:e1008484. [PMID: 32357182 PMCID: PMC7219791 DOI: 10.1371/journal.ppat.1008484] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/13/2020] [Accepted: 03/18/2020] [Indexed: 12/26/2022] Open
Abstract
The flaviviruses pose serious threats to human health. Being a natural fusion of a methyltransferase (MTase) and an RNA-dependent RNA polymerase (RdRP), NS5 is the most conserved flavivirus protein and an important antiviral target. Previously reported NS5 structures represented by those from the Japanese encephalitis virus (JEV) and Dengue virus serotype 3 (DENV3) exhibit two apparently different global conformations, defining two sets of intra-molecular MTase-RdRP interactions. However, whether these NS5 conformations are conserved in flaviviruses and their specific functions remain elusive. Here we report two forms of DENV serotype 2 (DENV2) NS5 crystal structures representing two conformational states with defined analogies to the JEV-mode and DENV3-mode conformations, respectively, demonstrating the conservation of both conformation modes and providing clues for how different conformational states may be interconnected. Data from in vitro polymerase assays further demonstrate that perturbing the JEV-mode but not the DENV3-mode intra-molecular interactions inhibits catalysis only at initiation, while the cell-based virological analysis suggests that both modes of interactions are important for virus proliferation. Our work highlights the role of MTase as a unique intra-molecular initiation factor specifically only through the JEV-mode conformation, providing an example of conformation-based crosstalk between naturally fused protein functional modules.
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Affiliation(s)
- Jiqin Wu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Han-Qing Ye
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiu-Yan Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zhang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
- Drug Discovery Center for Infectious Diseases, Nankai University, Tianjin, China
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4
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Gao X, Zhu K, Wojdyla JA, Chen P, Qin B, Li Z, Wang M, Cui S. Crystal structure of the NS3-like helicase from Alongshan virus. IUCRJ 2020; 7:375-382. [PMID: 32431821 PMCID: PMC7201283 DOI: 10.1107/s2052252520003632] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/11/2020] [Indexed: 05/05/2023]
Abstract
Alongshan virus (ALSV) is an emerging human pathogen that was identified in China and rapidly spread to the European continent in 2019, raising concerns about public health. ALSV belongs to the distinct Jingmenvirus group within the Flaviviridae family with segmented RNA genomes. While segments 2 and 4 of the ALSV genome encode the VP1-VP3 proteins of unknown origin, segments 1 and 3 encode the NS2b-NS3 and NS5 proteins, which are related to Flavivirus nonstructural proteins, suggesting an evolutionary link between segmented and unsegmented viruses within the Flaviviridae family. Here, the enzymatic activity of the ALSV NS3-like helicase (NS3-Hel) was characterized and its crystal structure was determined to 2.9 Å resolution. ALSV NS3-Hel exhibits an ATPase activity that is comparable to those measured for Flavivirus NS3 helicases. The structure of ALSV NS3-Hel exhibits an overall fold similar to those of Flavivirus NS3 helicases. Despite the limited amino-acid sequence identity between ALSV NS3-Hel and Flavivirus NS3 helicases, structural features at the ATPase active site and the RNA-binding groove remain conserved in ALSV NS3-Hel. These findings provide a structural framework for drug design and suggest the possibility of developing a broad-spectrum antiviral drug against both Flavivirus and Jingmenvirus.
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Affiliation(s)
- Xiaopan Gao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Kaixiang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | | | - Pu Chen
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Bo Qin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Ziheng Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
| | - Meitian Wang
- Swiss Light Source at the Paul Scherrer Institute, CH-5232 Villigen, Switzerland
| | - Sheng Cui
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People’s Republic of China
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5
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Abstract
Zika virus (ZIKV) was once considered an obscure member of the large and diverse family of mosquito-borne flaviviruses, and human infections with ZIKV were thought to be sporadic, with mild and self-limiting symptoms. The large-scale ZIKV epidemics in the Americas and the unexpected uncovering of a link to congenital birth defects escalated ZIKV infections to the status of a global public health emergency. Recent studies that combined reverse genetics with modelling in multiple systems have provided evidence that ZIKV has acquired additional amino acid substitutions at the same time as congenital Zika syndrome and other birth defects were detected. In this Progress article, we summarize the evolution of ZIKV during its spread from Asia to the Americas and discuss potential links to pathogenesis.
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Sariyer IK, Gordon J, Burdo TH, Wollebo HS, Gianti E, Donadoni M, Bellizzi A, Cicalese S, Loomis R, Robinson JA, Carnevale V, Steiner J, Ozdener MH, Miller AD, Amini S, Klein ML, Khalili K. Suppression of Zika Virus Infection in the Brain by the Antiretroviral Drug Rilpivirine. Mol Ther 2019; 27:2067-2079. [PMID: 31653397 DOI: 10.1016/j.ymthe.2019.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 01/02/2023] Open
Abstract
Zika virus (ZIKV) infection is associated with microcephaly in neonates and Guillain-Barré syndrome in adults. ZIKV produces a class of nonstructural (NS) regulatory proteins that play a critical role in viral transcription and replication, including NS5, which possesses RNA-dependent RNA polymerase (RdRp) activity. Here we demonstrate that rilpivirine (RPV), a non-nucleoside reverse transcriptase inhibitor (NNRTI) used in the treatment of HIV-1 infection, inhibits the enzymatic activity of NS5 and suppresses ZIKV infection and replication in primary human astrocytes. Similarly, other members of the NNRTI family, including etravirine and efavirenz, showed inhibitory effects on viral infection of brain cells. Site-directed mutagenesis identified 14 amino acid residues within the NS5 RdRp domain (AA265-903), which are important for the RPV interaction and the inhibition of NS5 polymerase activity. Administration of RPV to ZIKV-infected interferon-alpha/beta receptor (IFN-A/R) knockout mice improved the clinical outcome and prevented ZIKV-induced mortality. Histopathological examination of the brains from infected animals revealed that RPV reduced ZIKV RNA levels in the hippocampus, frontal cortex, thalamus, and cerebellum. Repurposing of NNRTIs, such as RPV, for the inhibition of ZIKV replication offers a possible therapeutic strategy for the prevention and treatment of ZIKV-associated disease.
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Affiliation(s)
- Ilker Kudret Sariyer
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Jennifer Gordon
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Tricia H Burdo
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Hassen S Wollebo
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Eleonora Gianti
- Department of Chemistry, Institute for Computational Molecular Science, College of Science and Technology, Temple University, 1901 N. 12(th) Street, Philadelphia, PA 19122, USA
| | - Martina Donadoni
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Anna Bellizzi
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Stephanie Cicalese
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Regina Loomis
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Jake A Robinson
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Vincenzo Carnevale
- Department of Chemistry, Institute for Computational Molecular Science, College of Science and Technology, Temple University, 1901 N. 12(th) Street, Philadelphia, PA 19122, USA
| | - Joseph Steiner
- Translational Neuroscience Center, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Mehmet H Ozdener
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA
| | - Andrew D Miller
- College of Veterinary Medicine, Cornell University, T5-006A Veterinary Research Tower, Ithaca, NY 14853, USA
| | - Shohreh Amini
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA
| | - Michael L Klein
- Department of Chemistry, Institute for Computational Molecular Science, College of Science and Technology, Temple University, 1901 N. 12(th) Street, Philadelphia, PA 19122, USA
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA.
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7
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Hu Y, Sun L. Systematic Analysis of Structure Similarity between Zika Virus and Other Flaviviruses. ACS Infect Dis 2019; 5:1070-1080. [PMID: 31038920 DOI: 10.1021/acsinfecdis.9b00047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Zika virus (ZIKV) infection has caused global concern because of its association with fetal microcephaly and serious neurological complications in adults since 2016. Currently, no specific anti-ZIKV therapy is available to control ZIKV infection. During the last couple of years, the intensive investigation of ZIKV structure has provided significant information for structure-based vaccine and drug design. In this review, we summarized the research progress on the structures of ZIKV and its component proteins. We analyzed the structure identity and the differences between ZIKV and other flaviviruses. This information is crucial to guiding structure-based anti-ZIKV inhibitors and vaccine discovery.
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Affiliation(s)
- Yuxia Hu
- The Fifth People’s Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 20032, China
| | - Lei Sun
- The Fifth People’s Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, 131 Dongan Road, Shanghai 20032, China
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8
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Fang J, Jing X, Lu G, Xu Y, Gong P. Crystallographic Snapshots of the Zika Virus NS3 Helicase Help Visualize the Reactant Water Replenishment. ACS Infect Dis 2019; 5:177-183. [PMID: 30672289 DOI: 10.1021/acsinfecdis.8b00214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Zika virus (ZIKV), a positive-strand RNA virus belonging to the Flavivirus genus, has become an urgent public health concern since recent outbreaks worldwide. Its genome replication is facilitated by the viral NS3 protein bearing helicase function. The NS3 helicase uses energy derived from adenosine triphosphate (ATP) hydrolysis to unwind RNA duplexed regions. Structural studies of the flavivirus NS3 helicases have suggested a conserved mechanism of ATP hydrolysis. However, the process of the reactant water replenishment, a key part of the hydrolysis cycle, remains elusive. Here, we report two high-resolution crystal structures of ZIKV NS3 helicase in complex with adenosine diphosphate (ADP) and Mn2+, one with the reactant water already loaded as previously observed and the other with the water molecule still in a loading state. These data suggest that the reactant water replenishment can occur between the release of phosphate and the release of ADP and improves the structural basis of the NS3 ATP hydrolysis cycle.
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Affiliation(s)
- Junnan Fang
- The Joint Center of Translational
Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women
and Children’s Medical Center, No. 318 Renminzhonglu, Guangzhou, Guangdong 510623, China
- The Joint Center of Translational Precision Medicine, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei, 430071, China
| | - Xuping Jing
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Xu
- The Joint Center of Translational
Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women
and Children’s Medical Center, No. 318 Renminzhonglu, Guangzhou, Guangdong 510623, China
- The Joint Center of Translational Precision Medicine, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei, 430071, China
| | - Peng Gong
- The Joint Center of Translational
Precision Medicine, Guangzhou Institute of Pediatrics, Guangzhou Women
and Children’s Medical Center, No. 318 Renminzhonglu, Guangzhou, Guangdong 510623, China
- The Joint Center of Translational Precision Medicine, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei, 430071, China
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, No. 44 Xiao Hong Shan, Wuhan, Hubei 430071, China
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