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Miura K, Suzuki Y, Ishida K, Arakawa M, Wu H, Fujioka Y, Emi A, Maeda K, Hamajima R, Nakano T, Tenno T, Hiroaki H, Morita E. Distinct motifs in the E protein are required for SARS-CoV-2 virus particle formation and lysosomal deacidification in host cells. J Virol 2023; 97:e0042623. [PMID: 37830820 PMCID: PMC10617393 DOI: 10.1128/jvi.00426-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has caused a global public health crisis. The E protein, a structural protein found in this virus particle, is also known to be a viroporin. As such, it forms oligomeric ion channels or pores in the host cell membrane. However, the relationship between these two functions is poorly understood. In this study, we showed that the roles of E protein in virus particle and viroporin formation are distinct. This study contributes to the development of drugs that inhibit SARS-CoV-2 virus particle formation. Additionally, we designed a highly sensitive and high-throughput virus-like particle detection system using the HiBiT tag, which is a useful tool for studying the release of SARS-CoV-2.
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Affiliation(s)
- Koya Miura
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kotaro Ishida
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Masashi Arakawa
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Yoshihiko Fujioka
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Akino Emi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Koki Maeda
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
| | - Ryusei Hamajima
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Takeshi Tenno
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Aichi, Japan
- BeCellBar LLC, Nagoya, Aichi, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
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2
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Bai C, Zhong Q, Gao GF. Overview of SARS-CoV-2 genome-encoded proteins. SCIENCE CHINA-LIFE SCIENCES 2021; 65:280-294. [PMID: 34387838 PMCID: PMC8362648 DOI: 10.1007/s11427-021-1964-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) has spread rapidly throughout the world. SARS-CoV-2 is an enveloped, plus-stranded RNA virus with a single-stranded RNA genome of approximately 30,000 nucleotides. The SARS-CoV-2 genome encodes 29 proteins, including 16 nonstructural, 4 structural and 9 accessory proteins. To date, over 1,228 experimental structures of SARS-CoV-2 proteins have been deposited in the Protein Data Bank (PDB), including 16 protein structures, two functional domain structures of nucleocapsid (N) protein, and scores of complexes. Overall, they exhibit high similarity to SARS-CoV proteins. Here, we summarize the progress of structural and functional research on SARS-CoV-2 proteins. These studies provide structural and functional insights into proteins of SARS-CoV-2, and further elucidate the daedal relationship between different components at the atomic level in the viral life cycle, including attachment to the host cell, viral genome replication and transcription, genome packaging and assembly, and virus release. It is important to understand the structural and functional properties of SARS-CoV-2 proteins as it will facilitate the development of anti-CoV drugs and vaccines to prevent and control the current SARS-CoV-2 pandemic.
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Affiliation(s)
- Chongzhi Bai
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Central Laboratory, Shanxi Province Hospital of Traditional Chinese Medicine, Taiyuan, 030012, China.,Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China
| | - Qiming Zhong
- Central Laboratory, Shanxi Province Hospital of Traditional Chinese Medicine, Taiyuan, 030012, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,Shanxi Academy of Advanced Research and Innovation, Taiyuan, 030032, China.
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3
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Grant SN, Lester HA. Regulation of epithelial sodium channel activity by SARS-CoV-1 and SARS-CoV-2 proteins. Biophys J 2021; 120:2805-2813. [PMID: 34197807 PMCID: PMC8238646 DOI: 10.1016/j.bpj.2021.06.005] [Citation(s) in RCA: 18] [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: 12/15/2020] [Revised: 04/21/2021] [Accepted: 06/03/2021] [Indexed: 01/06/2023] Open
Abstract
Severe acute respiratory syndrome (SARS) coronavirus (CoV) 2 (SARS-CoV-2), which causes the coronavirus disease 2019, encodes several proteins whose roles are poorly understood. We tested their ability either to directly form plasma membrane ion channels or to change functions of two mammalian plasma membrane ion channels, the epithelial sodium channel (ENaC) and the α3β4 nicotinic acetylcholine receptor. In mRNA-injected Xenopus oocytes, none of nine SARS-CoV-2 proteins or two SARS-CoV-1 proteins produced conductances, nor did co-injection of several combinations. Immunoblots for ORF8, spike (S), and envelope (E) proteins revealed that the proteins are expressed at appropriate molecular weights. In experiments on coexpression with ENaC, three tested SARS proteins (SARS-CoV-1 E, SARS-CoV-2 E, and SARS-CoV-2 S) markedly decrease ENaC currents. SARS-CoV-1 S protein decreases ENaC currents modestly. Coexpressing the E proteins but not the S proteins with α3β4 nicotinic acetylcholine receptors significantly reduces acetylcholine-induced currents. ENaC inhibition does not occur if the SARS-CoV protein mRNAs are injected 24 h after the ENaC mRNAs, suggesting that SARS-CoV proteins affect early step(s) in functional expression of channel proteins. Consistent with the hypothesis that the SARS-CoV-2 S protein-induced ENaC inhibition involves competition for available protease, mutating the furin cleavage site in SARS-CoV-2 S protein partially relieves inhibition of ENaC currents. Extending previous suggestions that SARS proteins affect ENaC currents via protein kinase C (PKC) activation, PKC activation via phorbol 12-myristate 13-acetate decreases ENaC and α3β4 activity. Phorbol 12-myristate 13-acetate application reduced membrane capacitance ∼5%, presumably via increased endocytosis, but this decrease is much smaller than the SARS proteins' effects on conductances. Also, incubating oocytes in Gö-6976, a PKCα and PKCβ inhibitor, did not alter E or S protein-induced channel inhibition. We conclude that SARS-CoV-1 and SARS-CoV-2 proteins alter the function of human plasma membrane channels, via incompletely understood mechanisms. These interactions may play a role in the coronavirus 2019 pathophysiology.
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Affiliation(s)
- Stephen N Grant
- Division of Chemistry and Chemical Engineering, Pasadena, California
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
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4
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Danladi J, Sabir H. Innate immunity, inflammation activation and heat-shock protein in COVID-19 pathogenesis. J Neuroimmunol 2021; 358:577632. [PMID: 34186336 PMCID: PMC8196476 DOI: 10.1016/j.jneuroim.2021.577632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/22/2021] [Accepted: 06/10/2021] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2-induced COVID-19 is a serious pandemic of the 21st century, which has caused a devastating loss of lives and a global economic catastrophe. A successful vaccine against SARS-CoV-2 has suffered a delay due to lack of substantial knowledge about its mechanisms of action. Understanding the innate immune system against SARS-CoV-2 and the role of heat shock proteins' (HSP) inhibiting and resolution of inflammatory pathways may provide information to the low SARS-CoV-2 mortality rates in Africa. In addition, bats being a host to different viruses, including SARS-CoV-2 possess a well specialized IFN-innate antiviral inflammatory response, showing no signs of disease or pro-inflammatory cytokine storm. We discuss the molecular pathways in COVID-19 with a focus on innate immunity, inflammation, HSP responses, and suggest appropriate candidates for therapeutic targets and The contribution of the innate immune system to the efficacy of mRNA or vector based Corona immunizations.
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Affiliation(s)
- Jibrin Danladi
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
| | - Hemmen Sabir
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
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5
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Cao Y, Yang R, Lee I, Zhang W, Sun J, Wang W, Meng X. Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors. Protein Sci 2021; 30:1114-1130. [PMID: 33813796 PMCID: PMC8138525 DOI: 10.1002/pro.4075] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
The COVID-19 epidemic is one of the most influential epidemics in history. Understanding the impact of coronaviruses (CoVs) on host cells is very important for disease treatment. The SARS-CoV-2 envelope (E) protein is a small structural protein involved in many aspects of the viral life cycle. The E protein promotes the packaging and reproduction of the virus, and deletion of this protein weakens or even abolishes the virulence. This review aims to establish new knowledge by combining recent advances in the study of the SARS-CoV-2 E protein and by comparing it with the SARS-CoV E protein. The E protein amino acid sequence, structure, self-assembly characteristics, viroporin mechanisms and inhibitors are summarized and analyzed herein. Although the mechanisms of the SARS-CoV-2 and SARS-CoV E proteins are similar in many respects, specific studies on the SARS-CoV-2 E protein, for both monomers and oligomers, are still lacking. A comprehensive understanding of this protein should prompt further studies on the design and characterization of effective targeted therapeutic measures.
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Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
| | - Rui Yang
- Department of Infection and ImmunityTianjin Union Medical Center, Nankai University Affiliated HospitalTianjinPeople's Republic of China
| | - Imshik Lee
- College of PhysicsNankai UniversityTianjinPeople's Republic of China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Xiangfei Meng
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
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6
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Chen DZ, Fan SR, Yang BJ, Yao HC, Wang YT, Cai JY, Jing CX, Pan ZH, Luo M, Yuze YQ, Liu GJ, Hao XJ. Phenanthridine Derivative Host Heat Shock Cognate 70 Down-Regulators as Porcine Epidemic Diarrhea Virus Inhibitors. JOURNAL OF NATURAL PRODUCTS 2021; 84:1175-1184. [PMID: 33760626 DOI: 10.1021/acs.jnatprod.0c01252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) has become increasingly problematic around the world, not only for its hazards to livestock but also due to the possibility that it is a zoonotic disease. Although vaccine therapy has made some progress toward PEDV control, additional effective therapeutic strategies against PEDV are needed, such as the development of chemotherapeutic agents. The aim of this work was to identify novel anti-PEDV agents by designing and synthesizing a series of phenanthridine derivatives. Among them, three compounds (compounds 1, 2, and 4) were identified as potent anti-PEDV agents exhibiting suppression of host cell heat shock cognate 70 (Hsc70) expression. Mechanism studies revealed that host Hsc70 is involved in the replication of PEDV, and its expression can be suppressed by destabilization of the mRNA, resulting in inhibition of PEDV replication. Activity against PEDV in vivo in PEDV-infected piglets suggested that phenanthridine derivatives are the first host-acting potential anti-PEDV agents.
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Affiliation(s)
- Duo-Zhi Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Shi-Rui Fan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Bi-Juan Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Huo-Chun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yi-Ting Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jie-Yun Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Chen-Xu Jing
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Zi-Hao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Miao Luo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Yan-Qiu Yuze
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Guang-Jin Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiao-Jiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
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7
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Das G, Das T, Chowdhury N, Chatterjee D, Bagchi A, Ghosh Z. Repurposed drugs and nutraceuticals targeting envelope protein: A possible therapeutic strategy against COVID-19. Genomics 2020; 113:1129-1140. [PMID: 33189776 PMCID: PMC7661923 DOI: 10.1016/j.ygeno.2020.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/06/2020] [Accepted: 11/09/2020] [Indexed: 01/25/2023]
Abstract
COVID-19 pandemic caused by SARS-CoV-2 has already claimed millions of lives worldwide due to the absence of a suitable anti-viral therapy. The CoV envelope (E) protein, which has not received much attention so far, is a 75 amino acid long integral membrane protein involved in assembly and release of the virus inside the host. Here we have used artificial intelligence (AI) and pattern recognition techniques for initial screening of FDA approved pharmaceuticals and nutraceuticals to target this E protein. Subsequently, molecular docking simulations have been performed between the ligands and target protein to screen a set of 9 ligand molecules. Finally, we have provided detailed insight into their mechanisms of action related to the varied symptoms of infected patients.
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Affiliation(s)
- Gourab Das
- Division of Bioinformatics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700 054, India.
| | - Troyee Das
- Division of Bioinformatics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700 054, India.
| | - Nilkanta Chowdhury
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India.
| | - Durbadal Chatterjee
- Division of Bioinformatics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700 054, India.
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India.
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700 054, India.
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8
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Dey D, Borkotoky S, Banerjee M. In silico identification of Tretinoin as a SARS-CoV-2 envelope (E) protein ion channel inhibitor. Comput Biol Med 2020; 127:104063. [PMID: 33126128 PMCID: PMC7574788 DOI: 10.1016/j.compbiomed.2020.104063] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/25/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Viroporins are oligomeric, pore forming, viral proteins that play critical roles in the life cycle of pathogenic viruses. Viroporins like HIV-1 Vpu, Alphavirus 6 K, Influenza M2, HCV p7, and Picornavirus 2B, form discrete aqueous passageways which mediate ion and small molecule transport in infected cells. The alterations in host membrane structures induced by viroporins is essential for key steps in the virus life cycle like entry, replication and egress. Any disruption in viroporin functionality severely compromises viral pathogenesis. The envelope (E) protein encoded by coronaviruses is a viroporin with ion channel activity and has been shown to be crucial for the assembly and pathophysiology of coronaviruses. We used a combination of virtual database screening, molecular docking, all-atom molecular dynamics simulation and MM-PBSA analysis to test four FDA approved drugs - Tretinoin, Mefenamic Acid, Ondansetron and Artemether - as potential inhibitors of ion channels formed by SARS-CoV-2 E protein. Interaction and binding energy analysis showed that electrostatic interactions and polar solvation energy were the major driving forces for binding of the drugs, with Tretinoin being the most promising inhibitor. Tretinoin bound within the lumen of the channel formed by E protein, which is lined by hydrophobic residues like Phe, Val and Ala, indicating its potential for blocking the channel and inhibiting the viroporin functionality of E. In control simulations, tretinoin demonstrated a lower binding energy with a known target as compared to SARS-CoV-2 E protein. This work thus highlights the possibility of exploring Tretinoin as a potential SARS-CoV-2 E protein ion channel blocker and virus assembly inhibitor, which could be an important therapeutic strategy in the treatment for coronaviruses. Screened a database of 1806 small molecule compounds from DrugBank for potential SARS CoV-2 E protein inhibitors. Tested four FDA-approved drugs Tetinoin, Mefenamic acid, Ondansetron and Artemether as SARS CoV-2 E protein inhibitors. Used a combination of molecular docking, MD simulations and MM-PBSA analysis to propose Tretinoin as a promising inhibitor.
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Affiliation(s)
- Debajit Dey
- School of Medicine, University of Maryland Baltimore, United States
| | - Subhomoi Borkotoky
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India.
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9
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McClenaghan C, Hanson A, Lee SJ, Nichols CG. Coronavirus Proteins as Ion Channels: Current and Potential Research. Front Immunol 2020; 11:573339. [PMID: 33154751 PMCID: PMC7586316 DOI: 10.3389/fimmu.2020.573339] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/22/2020] [Indexed: 01/22/2023] Open
Abstract
Coronavirus (CoV) outbreaks have recently emerged as a global public health threat due to their exceptional zoonotic potential — a feature arising from their ability to infect a diverse range of potential hosts combined with their high capacity for mutation and recombination. After Severe Acute Respiratory Syndrome (SARS) CoV-1 in 2003 and Middle East Respiratory Syndrome (MERS) CoV in 2012, with the current SARS-CoV-2 pandemic we are now in the midst of the third deadly international CoV outbreak in less than 20 years. Coronavirus outbreaks present a critical threat to global public health and an urgent necessity for therapeutic options. Here, we critically examine the current evidence for ion channel activity in CoV proteins and the potential for modulation as a therapeutic approach.
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Affiliation(s)
- Conor McClenaghan
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Alex Hanson
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Sun-Joo Lee
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Colin G Nichols
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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10
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Senger MR, Evangelista TCS, Dantas RF, Santana MVDS, Gonçalves LCS, de Souza Neto LR, Ferreira SB, Silva-Junior FP. COVID-19: molecular targets, drug repurposing and new avenues for drug discovery. Mem Inst Oswaldo Cruz 2020; 115:e200254. [PMID: 33027420 PMCID: PMC7534958 DOI: 10.1590/0074-02760200254] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/01/2020] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly contagious infection that may break the healthcare system of several countries. Here, we aimed at presenting a critical view of ongoing drug repurposing efforts for COVID-19 as well as discussing opportunities for development of new treatments based on current knowledge of the mechanism of infection and potential targets within. Finally, we also discuss patent protection issues, cost effectiveness and scalability of synthetic routes for some of the most studied repurposing candidates since these are key aspects to meet global demand for COVID-19 treatment.
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Affiliation(s)
- Mario Roberto Senger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Tereza Cristina Santos Evangelista
- Universidade Federal do Rio de Janeiro, Instituto de Química,
Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ,
Brasil
| | - Rafael Ferreira Dantas
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Marcos Vinicius da Silva Santana
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Luiz Carlos Saramago Gonçalves
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Lauro Ribeiro de Souza Neto
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
| | - Sabrina Baptista Ferreira
- Universidade Federal do Rio de Janeiro, Instituto de Química,
Laboratório de Síntese Orgânica e Prospecção Biológica, Rio de Janeiro, RJ,
Brasil
| | - Floriano Paes Silva-Junior
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório
de Bioquímica Experimental e Computacional de Fármacos, Rio de Janeiro, RJ,
Brasil
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11
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Artika IM, Dewantari AK, Wiyatno A. Molecular biology of coronaviruses: current knowledge. Heliyon 2020; 6:e04743. [PMID: 32835122 PMCID: PMC7430346 DOI: 10.1016/j.heliyon.2020.e04743] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) late December 2019 in Wuhan, China, marked the third introduction of a highly pathogenic coronavirus into the human population in the twenty-first century. The constant spillover of coronaviruses from natural hosts to humans has been linked to human activities and other factors. The seriousness of this infection and the lack of effective, licensed countermeasures clearly underscore the need of more detailed and comprehensive understanding of coronavirus molecular biology. Coronaviruses are large, enveloped viruses with a positive sense single-stranded RNA genome. Currently, coronaviruses are recognized as one of the most rapidly evolving viruses due to their high genomic nucleotide substitution rates and recombination. At the molecular level, the coronaviruses employ complex strategies to successfully accomplish genome expression, virus particle assembly and virion progeny release. As the health threats from coronaviruses are constant and long-term, understanding the molecular biology of coronaviruses and controlling their spread has significant implications for global health and economic stability. This review is intended to provide an overview of our current basic knowledge of the molecular biology of coronaviruses, which is important as basic knowledge for the development of coronavirus countermeasures.
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Affiliation(s)
- I. Made Artika
- Biosafety Level 3 Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Darmaga Campus, Bogor, 16680, Indonesia
| | - Aghnianditya Kresno Dewantari
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
| | - Ageng Wiyatno
- Emerging Virus Research Unit, Eijkman Institute for Molecular Biology, Jalan Diponegoro 69, Jakarta, 10430, Indonesia
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Alam I, Kamau AA, Kulmanov M, Jaremko Ł, Arold ST, Pain A, Gojobori T, Duarte CM. Functional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2. Front Cell Infect Microbiol 2020; 10:405. [PMID: 32850499 PMCID: PMC7396417 DOI: 10.3389/fcimb.2020.00405] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 06/30/2020] [Indexed: 11/13/2022] Open
Abstract
The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social, and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells. The S proteins from SARS and SARS-CoV-2 are similar, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-specific neutralizing antibodies to inhibit SARS-CoV-2. Here we used comparative pangenomic analysis of all sequenced reference Betacoronaviruses, complemented with functional and structural analyses. This analysis reveals that, among all core gene clusters present in these viruses, the envelope protein E shows a variant cluster shared by SARS and SARS-CoV-2 with two completely-conserved key functional features, namely an ion-channel, and a PDZ-binding motif (PBM). These features play a key role in the activation of the inflammasome causing the acute respiratory distress syndrome, the leading cause of death in SARS and SARS-CoV-2 infections. Together with functional pangenomic analysis, mutation tracking, and previous evidence, on E protein as a determinant of pathogenicity in SARS, we suggest E protein as an alternative therapeutic target to be considered for further studies to reduce complications of SARS-CoV-2 infections in COVID-19.
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Affiliation(s)
- Intikhab Alam
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Allan A. Kamau
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maxat Kulmanov
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Arnab Pain
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takashi Gojobori
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos M. Duarte
- Biological and Environmental Science and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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13
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Abstract
BACKGROUND Coronaviruses (CoVs) primarily cause enzootic infections in birds and mammals but, in the last few decades, have shown to be capable of infecting humans as well. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and, more recently, Middle-East respiratory syndrome (MERS) has demonstrated the lethality of CoVs when they cross the species barrier and infect humans. A renewed interest in coronaviral research has led to the discovery of several novel human CoVs and since then much progress has been made in understanding the CoV life cycle. The CoV envelope (E) protein is a small, integral membrane protein involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis. Recent studies have expanded on its structural motifs and topology, its functions as an ion-channelling viroporin, and its interactions with both other CoV proteins and host cell proteins. MAIN BODY This review aims to establish the current knowledge on CoV E by highlighting the recent progress that has been made and comparing it to previous knowledge. It also compares E to other viral proteins of a similar nature to speculate the relevance of these new findings. Good progress has been made but much still remains unknown and this review has identified some gaps in the current knowledge and made suggestions for consideration in future research. CONCLUSIONS The most progress has been made on SARS-CoV E, highlighting specific structural requirements for its functions in the CoV life cycle as well as mechanisms behind its pathogenesis. Data shows that E is involved in critical aspects of the viral life cycle and that CoVs lacking E make promising vaccine candidates. The high mortality rate of certain CoVs, along with their ease of transmission, underpins the need for more research into CoV molecular biology which can aid in the production of effective anti-coronaviral agents for both human CoVs and enzootic CoVs.
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Affiliation(s)
- Dewald Schoeman
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - Burtram C Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa.
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14
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Ivancic-Jelecki J, Slovic A, Ljubin-Sternak S, Mlinarić Galinović G, Forcic D. Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene. Virol J 2018; 15:109. [PMID: 30021648 PMCID: PMC6052705 DOI: 10.1186/s12985-018-1020-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/10/2018] [Indexed: 11/10/2022] Open
Abstract
Background Small hydrophobic (SH) gene is one of the mostly diverse genomic regions of human respiratory syncytial virus (HRSV). Its coding region constitutes less than 50% of the complete gene length, enabling SH gene to be highly variable and the SH protein highly conserved. In standard HRSV molecular epidemiology studies, solely sequences of the second hypervariable region of the glycoprotein gene (HVR2) are analyzed. To what extent do the strains identical in HVR2 differ elsewhere in genomes is rarely investigated. Our goal was to investigate whether diversity and inter-genotype differences observed for HVR2 are also present in the SH gene. Methods We sequenced 198 clinical samples collected within a limited area and time frame. In this HRSV collection, rapid and significant changes in HVR2 occurred. Results Over 20% of strains from this pool (containing HRSV genotypes NA1, ON1, GA5, BA9 and BA10) would be incorrectly assumed to be identical to another strain if only the HVR2 region was analysed. The majority of differences found in SH gene were located in the 5′ untranslated region (UTR). Seven indels were detected, one was genotype GA5 specific. An in-frame deletion of 9 nucleotides (coding for amino acids 49–51) was observed in one of group A strains. Fifteen different SH protein sequences were detected; 68% of strains possessed the consensus sequence and most of others differed from the consensus in only one amino acid (only 4 strains differed in 2 amino acids). The majority of differing amino acids in group A viruses had the same identity as the corresponding amino acids in group B strains. When analysis was restricted to strains with identical HVR2 nucleotide sequences and differing SH protein sequences, 75% of differences observed in the SH ectodomain were located within region coding for amino acids 49–51. Conclusions Basing HRSV molecular epidemiology studies solely on HVR2 largely underestimates the complexity of circulating virus populations. In strain identification, broadening of the genomic target sequence to SH gene would provide a more comprehensive insight into viral pool versatility and its evolutionary processes. Electronic supplementary material The online version of this article (10.1186/s12985-018-1020-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jelena Ivancic-Jelecki
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Rockefellerova 10, 10000, Zagreb, Croatia. .,Scientific Center of Excellence for Viral Immunology and Vaccines, CerVirVac, Zagreb, Croatia.
| | - Anamarija Slovic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Rockefellerova 10, 10000, Zagreb, Croatia.,Scientific Center of Excellence for Viral Immunology and Vaccines, CerVirVac, Zagreb, Croatia
| | - Sunčanica Ljubin-Sternak
- Teaching Institute of Public Health "Dr. Andrija Štampar", Mirogojska 8, 10000, Zagreb, Croatia.,School of Medicine University of Zagreb, Šalata 3, 10000, Zagreb, Croatia
| | - Gordana Mlinarić Galinović
- School of Medicine University of Zagreb, Šalata 3, 10000, Zagreb, Croatia.,Croatian National Institute of Public Health, Rockefellerova 12, 10000, Zagreb, Croatia
| | - Dubravko Forcic
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Rockefellerova 10, 10000, Zagreb, Croatia.,Scientific Center of Excellence for Viral Immunology and Vaccines, CerVirVac, Zagreb, Croatia
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To J, Surya W, Fung TS, Li Y, Verdià-Bàguena C, Queralt-Martin M, Aguilella VM, Liu DX, Torres J. Channel-Inactivating Mutations and Their Revertant Mutants in the Envelope Protein of Infectious Bronchitis Virus. J Virol 2017; 91:e02158-16. [PMID: 27974570 PMCID: PMC5309962 DOI: 10.1128/jvi.02158-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/06/2016] [Indexed: 02/06/2023] Open
Abstract
It has been shown previously in the severe acute respiratory syndrome coronavirus (SARS-CoV) that two point mutations, N15A and V25F, in the transmembrane domain (TMD) of the envelope (E) protein abolished channel activity and led to in vivo attenuation. Pathogenicity was recovered in mutants that also regained E protein channel activity. In particular, V25F was rapidly compensated by changes at multiple V25F-facing TMD residues located on a neighboring monomer, consistent with a recovery of oligomerization. Here, we show using infected cells that the same mutations, T16A and A26F, in the gamma-CoV infectious bronchitis virus (IBV) lead to, in principle, similar results. However, IBV E A26F did not abolish oligomer formation and was compensated by mutations at N- and C-terminal extramembrane domains (EMDs). The C-terminal EMD mutations clustered along an insertion sequence specific to gamma-CoVs. Nuclear magnetic resonance data are consistent with the presence of only one TMD in IBV E, suggesting that recovery of channel activity and fitness in these IBV E revertant mutants is through an allosteric interaction between EMDs and TMD. The present results are important for the development of IBV live attenuated vaccines when channel-inactivating mutations are introduced in the E protein.IMPORTANCE The ion channel activity of SARS-CoV E protein is a determinant of virulence, and abolishment of channel activity leads to viral attenuation. E deletion may be a strategy for generating live attenuated vaccines but can trigger undesirable compensatory mechanisms through modifications of other viral proteins to regain virulence. Therefore, a more suitable approach may be to introduce small but critical attenuating mutations. For this, the stability of attenuating mutations should be examined to understand the mechanisms of reversion. Here, we show that channel-inactivating mutations of the avian infectious bronchitis virus E protein introduced in a recombinant virus system are deficient in viral release and fitness and that revertant mutations also restored channel activity. Unexpectedly, most of the revertant mutations appeared at extramembrane domains, particularly along an insertion specific for gammacoronaviruses. Our structural data propose a single transmembrane domain in IBV E, suggesting an allosteric interaction between extramembrane and transmembrane domains.
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Affiliation(s)
- Janet To
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - To Sing Fung
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yan Li
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Carmina Verdià-Bàguena
- Department of Physics, Laboratory of Molecular Biophysics. Universitat Jaume I, Castelló, Spain
| | - Maria Queralt-Martin
- Department of Physics, Laboratory of Molecular Biophysics. Universitat Jaume I, Castelló, Spain
| | - Vicente M Aguilella
- Department of Physics, Laboratory of Molecular Biophysics. Universitat Jaume I, Castelló, Spain
| | - Ding Xiang Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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16
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Abstract
Since the discovery that certain small viral membrane proteins, collectively termed as viroporins, can permeabilize host cellular membranes and also behave as ion channels, attempts have been made to link this feature to specific biological roles. In parallel, most viroporins identified so far are virulence factors, and interest has focused toward the discovery of channel inhibitors that would have a therapeutic effect, or be used as research tools to understand the biological roles of viroporin ion channel activity. However, this paradigm is being shifted by the difficulties inherent to small viral membrane proteins, and by the realization that protein-protein interactions and other diverse roles in the virus life cycle may represent an equal, if not, more important target. Therefore, although targeting the channel activity of viroporins can probably be therapeutically useful in some cases, the focus may shift to their other functions in following years. Small-molecule inhibitors have been mostly developed against the influenza A M2 (IAV M2 or AM2). This is not surprising since AM2 is the best characterized viroporin to date, with a well-established biological role in viral pathogenesis combined the most extensive structural investigations conducted, and has emerged as a validated drug target. For other viroporins, these studies are still mostly in their infancy, and together with those for AM2, are the subject of the present review.
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Emerging Roles of Viroporins Encoded by DNA Viruses: Novel Targets for Antivirals? Viruses 2015; 7:5375-87. [PMID: 26501313 PMCID: PMC4632388 DOI: 10.3390/v7102880] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/02/2015] [Accepted: 10/12/2015] [Indexed: 12/20/2022] Open
Abstract
Studies have highlighted the essential nature of a group of small, highly hydrophobic, membrane embedded, channel-forming proteins in the life cycles of a growing number of RNA viruses. These viroporins mediate the flow of ions and a range of solutes across cellular membranes and are necessary for manipulating a myriad of host processes. As such they contribute to all stages of the virus life cycle. Recent discoveries have identified proteins encoded by the small DNA tumor viruses that display a number of viroporin like properties. This review article summarizes the recent developments in our understanding of these novel viroporins; describes their roles in the virus life cycles and in pathogenesis and speculates on their potential as targets for anti-viral therapeutic intervention.
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