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Hossain MS, Shovon MTI, Hasan MR, Hakim FT, Hasan MM, Esha SA, Tasnim S, Nazir MS, Akhter F, Ali MA, Halim MA. Therapeutic Potential of Antiviral Peptides against the NS2B/NS3 Protease of Zika Virus. ACS OMEGA 2023; 8:35207-35218. [PMID: 37779969 PMCID: PMC10536883 DOI: 10.1021/acsomega.3c04903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
The NS2B/NS3 protease is highly conserved among various proteases of the Zika virus, making it an important therapeutic target for developing broad-spectrum antiviral drugs. The NS2B/NS3 protease is a crucial enzyme in the replication cycle of Zika virus and plays a significant role in viral maturation and assembly. Inhibiting the activity of this protease can potentially prevent viral replication, making it an attractive target for developing therapies against Zika virus infection. This work screens 429 antiviral peptides in comparison with substrate peptide against the NS2B/NS3 of Zika virus using molecular docking and molecular dynamics (MD) simulation. Based on the docking screening, MD simulation conducted for the best four peptides including AVP0239, AVP0642, AVP0660, and AVP2044, could be effective against NS2B/NS3. These results were compared with the control substrate peptide. Further analysis indicates that AVP0642 and AVP2044 are the most promising candidates. The interaction analysis showed that the catalytic site residues including His51, Asp75, Ser135 and other non-catalytic residues such as Asp129, Asp83, and Asp79 contribute substantial interactions. Hydrogen bonds (41%) and hydrophobic interactions (33%) are observed as the prominent non-covalent interaction prompting the peptide-protein complex formation. Furthermore, the structure-activity relationship (SAR) illustrates that positively charged (Lys, Arg) residues in the peptides dominate the interactions. This study provides the basis for developing novel peptide-based protease inhibitors for Zika virus.
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Affiliation(s)
- Md. Shahadat Hossain
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Tanjil Islam Shovon
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Rafid Hasan
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Fuad Taufiqul Hakim
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Mohammad Mehedi Hasan
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Sadia Afrose Esha
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Sabiha Tasnim
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Shahoriar Nazir
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Fahmida Akhter
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department
of Chemistry and Biochemistry, Kennesaw
State University, Kennesaw, Georgia 30144, United States
| | - Mohammad A. Halim
- Department
of Chemistry and Biochemistry, Kennesaw
State University, Kennesaw, Georgia 30144, United States
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Chen T, Yang H, Liu P, Hamiti M, Zhang X, Xu Y, Quan W, Zhang Y, Yu W, Jiao L, Du T, Xi J, Yin B, Zhou W, Lu S, Peng X. Splicing factor SF3B3, a NS5-binding protein, restricts ZIKV infection by targeting GCH1. Virol Sin 2022; 38:222-232. [PMID: 36572150 PMCID: PMC10176263 DOI: 10.1016/j.virs.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Zika virus (ZIKV), a positive-sense single-stranded RNA virus, causes congenital ZIKV syndrome in children and Guillain-Barré Syndrome (GBS) in adults. ZIKV expresses nonstructural protein 5 (NS5), a large protein that is essential for viral replication. ZIKV NS5 confers the ability to evade interferon (IFN) signalling; however, the exact mechanism remains unclear. In this study, we employed affinity pull-down and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses and found that splicing factor 3b subunit 3 (SF3B3) is associated with the NS5-Flag pull-down complex through interaction with NS5. Functional assays showed that SF3B3 overexpression inhibited ZIKV replication by promoting IFN-stimulated gene (ISG) expression whereas silencing of SF3B3 inhibited expression of ISGs to promote ZIKV replication. GTP cyclohydrolase I (GCH1) is the first and rate-limiting enzyme in tetrahydrobiopterin (BH4) biosynthesis. NS5 upregulates the expression of GCH1 during ZIKV infection. And GCH1 marginally promoted ZIKV replication via the IFN pathway. Additionally, GCH1 expression is related to the regulation of SF3B3. Overexpression of the SF3B3 protein effectively reduced GCH1 protein levels, whereas SF3B3 knockdown increased its levels. These findings indicated that ZIKV NS5 binding protein SF3B3 contributed to the host immune response against ZIKV replication by modulating the expression of GCH1.
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Affiliation(s)
- Tanxiu Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China; Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, 330029, China
| | - Hao Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Penghui Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Moliduer Hamiti
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xintian Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Yi Xu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Wenqi Quan
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Yong Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Wenhai Yu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Li Jiao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Tingfu Du
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Juemin Xi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China
| | - Bin Yin
- The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Wei Zhou
- Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, 330029, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China.
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, 650031, China; The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Kousa YA, Hossain RA. Causes of Phenotypic Variability and Disabilities after Prenatal Viral Infections. Trop Med Infect Dis 2021; 6:tropicalmed6020095. [PMID: 34205913 PMCID: PMC8293342 DOI: 10.3390/tropicalmed6020095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/25/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022] Open
Abstract
Prenatal viral infection can lead to a spectrum of neurodevelopmental disabilities or fetal demise. These can include microencephaly, global developmental delay, intellectual disability, refractory epilepsy, deafness, retinal defects, and cortical-visual impairment. Each of these clinical conditions can occur on a semi-quantitative to continuous spectrum, from mild to severe disease, and often as a collective of phenotypes. Such serious outcomes result from viruses’ overlapping neuropathology and hosts’ common neuronal and gene regulatory response to infections. The etiology of variability in clinical outcomes is not yet clear, but it may be related to viral, host, vector, and/or environmental risk and protective factors that likely interact in multiple ways. In this perspective of the literature, we work toward understanding the causes of phenotypic variability after prenatal viral infections by highlighting key aspects of the viral lifecycle that can affect human disease, with special attention to the 2015 Zika pandemic. Therefore, this work offers important insights into how viral infections and environmental teratogens affect the prenatal brain, toward our ultimate goal of preventing neurodevelopmental disabilities.
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Affiliation(s)
- Youssef A. Kousa
- Division of Neurology, Children’s National Hospital, Washington, DC 20010, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA
- Correspondence:
| | - Reafa A. Hossain
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20892, USA;
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