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Sureshan M, Prabhu D, Joshua SN, Sasikumar SV, Rajamanikandan S, Govindhapriya M, Umadevi V, Kadhirvel S. Discovery of plant-based phytochemical as effective antivirals that target the non-structural protein C of the Nipah virus through computational methods. J Biomol Struct Dyn 2024; 42:3568-3578. [PMID: 37222609 DOI: 10.1080/07391102.2023.2214236] [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: 02/01/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
Nipah Virus (NiV) belongs to the Paramyxoviridae family and was first identified during an outbreak in Malaysia. Some initial symptoms include mild fever, headache and sore throat, which could escalate to respiratory illness and brain inflammation. The mortality rate of NiV infection can range from 40% to 75%, which is quite high. This is mainly due to the lack of efficient drugs and vaccines. In most instances, NiV is transmitted from animals to humans. Non-Structural Proteins (C, V and W) of the Nipah virus impede the host immune response by obstructive the JAK/STAT pathway. However, Non-Structural Proteins - C (NSP-C) plays a vital role in NiV pathogenesis, which includes IFN antagonist activity and viral RNA production. In the present study, the full-length structure of NiV-NSP-C was predicted using computational modelling, and the stability of the structure was analysed using 200 ns molecular dynamic (MD) simulation. Further, the structure-based virtual screening identified five potent phytochemicals (PubChem CID: 9896047, 5885, 117678, 14887603 and 5461026) with better binding affinity against NiV-NSP-C. DFT studies clearly showed that the phytochemicals had higher chemical reactivity, and the complex MD simulation depicted that the identified inhibitors exhibited stable binding with NiV-NSP-C. Furthermore, experimental validation of these identified phytochemicals would likely control the infection of NiV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muthusamy Sureshan
- Biomolecular Crystallography Lab, Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Dhamodharan Prabhu
- Centre for Drug Discovery; Department of Biotechnology; Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, India
| | - Sharon Nissi Joshua
- Biomolecular Crystallography Lab, Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Shruti Vardhini Sasikumar
- Biomolecular Crystallography Lab, Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Sundarraj Rajamanikandan
- Centre for Drug Discovery; Department of Biotechnology; Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, India
| | | | - Venkatachalam Umadevi
- Faculty of Physics, Dr. Mahalingam College of Engineering and Technology, Pollachi, India
| | - Saraboji Kadhirvel
- Department of Computational Sciences, Central University of Punjab, Bathinda, Punjab, India
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Type I and Type II Interferon Antagonism Strategies Used by Paramyxoviridae: Previous and New Discoveries, in Comparison. Viruses 2022; 14:v14051107. [PMID: 35632848 PMCID: PMC9145045 DOI: 10.3390/v14051107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
Paramyxoviridae is a viral family within the order of Mononegavirales; they are negative single-strand RNA viruses that can cause significant diseases in both humans and animals. In order to replicate, paramyxoviruses–as any other viruses–have to bypass an important protective mechanism developed by the host’s cells: the defensive line driven by interferon. Once the viruses are recognized, the cells start the production of type I and type III interferons, which leads to the activation of hundreds of genes, many of which encode proteins with the specific function to reduce viral replication. Type II interferon is produced by active immune cells through a different signaling pathway, and activates a diverse range of genes with the same objective to block viral replication. As a result of this selective pressure, viruses have evolved different strategies to avoid the defensive function of interferons. The strategies employed by the different viral species to fight the interferon system include a number of sophisticated mechanisms. Here we analyzed the current status of the various strategies used by paramyxoviruses to subvert type I, II, and III interferon responses.
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Thakur V, Thakur P, Ratho RK. Nipah Outbreak: Is it the beginning of another pandemic in the era of COVID-19 and Zika. Brain Behav Immun 2022; 99:25-26. [PMID: 34562598 PMCID: PMC8506197 DOI: 10.1016/j.bbi.2021.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/18/2021] [Accepted: 09/18/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Vikram Thakur
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), 160012 Chandigarh, India; Viral Regional Diagnostic Laboratory (VRDL), Government Medical College, 147001 Patiala, India.
| | - Pryanka Thakur
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), 160012 Chandigarh, India
| | - Radha Kanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), 160012 Chandigarh, India.
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Esmail S, Danter W. Viral pandemic preparedness: A pluripotent stem cell-based machine-learning platform for simulating SARS-CoV-2 infection to enable drug discovery and repurposing. Stem Cells Transl Med 2021; 10:239-250. [PMID: 32961040 PMCID: PMC7537153 DOI: 10.1002/sctm.20-0181] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/05/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023] Open
Abstract
Infection with the SARS-CoV-2 virus has rapidly become a global pandemic for which we were not prepared. Several clinical trials using previously approved drugs and drug combinations are urgently under way to improve the current situation. A vaccine option has only recently become available, but worldwide distribution is still a challenge. It is imperative that, for future viral pandemic preparedness, we have a rapid screening technology for drug discovery and repurposing. The primary purpose of this research project was to evaluate the DeepNEU stem-cell based platform by creating and validating computer simulations of artificial lung cells infected with SARS-CoV-2 to enable the rapid identification of antiviral therapeutic targets and drug repurposing. The data generated from this project indicate that (a) human alveolar type lung cells can be simulated by DeepNEU (v5.0), (b) these simulated cells can then be infected with simulated SARS-CoV-2 virus, (c) the unsupervised learning system performed well in all simulations based on available published wet lab data, and (d) the platform identified potentially effective anti-SARS-CoV2 combinations of known drugs for urgent clinical study. The data also suggest that DeepNEU can identify potential therapeutic targets for expedited vaccine development. We conclude that based on published data plus current DeepNEU results, continued development of the DeepNEU platform will improve our preparedness for and response to future viral outbreaks. This can be achieved through rapid identification of potential therapeutic options for clinical testing as soon as the viral genome has been confirmed.
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Singh RK, Dhama K, Chakraborty S, Tiwari R, Natesan S, Khandia R, Munjal A, Vora KS, Latheef SK, Karthik K, Singh Malik Y, Singh R, Chaicumpa W, Mourya DT. Nipah virus: epidemiology, pathology, immunobiology and advances in diagnosis, vaccine designing and control strategies - a comprehensive review. Vet Q 2019. [PMID: 31006350 PMCID: PMC6830995 DOI: 10.1080/01652176.2019.1580827] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Nipah (Nee-pa) viral disease is a zoonotic infection caused by Nipah virus (NiV), a paramyxovirus belonging to the genus Henipavirus of the family Paramyxoviridae. It is a biosafety level-4 pathogen, which is transmitted by specific types of fruit bats, mainly Pteropus spp. which are natural reservoir host. The disease was reported for the first time from the Kampung Sungai Nipah village of Malaysia in 1998. Human-to-human transmission also occurs. Outbreaks have been reported also from other countries in South and Southeast Asia. Phylogenetic analysis affirmed the circulation of two major clades of NiV as based on currently available complete N and G gene sequences. NiV isolates from Malaysia and Cambodia clustered together in NiV-MY clade, whereas isolates from Bangladesh and India clusterered within NiV-BD clade. NiV isolates from Thailand harboured mixed population of sequences. In humans, the virus is responsible for causing rapidly progressing severe illness which might be characterized by severe respiratory illness and/or deadly encephalitis. In pigs below six months of age, respiratory illness along with nervous symptoms may develop. Different types of enzyme-linked immunosorbent assays along with molecular methods based on polymerase chain reaction have been developed for diagnostic purposes. Due to the expensive nature of the antibody drugs, identification of broad-spectrum antivirals is essential along with focusing on small interfering RNAs (siRNAs). High pathogenicity of NiV in humans, and lack of vaccines or therapeutics to counter this disease have attracted attention of researchers worldwide for developing effective NiV vaccine and treatment regimens.
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Affiliation(s)
- Raj Kumar Singh
- a ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Kuldeep Dhama
- b Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Sandip Chakraborty
- c Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry , West Tripura , India
| | - Ruchi Tiwari
- d Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences , Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Senthilkumar Natesan
- e Biomac Life Sciences Pvt Ltd. , Indian Institute of Public Health Gandhinagar , Gujarat , India
| | - Rekha Khandia
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Ashok Munjal
- f Department of Biochemistry and Genetics , Barkatullah University , Bhopal , India
| | - Kranti Suresh Vora
- g Wheels India Niswarth (WIN) Foundation, Maternal and Child Health (MCH) , University of Canberra , Gujarat , India
| | - Shyma K Latheef
- b Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Kumaragurubaran Karthik
- h Central University Laboratory , Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - Yashpal Singh Malik
- i Division of Biological Standardization , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Rajendra Singh
- b Division of Pathology , ICAR-Indian Veterinary Research Institute , Bareilly , India
| | - Wanpen Chaicumpa
- j Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine, Siriraj Hospital , Mahidol University , Bangkok , Thailand
| | - Devendra T Mourya
- k National Institute of Virology , Ministry of Health and Family Welfare, Govt of India , Pune , India
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Clayton BA. Nipah virus: transmission of a zoonotic paramyxovirus. Curr Opin Virol 2017; 22:97-104. [PMID: 28088124 DOI: 10.1016/j.coviro.2016.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 12/14/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
Abstract
Nipah virus is a recently-recognised, zoonotic paramyxovirus that causes severe disease and high fatality rates in people. Outbreaks have occurred in Malaysia, Singapore, India and Bangladesh, and a putative Nipah virus was also recently associated with human disease in the Philippines. Worryingly, human-to-human transmission is common in Bangladesh, where outbreaks occur with near-annual frequency. Onward human transmission of Nipah virus in Bangladesh is associated with close contact with clinically-unwell patients or their infectious secretions. While Nipah virus isolates associated with outbreaks of human infection have not resulted in sustained transmission to date, specific exposures carry a high risk of person-to-person transmission, an observation which is supported by recent findings in animal models. Novel paramyxoviruses continue to emerge from wildlife hosts, and represent an ongoing threat to human health globally.
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Affiliation(s)
- Bronwyn Anne Clayton
- Commonwealth Scientific and Industrial Research Organisation, Australian Animal Health Laboratory, East Geelong, Victoria 3219, Australia.
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Pernet O, Schneider BS, Beaty SM, LeBreton M, Yun TE, Park A, Zachariah TT, Bowden TA, Hitchens P, Ramirez CM, Daszak P, Mazet J, Freiberg AN, Wolfe ND, Lee B. Evidence for henipavirus spillover into human populations in Africa. Nat Commun 2014; 5:5342. [PMID: 25405640 PMCID: PMC4237230 DOI: 10.1038/ncomms6342] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 09/19/2014] [Indexed: 02/06/2023] Open
Abstract
Zoonotic transmission of lethal henipaviruses (HNVs) from their natural fruit bat reservoirs to humans has only been reported in Australia and South/Southeast Asia. However, a recent study discovered numerous HNV clades in African bat samples. To determine the potential for HNV spillover events among humans in Africa, here we examine well-curated sets of bat (Eidolon helvum, n=44) and human (n=497) serum samples from Cameroon for Nipah virus (NiV) cross-neutralizing antibodies (NiV-X-Nabs). Using a vesicular stomatitis virus (VSV)-based pseudoparticle seroneutralization assay, we detect NiV-X-Nabs in 48% and 3–4% of the bat and human samples, respectively. Seropositive human samples are found almost exclusively in individuals who reported butchering bats for bushmeat. Seropositive human sera also neutralize Hendra virus and Gh-M74a (an African HNV) pseudoparticles, as well as live NiV. Butchering bat meat and living in areas undergoing deforestation are the most significant risk factors associated with seropositivity. Evidence for HNV spillover events warrants increased surveillance efforts. Henipaviruses (HNVs) infect bats in Asia and Africa, but transmission to humans (often with lethal consequences) is known only in Asia. Here the authors show that 3% of human serum samples from certain areas in Cameroon contain antibodies against HNV, indicating spillover into the human population.
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Affiliation(s)
- Olivier Pernet
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
| | - Bradley S Schneider
- Global Viral/Metabiota Laboratory Sciences, San Francisco, California 90104, USA
| | - Shannon M Beaty
- 1] Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA [2] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Matthew LeBreton
- Global Viral/Metabiota Laboratory Sciences, San Francisco, California 90104, USA
| | - Tatyana E Yun
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Arnold Park
- 1] Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA [2] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Trevor T Zachariah
- Brevard Zoo Veterinary Services, Brevard Zoo, Melbourne, 32940 Florida, USA
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Peta Hitchens
- Department of Medicine and Epidemiology, School of Veterinary Medicine, UC Davis, Davis, California 95616, USA
| | - Christina M Ramirez
- Department of Biostatistics, School of Public Health, UCLA, Los Angeles, California 90095, USA
| | - Peter Daszak
- EcoHealth Alliance, New York, New York 10001, USA
| | - Jonna Mazet
- Department of Medicine and Epidemiology, School of Veterinary Medicine, UC Davis, Davis, California 95616, USA
| | - Alexander N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Nathan D Wolfe
- Global Viral/Metabiota Laboratory Sciences, San Francisco, California 90104, USA
| | - Benhur Lee
- 1] Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA [2] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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