NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus

Gupta, Amit; Kumar, Archit; Rajput, Abhishek; Kaur, Karambir; Dar, Showkat Ahmad; Thakur, Ashwani Kumar; Megha, Kirti; Kumar, Manoj

doi:10.1093/database/baz159

Cited by 9 publications

(10 citation statements)

References 63 publications

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“…AEFFSFFRTF, IPFLFLSAY, ETDDYNGIY, SQNLLVTSY) show a match with previous studies[35][36][37][38], indicating consensus of epitope screening by different approaches and methods (Supplementary table…”

supporting

confidence: 83%

“…Along with the B cell, the T cell also play a critical role in immune response against NiV infection. In recent studies a number of B cell and T cell epitopes from the NIPAH proteome have been reported [27][28][29][30][31][32][33][34][35][36][37][38]. Further different approaches were proposed for the design of multi epitope vaccines [39,44].…”

Section: Introductionmentioning

confidence: 99%

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Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health

Srivastava

Saxena

Kolbe

2021

Preprint

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Nipah virus (NiV) is an emerging zoonotic virus responsible to cause several serious outbreaks in South Asian region with high mortality rate of 40 to 90% since 2001. NiV infection causes lethal encephalitis and respiratory disease with the symptom of endothelial cell-cell fusion. No specific vaccine has yet been reported against NiV infection. Recently, some Multi-Epitope Vaccines (MEV) has been proposed but they involve limited number of epitopes which further limits the potential of vaccine. To address the urgent need for a specific and effective vaccine against NiV infection, in the present study, we have design two multi-epitope vaccines (MEVs) composed of 33 Cytotoxic T lymphocyte (CTL) epitopes and 38 Helper T lymphocyte (HTL) epitopes. Both the MEVs carry potential B cell linear epitope overlapping regions, B cell discontinuous epitopes as well as IFN-γ inducing epitopes. Hence the designed MEVs carry potential to elicit cell-mediated as well as humoral immune response. Selected CTL and HTL epitopes were validated for their stable molecular interactions with HLA class I and II alleles as well as in case of CTL epitopes, with human transporter associated with antigen processing (TAP). Human β-defensin 2 and β-defensin 3 were used as adjuvants to enhance the immune response of both the MEVs. The molecular dynamics simulation study of MEVs-TLR3(ECD) (Toll-Like Receptor 3 Ectodomain) complex indicated stable molecular interaction. Further, the codon optimized cDNA of both the MEVs has shown high expression potential in the mammalian host cell line (Human). Hence for further studies, both the design of CTL and HTL MEVs could be cloned, expressed and tried for in-vivo validations (animal trails) as potential vaccine candidates against NiV infection.

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supporting

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health

Srivastava

Saxena

Kolbe

2021

Preprint

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“…Additionally, the drugs designed for multiple protein targets are extensively preferable for the treatment of infectious, inherited and complex diseases due to low treatment cost, less drug dosage and minimal side effect and drug–drug interactions. Therefore, with the immediate requirement of multi-targeted strategies against the novel coronavirus SARS-CoV-2, with either biologically active drug-like molecules or approved drugs are in pressing priority [ 6 , 24 , 25 ]. Recent advancements in the computational techniques have proven their efficiency for identifying the potential drug candidates [ 7 , 26–28 ].…”

Section: Introductionmentioning

confidence: 99%

Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach

Mishra

Pandey

Sharma

et al. 2020

Briefings in Bioinformatics

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The global pandemic crisis, coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed the lives of millions of people across the world. Development and testing of anti-SARS-CoV-2 drugs or vaccines have not turned to be realistic within the timeframe needed to combat this pandemic. Here, we report a comprehensive computational approach to identify the multi-targeted drug molecules against the SARS-CoV-2 proteins, whichare crucially involved in the viral–host interaction, replication of the virus inside the host, disease progression and transmission of coronavirus infection. Virtual screening of 75 FDA-approved potential antiviral drugs against the target proteins, spike (S) glycoprotein, human angiotensin-converting enzyme 2 (hACE2), 3-chymotrypsin-like cysteine protease (3CL pro ), cathepsin L (CTSL), nucleocapsid protein, RNA-dependent RNA polymerase (RdRp) and non-structural protein 6 (NSP6), resulted in the selection of seven drugs which preferentially bind to the target proteins. Further, the molecular interactions determined by molecular dynamics simulation revealed that among the 75 drug molecules, catechin can effectively bind to 3CL pro , CTSL, RBD of S protein, NSP6 and nucleocapsid protein. It is more conveniently involved in key molecular interactions, showing binding free energy (Δ G bind ) in the range of −5.09 kcal/mol (CTSL) to −26.09 kcal/mol (NSP6). At the binding pocket, catechin is majorly stabilized by the hydrophobic interactions, displays Δ E vdW values: −7.59 to −37.39 kcal/mol. Thus, the structural insights of better binding affinity and favorable molecular interaction of catechin toward multiple target proteins signify that catechin can be potentially explored as a multi-targeted agent against COVID-19.

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“…The world is currently undergoing and living with the great threat of pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which has newly emerged from Wuhan, Hubei province, China ( Du Toit, 2020 ; Hui et al, 2020 ; Wang C. et al, 2020 ). Apart from this, in recent years, we have also witnessed sporadic outbreaks and epidemics of various lethal viruses, i.e., Ebola, Zika, Nipah, etc ( Gupta et al, 2016 , 2020 ). The current pandemic of SARS-CoV-2 (also named as 2019-nCoV) is now reported to spread over 199 countries and to be responsible for excessive economic loss worldwide ( Zhang and Liu, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

CoronaVR: A Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2

et al. 2020

Self Cite

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In December 2019, the Chinese city of Wuhan was the center of origin of a pneumonialike disease outbreak with an unknown causative pathogen. The CDC, China, managed to track the source of infection to a novel coronavirus (2019-nCoV; SARS-CoV-2) that shares approximately 79.6% of its genome with SARS-CoV. The World Health Organization (WHO) initially declared COVID-19 as a Public Health Emergency of International Concern (PHEIC) and later characterized it as a global pandemic on March 11, 2020. Due to the novel nature of this virus, there is an urgent need for vaccines and therapeutics to control the spread of SARS-CoV-2 and its associated disease, COVID-19. Global efforts are underway to circumvent its further spread and treat COVID-19 patients through experimental vaccine formulations and therapeutic interventions, respectively. In the absence of any effective therapeutics, we have devised h bioinformatics-based approaches to accelerate global efforts in the fight against SARS-CoV-2 and to assist researchers in the initial phase of vaccine and therapeutics development. In this study, we have performed comprehensive meta-analyses and developed an integrative resource, "CoronaVR" (http://bioinfo.imtech.res.in/manojk/ coronavr/). Predominantly, we identified potential epitope-based vaccine candidates, siRNA-based therapeutic regimens, and diagnostic primers. The resource is categorized into the main sections "Genomes," "Epitopes," "Therapeutics," and Primers." The genome section harbors different components, viz, genomes, a genome browser, phylogenetic analysis, codon usage, glycosylation sites, and structural analysis. Under the umbrella of epitopes, subdivisions , namely cross-protective epitopes, B-cell (linear/discontinuous), T-cell (CD4 + /CD8 +), CTL, and MHC binders, are presented. The therapeutics section has different subsections like siRNA, miRNAs, and sgRNAs. Further, experimentally confirmed and designed diagnostic primers are earmarked in the primers section. Our study provided a set of shortlisted B-cell and T-cell (CD4 +

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NipahVR: a resource of multi-targeted putative therapeutics and epitopes for the Nipah virus

Cited by 9 publications

References 63 publications

Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health

Exploring the structural basis to develop efficient multi-epitope vaccines displaying interaction with HLA and TAP and TLR3 molecules to prevent NIPAH infection, a global threat to human health

Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach

CoronaVR: A Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2

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