Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach

Bappy, Syed Shahariar; Sultana, Sorna; Adhikari, Juthi; Mahmud, Shafi; Khan, Mukhtar A.; Kibria, K. M. Kaderi; Rahman, Md. Masuder; Shibly, Abu Zaffar

doi:10.1080/07391102.2020.1726815

Cited by 33 publications

(18 citation statements)

References 85 publications

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“…Henceforth, in the current approach, we have checked the propensity of the multi-epitope vaccine construct of the Nipah virus and human TLR3 complex. This epitope-based vaccine development approach has been explored and proved to be promising in a number of diseases caused by viruses like Herpes simplex virus (Hasan et al, 2019;Kumar et al, 2019), Yellow Fever Virus (Tosta et al, 2019), SARS Coronavirus (Srivastava et al, 2019), Chikungunya (Bappy et al, 2020), Dengue (Sabetian, Nezafat, Dorosti, Zarei, & Ghasemi, 2019), Alkhurma hemorrhagic fever virus (Ul-Rahman & Shabbir, 2019), etc. as well as by other pathogens including Leishmania donovani (Khatoon et al, 2019), Elizabethkingia anophelis (Nain et al, 2019), Flavobacterium columnare (Bhattacharya et al, 2020), Bacillus anthracis (Gupta, Khatoon, Mishra, Verma, & Prajapati, 2019), Streptococcus pneumoniae (Dorosti et al, 2019), Helicobacter pylori (Pasala et al, 2019), etc.…”

Section: Introductionmentioning

confidence: 99%

Designing of a multi-epitope vaccine candidate against Nipah virus by in silico approach: a putative prophylactic solution for the deadly virus

Majee

Jain

Kumar

2020

Journal of Biomolecular Structure and Dynamics

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Nipah virus (NPV) is one of the most notorious viruses with a very high fatality rate. Because of the recurrent advent of this virus and its severe neurological implications, often leading to high mortality, the WHO R&D Blueprint, 2018 has listed the Nipah virus as one of the emerging infectious diseases requiring urgent research and development effort. Yet there is a major layback in the development of effective vaccines or drugs against NPV. In this study, we have designed a stable multivalent vaccine combining several T-cell and B-cell epitopes of the essential Nipah viral proteins with the help of different ligands and adjuvants which can effectively induce both humoral and cellular immune responses in human. Different advanced immune-informatic tools confirm the stability, high immunogenicity and least allergenicity of the vaccine candidate. The standard molecular dynamic cascade analysis validates the stable interaction of the vaccine construct with the human Toll-like receptor 3 (TLR3) complex. Later, codon optimization and in silico cloning in a known pET28a vector system shows the possibility for the expression of this vaccine in a simple organism like E.coli. It is believed that with further in vitro and in vivo validation, this vaccine construct can pose to be a better prophylactic solution to the Nipah viral disease.

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Section: Introductionmentioning

confidence: 99%

Designing of a multi-epitope vaccine candidate against Nipah virus by in silico approach: a putative prophylactic solution for the deadly virus

Majee

Jain

Kumar

2020

Journal of Biomolecular Structure and Dynamics

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“…Molecular modelling especially docking and dynamic simulation study has become essential part in modern drug discovery pipeline(Bappy et al., 2020 ; Elfiky, 2020a ; Islam et al., 2019 ). Moreover, time and lab cost can significantly reduce by narrowing the drug molecule choices in in silico based drug discovery process (Talele et al., 2010 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study

Khan

Mahmud

Alam³

et al. 2020

Journal of Biomolecular Structure and Dynamics

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Recent outbreak of novel coronavirus and its rapid pandemic escalation in all over the world has drawn the attention to urgent need for effective drug development. However, due to prolonged vaccine and drug development procedure against a newly emerged devastating SARS-CoV-2 virus pathogen, repurposing of existing potential pertinent drug molecules would be preferable strategy to reduce mortality immediately and further development of new drugs to combat overall global Covid-19 crisis in all over the world. Herein, we have filtered 23 prospective drug candidates through literature review. Assessing evidences from molecular docking studies, it was clearly seen that, Epirubicin, Vapreotida, and Saquinavir exhibited better binding affinity against SARS-CoV-2 Main Protease than other drug molecules among the 23 potential inhibitors. However, 50 ns molecular dynamics simulation indicated the less mobile nature of the docked complex maintaining structural integrity. Our overall prediction findings indicate that Epirubicin, Vapreotida, and Saquinavir may inhibit COVID-19 by synergistic interactions in the active cavity and those results can pave the way in drug discovery although it has to be further validated by in-vitro and in-vivo investigations.

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“…The simulation was run by using 1.25 fs time step. The trajectories were saved after every 100 ps to analyze the root mean square deviation, root mean square fluctuations, hydrogen bond, radius of gyration, and solvent accessible surface area (Bappy et al, 2020;Khan et al, 2020;Islam et al, 2020;Mahmud et al, 2020a;Mahmud et al, 2020b;Mahmud et al, 2021b;Swargiary et al, 2020;Chowdhury et al, 2021;Rakib et al, 2021;Uddin et al, 2021).…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2

Mahmud

Paul

Biswas

et al. 2021

Front. Mol. Biosci.

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The recently emerged coronavirus (SARS-CoV-2) has created a crisis in world health, and economic sectors as an effective treatment or vaccine candidates are still developing. Besides, negative results in clinical trials and effective cheap solution against this deadly virus have brought new challenges. The viral protein, the main protease from SARS-CoV-2, can be effectively targeted due to its viral replication and pathogenesis role. In this study, we have enlisted 88 peptides from the AVPdb database. The peptide molecules were modeled to carry out the docking interactions. The four peptides molecules, P14, P39, P41, and P74, had more binding energy than the rest of the peptides in multiple docking programs. Interestingly, the active points of the main protease from SARS-CoV-2, Cys145, Leu141, Ser139, Phe140, Leu167, and Gln189, showed nonbonded interaction with the peptide molecules. The molecular dynamics simulation study was carried out for 200 ns to find out the docked complex’s stability where their stability index was proved to be positive compared to the apo and control complex. Our computational works based on peptide molecules may aid the future development of therapeutic options against SARS-CoV-2.

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Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach

Cited by 33 publications

References 85 publications

Designing of a multi-epitope vaccine candidate against Nipah virus by in silico approach: a putative prophylactic solution for the deadly virus

Designing of a multi-epitope vaccine candidate against Nipah virus by in silico approach: a putative prophylactic solution for the deadly virus

Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study

Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2

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