Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine

Ismail, Saba; Ahmad, Sajjad; Azam, Syed Sikander

doi:10.1016/j.molliq.2020.113612

Cited by 50 publications

(40 citation statements)

References 105 publications

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“…For a potential vaccine candidate, structural, non-structural and accessory proteins of the virus are suitable selections which induce protective immune responses [ [75] , [76] , [77] ]. There are many studies that propose epitope and multi-epitope based vaccines against SARS-CoV-2 via the application of various computational and immunoinformatics approaches [ [78] , [79] , [80] , [81] , [82] , [83] , [84] , [85] , [86] ]. After scanning the literature, we found most of the published studies concerning epitope prediction on the S protein [ 71 , 87 , 88 ].…”

Section: Discussionmentioning

confidence: 99%

Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2

Khan

Islam

Parihar

et al. 2021

Informatics in Medicine Unlocked

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmittable and pathogenic human coronavirus that caused a pandemic situation of acute respiratory syndrome, called COVID-19, which has posed a significant threat to global health security. The aim of the present study is to computationally design an effective peptide-based multi-epitope vaccine (MEV) against SARS-CoV-2. The overall model quality of the vaccine candidate, immunogenicity, allergenicity, and physiochemical analysis have been conducted and validated. Molecular dynamics studies confirmed the stability of the candidate vaccine. The docked complexes during the simulation revealed that a strong and stable binding interactions of MEV with human and mice toll-like receptors (TLR), TLR3 and TLR4. Finally, candidate vaccine codons have been optimized for their in silico cloning in E.coli expression system, to confirm increased expression. The proposed MEV can be a potential candidate against SARS-CoV-2, but experimental validation is needed to ensure its safety and immunogenicity status.

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Section: Discussionmentioning

confidence: 99%

Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2

Khan

Islam

Parihar

et al. 2021

Informatics in Medicine Unlocked

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“…Different computational models based on the molecular mechanism of the said problems, are available in the literature [ [14] , [15] , [16] , [17] ]. During this research, we developed a model comprising target cells ( X ), virus infected cells ( Y ), immune cells ( Z ), pro-inflammatory cytokines C, and, anti-inflammatory cytokine A .…”

Section: Mathematical Modelmentioning

confidence: 99%

Modeling and simulations of CoViD-19 molecular mechanism induced by cytokines storm during SARS-CoV2 infection

Ellahi

Nutini

et al. 2021

Journal of Molecular Liquids

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It is highly desired to explore the interventions of COVID-19 for early treatment strategies. Such interventions are still under consideration. A model is benchmarked research and comprises target cells, virus infected cells, immune cells, pro-inflammatory cytokines, and, anti-inflammatory cytokine. The interaction of the drug with the inflammatory sub-system is analyzed with the aid of kinetic modeling. The impact of drug therapy on the immune cells is modelled and the computational framework is verified with the aid of numerical simulations. The work includes a significant hypothesis that quantifies the complex dynamics of the infection, by relating it to the effect of the inflammatory syndrome generated by IL-6. In this paper we use the cancer immunoediting process: a dynamic process initiated by cancer cells in response to immune surveillance of the immune system that it can be conceptualized by an alternating movement that balances immune protection with immune evasion. The mechanisms of resistance to immunotherapy seem to broadly overlap with those used by cancers as they undergo immunoediting to evade detection by the immune system. In this process the immune system can both constrain and promote tumour development, which proceeds through three phases termed: (i) Elimination, (ii) Equilibrium, and, (iii) Escape [ 1 ]. We can also apply these concepts to viral infection, which, although it is not exactly “immunoediting”, has many points in common and helps to understand how it expands into an “untreated” host and can help in understanding the SARS-CoV2 virus infection and treatment model.

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“…Therefore, in the present study, molecular modelling-based approaches were employed to target NRP1 in order to identify novel hits against SARS-CoV-2 within a comprehensive marine natural products (CMNP) database ( https://www.cmnpd.org/ ). Computational structural biology and biophysical approaches are the most widely used approaches in drug discovery for the treatment of viral pathogens [ [16] , [17] , [18] , [19] , [20] , [21] , [22] , [23] , [24] , [25] ]. We used virtual drug screening approaches and binding free energy calculations to decipher the binding, possible mechanism, and long-term association strength between the identified drugs and NRP1.…”

Section: Introductionmentioning

confidence: 99%

Abrogation of SARS-CoV-2 interaction with host (NRP1) neuropilin-1 receptor through high-affinity marine natural compounds to curtail the infectivity: A structural-dynamics data

Humayun

Khan

Ahmad

et al. 2022

Computers in Biology and Medicine

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The evolution of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants around the globe has made the coronavirus disease 2019 (COVID-19) pandemic more worrisome, pressuring the health care system and resulting in an increased mortality rate. Recent studies recognized neuropilin-1 (NRP1) as a key facilitator in the invasion of the new SARS-CoV-2 into the host cell. Therefore, it is considered an imperative drug target for the treatment of COVID-19. Hence, a thorough analysis was needed to understand the impact and to guide new therapeutics development. In this study, we used structural and biomolecular simulation techniques to identify novel marine natural products which could block this receptor and stop the virus entry. We discovered that the binding affinity of CMNPD10175, CMNPD10017, CMNPD10114, CMNPD10115, CMNPD10020. CMNPD10018, CMNPD10153, CMNPD10149 CMNPD10464 and CMNPD10019 were substantial during the virtual screening (VS). We further explored these compounds by analyzing their absorption, distribution, metabolism, and excretion and toxicity (ADMET) properties and structural-dynamics features. Free energy calculations further established that all the compounds exhibit strong binding energy for NRP1. Consequently, we hypothesized that these compounds might be the best lead candidates for therapeutic interventions hindering virus binding to the host cell. This study provides a strong impetus to develop novel drugs against the SARS-CoV-2 by targeting NRP1.

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Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine

Cited by 50 publications

References 105 publications

Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2

Immunoinformatics and molecular modeling approach to design universal multi-epitope vaccine for SARS-CoV-2

Modeling and simulations of CoViD-19 molecular mechanism induced by cytokines storm during SARS-CoV2 infection

Abrogation of SARS-CoV-2 interaction with host (NRP1) neuropilin-1 receptor through high-affinity marine natural compounds to curtail the infectivity: A structural-dynamics data

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