Novel association of genetic variants in non-coding regulatory regions with HIV-1 infection

Waqar, Walifa; Altaf, Saba; Nazir, Sadia; Javed, Aneela

doi:10.1016/j.meegid.2020.104514

Cited by 1 publication

(1 citation statement)

References 47 publications

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“…Finalized epitopes were checked for their compatibility among themselves to determine the order of these epitopes in the final construct. For this purpose, HIV-1 mature proteins (from which epitopes were derived) nucleocapsid (PDB ID 5I1R) [ 59 ], reverse transcriptase (PDB ID 1HMV) [ 60 ], integrase (PDB ID 6U8Q) [ 61 ], and VPU (PDB ID 1VPU) [ 62 ] were downloaded from the RCSB PDB. Further methodology for the construction of a multi-epitope vaccine can be categorized into three steps: Epitopes and epitope combinations’ structure prediction.…”

Section: Methodsmentioning

confidence: 99%

Employing computational tools to design a multi-epitope vaccine targeting human immunodeficiency virus-1 (HIV-1)

Sher,

Sharif,

Zaheer

et al. 2023

BMC Genomics

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Background Despite being in the 21st century, the world has still not been able to vanquish the global AIDS epidemic, and the only foreseeable solution seems to be a safe and effective vaccine. Unfortunately, vaccine trials so far have returned unfruitful results, possibly due to their inability to induce effective cellular, humoral and innate immune responses. The current study aims to tackle these limitations and propose the desired vaccine utilizing immunoinformatic approaches that have returned promising results in designing vaccines against various rapidly mutating organisms. For this, all polyprotein and protein sequences of HIV-1 were retrieved from the LANL (Los Alamos National Laboratory) database. The consensus sequence was generated after alignment and used to predict epitopes. Conserved, antigenic, non-allergenic, T-cell inducing, B-cell inducing, IFN-ɣ inducing, non-human homologous epitopes were selected and combined to propose two vaccine constructs i.e., HIV-1a (without adjuvant) and HIV-1b (with adjuvant). Results HIV-1a and HIV-1b were subjected to antigenicity, allergenicity, structural quality analysis, immune simulations, and MD (molecular dynamics) simulations. Both proposed multi-epitope vaccines were found to be antigenic, non-allergenic, stable, and induce cellular, humoral, and innate immune responses. TLR-3 docking and in-silico cloning of both constructs were also performed. Conclusion Our results indicate HIV-1b to be more promising than HIV-1a; experimental validations can confirm the efficacy and safety of both constructs and in-vivo efficacy in animal models. Graphical Abstract

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