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Inactivation of cell-free HIV-1 by designing potent peptides based on mutations in the CD4 binding site

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Abstract

Human immunodeficiency virus type 1 (HIV-1) is a major global health problem, with over 38 million people infected worldwide. Current anti-HIV-1 drugs are limited in their ability to prevent the virus from replicating inside host cells, making them less effective as preventive measures. In contrast, viral inhibitors that inactivate the virus before it can bind to a host cell have great potential as drugs. In this study, we aimed to design mutant peptides that could block the interaction between gp120 and the CD4 receptor on host cells, thus preventing HIV-1 infection. We designed a 20-amino-acid peptide that mimicked the amino acids of the CD4 binding site and docked it to gp120. Molecular dynamics simulations were performed to calculate the energy of MMPBSA (Poisson–Boltzmann Surface Area) for each residue of the peptide, and unfavorable energy residues were identified as potential mutation points. Using MAESTRO (Multi AgEnt STability pRedictiOn), we measured ΔΔG (change in the change in Gibbs free energy) for mutations and generated a library of 240 mutated peptides using OSPREY software. The peptides were then screened for allergenicity and binding affinity. Finally, molecular dynamics simulations (via GROMACS 2020.2) and control docking (via HADDOCK 2.4) were used to evaluate the ability of four selected peptides to inhibit HIV-1 infection. Three peptides, P3 (AHRQIRQWFLTRGPNRSLWQ), P4 (VHRQIRQWFLTRGPNRSLWQ), and P9 (AHRQIRQMFLTRGPNRSLWQ), showed practical and potential as HIV inhibitors, based on their binding affinity and ability to inhibit infection. These peptides have the ability to inactivate the virus before it can bind to a host cell, thus representing a promising approach to HIV-1 prevention. Our findings suggest that mutant peptides designed to block the interaction between gp120 and the CD4 receptor have potential as HIV-1 inhibitors. These peptides could be used as preventive measures against HIV-1 transmission, and further research is needed to evaluate their safety and efficacy in clinical settings.

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Acknowledgements

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  1. Department of Biology, Faculty of Science, Bu-Ali Sina, University, Hamedan, Iran

    Fatemeh Sabzian-Molaei

  2. Social Determinants of Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran

    Mohammad Amin Ahmadi & Mohammad Sabzian-Molaei

  3. Department of Biology, Oberlin College, Oberlin, OH, 44074, USA

    Zahra Nikfarjam

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Sabzian-Molaei, F., Ahmadi, M.A., Nikfarjam, Z. et al. Inactivation of cell-free HIV-1 by designing potent peptides based on mutations in the CD4 binding site. Med Biol Eng Comput 62, 423–436 (2024). https://doi.org/10.1007/s11517-023-02950-8

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