Molecular Modeling and Screening of Antiviral peptides for HIV-Glycoprotein (gp41) using Hpepdock software for the therapy of AIDS (Acquired ImmunoDeficiency Syndrome)

Abstract

Aim: To determine the binding affinity (Kcal/mol) for various antiviral peptides to target AIDS (Acquired Immunodeficiency Syndrome) gp41 protein. Materials and methods: The three-dimensional coordinates of gp41 protein were retrieved from Protein data bank(PDB ID 3VIE). The structures of 16 antiviral peptides were modeled using Hpepdock software. The Hpepdock software was used to perform a molecular docking investigation of gp41 with antiviral peptides. This software uses an algorithm to produce output complexes based on peptide conformations and orientations.The power calculation was done by clinical.cal.com, comparing binding affinity (kal/mol) for HIV virus gp41 protein Alpha error-threshold 0.05 power is 80% and for enrollment ratio-1. Results: Molecular docking analysis revealed that antiviral peptides namely, P9R peptide 3, M1 peptide 1 and P9 peptide 3 could bind gp41 protein with higher affinity in comparison with the reference Macrocyclic iHA-100 peptide. The antiviral peptides of P9R Peptide 3, M1 peptide 1 and P9 Peptide 3 with p=0.029, p<0.05 significant ( -192.321Kcal/mol), p=0.918, p>0.05 insignificant (-179.685Kcal/ mol), p=0.029 p<0.05 significant (-172.523Kcal/mol) showed better results in comparison to reference Macrocyclic iHA-100 peptide ( -207.052 Kcal/mol). Conclusion: The identified novel antiviral peptides could effectively inhibit gp41 protein than other drugs in the market to treat AIDS(acquired immunodeficiency syndrome) disease.