Majority of the HIV medications help people live longer and healthier lives. HIV can be prevented at various stages using different types of antiviral drugs, that are either Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTI) or as Nucleoside Reverse Transcriptase inhibitors (NRTIs) or combination drugs. However, there are several short term as well as long term effects associated with majority of the drugs used for the treatment of HIV. Nevirapine (NVP) is one such drug that is used as a Non-Nucleoside Reverse transcriptase (NNRTI) that treats the Human immunodeficiency virus 1 (HIV-1). One such long term effect of Nevirapine is, it does not completely suppress HIV-1, and mutations in the HIV-1 protein reverse transcriptase lead to resistance. The method used in this investigation focuses finding a more suitable NNRTI that is less likely to have such drug resistance. One such study involves Structure Based Drug Design (SBDD) of Cocrystallized structure of Nevirapine with the available PDB (Protein Data Bank). Molecular docking is one of the most commonly used methods in SBDD due to its capability of predicting the binding conformation of ligands to the appropriate target binding site. To investigate the binding mode of the NNRTI inhibitors, molecular docking simulations were performed by means of the software MOE In the cocrystallized molecules water was deleted and all polar hydrogens were added using the appropriate tool in the builder module of MOE (Molecular Operating Environment). Modifying substituents with different fragments that fits in the receptor packet were selected from the listed fragments in the builder besides using various other modifications. Several Physico chemical Ligand properties such as LogP -log of the octanol/water partition coefficient and Log D The octanol/water distribution coefficient at pH 7, log S -log of the aqueous solubility (mol/L), estimated strain energy for a given conformation (kcal/mol) were calculated. The binding affinities were also estimated using the GBVI/WSA dG scoring function in kcal/mol. The modeling results suggest that the observed SAR may be explained by a possible interaction of the selected modification of the ligand. Conformational search to find the most suitable conformation using docking process will be used to study the mechanism of binding of the ligands to the receptor.

Structure activity relationship(SAR) studies of Nevirapine using computational methods

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.