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Human immunodeficiency virus type 1 (HIV-1) is the causative agent for acquired immunodeficiency syndrome (AIDS). In 2020, South Africa recorded an estimated 8,2 million people living with HIV. This extensive figure is a red flag to the country, as it causes serious economic burden to its health care system. In the quest for finding a suitable inhibitor for HIV-1 protease, computer aided drug design (CADD) approachstands out to be one of the leading fields of study in pursuit of a new drug for HIV. The Lipinski rule of five was applied in screening the ninety-two plant extracts from Ocium santum, Carica papaya, Persea Americana, Azadirachta indica and Spondias mombin medicinal plants, and forty-six of the compounds complied with this rule. Afterwards, a ligand-based pharmacophore was constructed based on the active properties of the three (3) best binding compound obtained from the screened ZINC compounds (Zinc_001456687980, Zinc_001445792073 and Zinc_001461099137). Then the compounds with less than 0.5 RMSD were picked out. The best 10 compounds were docked and compared with a drug that is already in the market, dolutegravir. 3, 5-di-O-galloyl-4- O-digalloylquinic acid 3,5,4,4-Tetragqa (-8.6), epicatechin (-8) and quercitrin (-8) obtained the highest binding affinity.Even though Tetragqa had the highest binding affinity, it failing the test because of its large molecular weight. The safety evaluation and other chemical parameters that included the lipophilicity, physicochemical other properties of these compounds was performed through SwissADME/T web server. On the best top three binding compounds, only epicatechin (-8) had promising features of a drug candidate. However, the remaining compounds from the best 10 compounds were also analysed using the SwissADME/T tools, whereby two of them (juglanin and catechin) satisfied the ADMET prediction analysis. Catechin showed some promising features as well after it displayed good druglike properties, suitable for a novel compound. Lastly, molecular dynamics simulation was then performed on the three lead compounds namely; epicatechin, juglanin andcatechin against dolutegravir. The ligand protein interaction between catechin and the protein displayed minimal shift of the protein during the simulation that was performed over 100ns, signifying a strong complex association.

pakistan journal of medical and health sciences

Computational Studies for Selected Medicinal Plants against Dolutegravir using Ligand Based Pharmacophore, Molecular Docking, ADMET Predictionsand Molecular Dynamics Simulation