PARAMETER OPTIMIZATION AND VIRTUAL SCREENING INDONESIAN HERBAL DATABASE AS HUMAN IMMUNODEFICIENCY VIRUS -1 INTEGRASE INHIBITOR USING AUTODOCK AND VINA


Arry Yanuar, Rezi Riadhi Syahdi, Widya Dwi Aryati

Abstract


Objective: Human immunodeficiency virus (HIV-1) is a virus that causes acquired immunodeficiency syndrome, a disease considered to be one of the
most dangerous because of its high mortality, morbidity, and infectivity. The emergence of mutant HIV strains has led treatment to target protease
as reverse transcriptase and integrase enzyme become less effective. This study aims to provide knowledge about the potential of HIV-1 integrase
inhibitors for use as guiding compounds in the development of new anti-HIV drugs.
Methods: This study used AutoDock and AutoDock Vina for virtual screening of the Indonesian herbal database for inhibitors of HIV-1 integrase and
is validated using a database of the directory of useful decoys. Optimization was accomplished by selecting the grid size, the number of calculations,
and the addition of two water molecules and a magnesium atom as cofactor.
Results: This study determined that the best grid box size is 21.1725×21.1725×21.1725 in unit space size (1 unit space equals to macromolecules 1Ǻ),
using AutoDock Vina with EF and AUC values, 3.93 and 0.693, respectively. Three important water molecules have meaning in molecular docking
around the binding pocket.
Conclusions: This study obtained the top ten ranked compounds using AutoDock Vina. The compounds include: Casuarinin; Myricetin-3-O-(2’’,6’’-
di-O-α-rhamnosyl)-β-glucoside; 5,7,2’,4’-tetrahydroxy-6,3’-diprenylisoflavone 5-O-(4’’-rhamnosylrhamnoside); myricetin 3-robinobioside; cyanidin
3-[6-(6-ferulylglucosyl)-2-xylosylgalactoside]; mesuein, cyanidin 7-(3-glucosyl-6-malonylglucoside)-4’-glucoside; kaempferol 3-[glucosyl-(1→3)-
rhamnosyl-(1→6)-galactoside]; 3-O-galloylepicatechin-(4-β→8)-epicatechin-3-O-gallate; and quercetin 4’-glucuronide.


Keywords


Virtual Screening, Indonesian Natural Product, Human immunodeficiency virus-1 integrase, Molecular docking.

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About this article

Title

PARAMETER OPTIMIZATION AND VIRTUAL SCREENING INDONESIAN HERBAL DATABASE AS HUMAN IMMUNODEFICIENCY VIRUS -1 INTEGRASE INHIBITOR USING AUTODOCK AND VINA

Keywords

Virtual Screening, Indonesian Natural Product, Human immunodeficiency virus-1 integrase, Molecular docking.

DOI

10.22159/ijap.2017.v9s1.51_57

Date

30-10-2017

Additional Links

Manuscript Submission

Journal

International Journal of Applied Pharmaceutics
Vol. 9, Special Issue (Oct.), 2017 [PTMDS 2017] Page: 90-93

Online ISSN

0975-7058

Statistics

11 Views | 16 Downloads

Authors & Affiliations

Arry Yanuar
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.
Indonesia

Rezi Riadhi Syahdi
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.
India

Widya Dwi Aryati
Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.
Indonesia


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