Virtual binding of flavonoids to NS5 dengue virus mRNA 2'-O- Methyltransferase domain using Autodock software

Date

4-2009

Degree

Bachelor of Science in Agricultural Chemistry

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Ernesto J Del Rosario

Abstract

The molecular docking of flavonoids to NS5 Dengue Virus mRNA 2'-o-methyltransferase domain was studied using Autodock Software. The three-dimensional crystal structure of NSSMTaseDV, was obtained from the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The structures of the ligands were drawn and optimized using HyperChem Software. Control dockings were done in order to validate the energy calculations by docking ethylbenzene T4-Lysozyme and the binding site by docking S-adenosyl-L-methionine (SAM) and Ribavirin 5-Triphosphate to NSSMTaseDV Sixty seven out of the seventy six ligands docked at the SAH/SAM binding site gave more favorable docking energies than SAM. The distances between the ligand molecule and amino acid residues in the binding site of the enzyme were measured, if the distance is less than 4.5 A, the residue is considered to have interaction with the ligand. Based on the calculated final docked energy, type of inhibition and the ligand-receptor interaction, the two most potent inhibitors are Kuwanon A and Glabranin. For Kuwanon A, the residues involved in the interaction were: SER 56, ARG 57, GLY 58, LYS 61, ASP 79, GLY 81, CYX 82, GLY 83, ARG 84, GLY 86, TRP 87, GLU 111, ASP 146, ILE 147, GLY 148, GLU 149, LYS 181, LEU 210, SER 211, ARG 212, THE 215 and GLU 217. The residues involved in the interaction of Mulberrin with the receptor were: SER 56, ARG 57, GLY 58, LYS 61, GLY 81, CYX 82, GLY 83, ARG 84, GLY 86, THR 104, GLY 106, HIS 110, GLU 111, ASP 146, ILE 17, GLY 148, GLU 149, SER 150, LYS 181, LEU 210, SER 211, ARG 212 and THR 215.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

LG 993.5 2009 C13 K35

Document Type

Thesis

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