"Virtual binding of synthetic nucleoside analogues and phyto -brassinosteroids to NS5 dengue Vvrus mRNA 2'-O- methyltransferase domain using autodock software"

Date

4-2007

Degree

Bachelor of Science in Chemistry

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Ernesto J. Del Rosario

Co-adviser

Dolores P Buquiran

Abstract

Molecular drug design is facilitated through virtual binding or "docking" of inhibitors. The molecular docking of phyto-brassinosteroids and synthetic nucleoside analogues was studied using the AutoDock Software. The three-dimensional crystal structure of NS5 Dengue Virus mRNA 2' -0-methyltransferase Domain (NS5MTaseuv) was obtained from the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB). The structures of the ligands were drawn using HyperChem Software. The same program was used to optimize the structures using Molecular Mechanics (AMBER) and Semi-Empirical (by PM3) methods. Two control dockings were performed to validate the method; the first control was for the validation of the binding site by docking S-adenosyl-L-homocysteine (SAH) and ribavirin-5' -triphosphate (RIP) to NS5MTasetw and the second was for the validation of energy calculation by docking ethylbenzene to T4-Lysozyme. The interactions made by the macromolecule-ligand complex were analyzed using Visual Molecular Display (VMD). Forty-eight ligands were observed to bind to the SAH/SAM binding site and showed more favorable docking energies than S-adenosyl-L-methionine (SAM). The ligand that gave the most negative docking energy, —16.19 ± 0.35 kcalimol, was 28- nortyphasterol. The ligand showed interactions with the following residues in the enzyme binding site: SER 56, ARG 57, GLY 58, LYS 61, GLY 81, CYS 82, GLY 83, ARG 84, GLY 85, GLY 86, TRP 87, THR 104, LYS 105, GLY 106, HIS 110, GLU 111, ASP 146, ILE 147, GLY 148, GLU 149, and LYS 181.

Language

Filipino

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

This document is currently not available here.

Share

COinS