Computational modeling of the binding of selected ligands to native insects chitinases using autodock software

Date

10-2004

Degree

Bachelor of Science in Chemistry

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Edwin P. Alcantara

Abstract

TESORERO, ALHYNN P. University of the Philippines Los Banos. October 2004 Molecular Modeling of the Binding of Selected Ligands to Native Insect Chitinases Using AutoDock Software.

Adviser Dr Edwin P Alcantara

Co-Adviser. Alma 0. Gonzales

Consultant: Dr. Ernesto J. del Rosario

Blind docking of four ligands, namely (GIcNAc)5, allosamidin (ALLO), demethylallosamidin (DEME), and cyclic-(L-Arg-D-Pro) (CAP) to three insect chitinases from Bombyx mori, Aedes aegypti and Manduca sexta was done using AutoDock software.

The common residues identified to be present in the active sites of complexes were: Trp, Asp, Ser, Tyr, and Arg. H-bonding primarily mediated the binding of ligands to catalytic residues in chitinases. Hydrophobic interactions of the methyl group with polar aromatic residues, as well as stacking of rings were also observed.

Calculations using flexible ligands generally gave lower values of △Gbinding, and compared to those for rigid ligands, which can be attributed to the steric strain caused by repulsive forces due to the flexibility of the atoms in the ligands.

Among the complexes studied, Al. sexta Chi-DEME for the rigid ligand had the most negative (10.51±0.78 kcal/mol). While (G1cNAc), has the least negative values of △Gbinding and Edocked for all insect chitinases.

Observations of docked structures reveal that CAP can act as a competitive inhibitor for all the three chitinases while ALLO and DEME are probably non-competitive inhibitors. Nevertheless, in the case of M. aorta chitinase, all the inhibitors d on closely similar binding pockets and could cause competitive inhibition of the enzyme.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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