Molecular dynamics simulations of complexes of human dipeptidyl peptidase III with inhibitors

Tir, Nora (2016) Molecular dynamics simulations of complexes of human dipeptidyl peptidase III with inhibitors. Diploma thesis, Faculty of Science > Department of Chemistry.

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Abstract

Dipeptidyl peptidase III (DPP III) is a zinc dependent peptidase which catalyses hydrolysis of the second N-terminal peptide bond of its substrates. DPP III is an enzyme of broad substrate specificity and it has been found in many organisms. Although its fundamental physiological role is unknown, it has been recognised in several processes of interest for the drug development. In this thesis, molecular dynamic simulations were done for the complexes of human DPP III with two inhibitors for which the percentages of inhibition have been measured for the Arg-Arg-2-naphthylamide synthetic substrate hydrolysis. Two enzyme conformations of different compactness were used for the simulations. Subsequently, the binding free energies were calculated in order to find out which one is more favorable for ligand binding and to obtain an insight into the ligand-protein interactions. The obtained results might be useful in future development and testing of potential inhibitors of this enzyme.

Item Type: Thesis (Diploma thesis)
Keywords: human dipeptidyl peptidase III, metallopeptidases, molecular dynamics,inhibitors,free energy of binding, substrate specificity
Supervisor: Tomić, Sanja
Date: 2016
Number of Pages: 50
Subjects: NATURAL SCIENCES > Chemistry
Divisions: Faculty of Science > Department of Chemistry
Depositing User: Branka Maravic
Date Deposited: 01 Jul 2016 09:27
Last Modified: 01 Jul 2016 09:27
URI: http://digre.pmf.unizg.hr/id/eprint/4942

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