Title: Homology modelling and docking studies of strictosidine β-D-glucosidase from Madagascar periwinkle (Catharanthus roseus Bunge)

Authors: Piotr Szymczyk; Grażyna Szymańska; Małgorzata Majewska; Izabela Weremczuk-Jeżyna; Michał Kołodziejczyk; Kamila Czarnecka; Paweł Szymański; Ewa Kochan

Addresses: Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, Medical University of Łódź, 90-151 Łódź, Poland ' Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, Medical University of Łódź, 90-151 Łódź, Poland ' Faculty of Pharmacy, Department of Biology and Pharmaceutical Botany, Medical University of Łódź, 90-151 Łódź, Poland ' Faculty of Pharmacy, Department of Biology and Pharmaceutical Botany, Medical University of Łódź, 90-151 Łódź, Poland ' Faculty of Pharmacy, Drug Technology Department, Medical University of Łódź, 90-151 Łódź, Poland ' Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Drug Analyses and Radiopharmacy, Medical University of Łódź, 90-151 Łódź, Poland ' Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Drug Analyses and Radiopharmacy, Medical University of Łódź, 90-151 Łódź, Poland ' Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, Medical University of Łódź, 90-151 Łódź, Poland

Abstract: Here, the structure of the enzyme and substrate binding site of C. roseus strictosidine β-D-glucosidase is reported. An homology model of C. roseus strictosidine β-D-glucosidase was built using the Discovery Studio 4.1 software package and rice Os3bglu6 β-glucosidase (PDB code: 3GNPA) as a template. The CDOCKER algorithm was used to dock the natural substrate, strictosidine, as well as an inhibitor D-glucono 1,5-lactone. Obtained structures were refined in the course of molecular dynamic simulation. Analysis of the acquired data provided information on the C. roseus strictosidine β-D-glucosidase amino acid residues interaction with the natural substrate and inhibitor. Our findings expand the basic knowledge of the structure of the C. roseus strictosidine β-D-glucosidase active site, and may also be used in the design of enzyme point mutations with improved stability and catalytic properties, or to change substrate specificity.

Keywords: homology modelling; ligand docking; enzyme-ligand interactions; alanine scanning; mutagenesis.

DOI: 10.1504/IJBRA.2022.10033607

International Journal of Bioinformatics Research and Applications, 2022 Vol.18 No.3, pp.234 - 269

Accepted: 29 Mar 2020
Published online: 22 Aug 2022 *

Full-text access for editors Access for subscribers Purchase this article Comment on this article