Molecular Docking of the Pneumococcal Main Autolysin (Lyta) and Deoxycholate Ligand Publisher Pubmed



Chalbatani GM¹ ; Karimaei S² ; Afshar D³ ; Moghadam SO⁴ ; Mahmoodzadeh H¹ ; Amini M² ; Shirkhoda M¹ Show Affiliations
Source: Pakistan Journal of Pharmaceutical Sciences Published:2020

Abstract

In the Streptococcus pneumoniae, the N-acetylmuramoyl-l-alanine amidase known as LytA protein is a main autolysin and in the presence of sodium deoxycholate, it activates and breaks S. pneumoniae cell wall. In the present study, the interaction between the LytA protein and deoxycholate as ligand was investigated. The Lyt A protein was retrieved from PDB databank and energetically minimized by Molegro Virtual Docker. The binding sites of LytA protein were detected and molecular docking carried out using MolDock algorithm. Finally, the number of hydrogen and electrostatic bonds were obtained for each predicted pose. A total of 5 binding sites predicted on LytA protein. The number of 5 predicted poses for each binding site also detected and molecular docking showed that all the poses have interactions (by H bonds) with deoxycholate. The interaction of the LytA protein with the deoxycholate ligand reveal five binding sites, which are involved in deoxycholate substrate recognition. © 2020 Pakistan Journal of Pharmaceutical Sciences. All rights reserved.