Insilco Analysis and Identification of Biosurfactants Effects on E. Coli K12 Proteins to Inhibit Biofilm

Abstract

Microbes have the tendency to attach on surface and developed biofilm. The act of producing biofilms is the social behavior of the microbes when they are in stress condition. Sometime this kind of aggregation of cell to produce biofilm leads to certain disease in human. Despite this, the biofilm producing bacteria also carried the attention due to its antibiotic resistance properties. To encounter this, an in-silico approach was carried out to targets biofilm producing proteins with the desirable biosurfactants, rhamnolipid. Rhanmnolipid, a glycolipid type of biosurfactants crystalline acid made up of β-hydroxyl fatty acid. It was taken as the desired ligand for various biofilm producing proteins. Certain in silico tools like UCSF CHIMERA, DISCOVERY STUDIO 4.1, AUTODOCK 4.0 and LIGPLOT were used to analyze the interaction between the targeted protein and desired ligand (rhamnolipid). A strong binding affinity has been deduced between the biofilm producing protein (pgaC) and ligands (rhamnolipid) as well as the binding pockets of the proteins were also revealed. The molecular docking approach revealed that rhamnolipid bind with certain proteins very efficiently. Out of the 14 selected proteins, 6 proteins that are pgaC (-8.91 kcal/mol), csgD (-7.75 kcal/mol), bdcA(-7.04 kcal/mol), pgaB(-7.30 kcal/mol), tabA(-6.08) and mqsA(-6.54 kcal/mol) were considered to be a quality target proteins for the bio surfactants. Strong effective interaction along with its bond angle and bond length was observed within 3.5 A0. Ligand optimization was obtained in order to make the molecule more potent. Analysis of the ADMET properties confirmed the micromolecule as a possible drug candidate. Thus the overall study suggested the optimized ligand molecule as a therapeutic target against microbial biofilm producing proteins.

Keywords: Biofilm, Bio surfactants, Insilco analysis, Chimera, Discovery studio, K-12