An In-silico study of rational drug design for Pseudomonas aeruginosa Rhamnosyltransferase A enzyme and transcriptional regulator rhlR enzyme via blocking formation of biofilm

Abstract

Ubiquitous, mobile, opportunistic pathogen named Pseudomonas aeruginosa which is gram negative is well-known for causing a plethora of nosocomial infections. It poses serious threats in immunocompromised hosts and is very difficult to treat in patients. It has become extremely difficult to eradicate it from hospitals due to its resistance towards antibiotics and disinfectants. Therefore, there is a dire need of innovative therapies to treat the multi-drug resistant bacterium. This pathogen easily develops biofilm which shows prominent resistance to antibiotics and this is why WHO has classified it as one of the ESKAPE infections. PAO1 has been of good use in understanding the biology of pseudomonas and is helpful in assessing the novel treatment. We used a rational drug design approach, in this study, to inhibit quorum sensing pathway, rhl, in pseudomonas aeruginosa PAO1 which is responsible for biofilm formation and rhamnolipid synthesis. We did so by suggesting inhibitory molecules against the two enzymes, Rhamnosyltransferase subunit A which is encoded by the gene rhlA and Regulatory protein RHLR encoded by the gene rhlR. Homology modelling was performed to obtain the 3D structure of the target proteins which were then refined. Various tools such as ERRAT and Ramachandran plot were used to assess the quality of the protein. Seventeen compounds for rhlA and eight for rhlR were extracted using Chembl and PubChem. Castp was used to analyze the ligand binding domain. Site specific docking was carried out to find the ligand showing the most negative binding affinity value with the enzyme that has been targeted. Two compounds against each protein were selected with the most negative binding affinity. These compounds were then checked for ADMET properties and bioavailability. Molecular dynamic simulation results further calculated the stability of the complex. The compounds explored are expected to be an effective drug against the target proteins in blocking the rhamnolipid synthesis and biofilm formation. Detailed laboratory experimentation is always necessary to bridge the gap between wet and dry laboratory studies and to ensure the validity of the obtained results.