Construction of 3D Model of Protein Drug Targets for Renibacterium Salmoninarum - a Bacterial Pathogen Causing Bacterial Kidney Disease in Young Salmonid Fish

Om Kumar , Keerthana G<, Ashitha B Arun , Ananya Joliholi and Lokesh Ravi*

Department of Botany, St. Joseph’s College (Autonomous), Bengaluru, India.

Corresponding Author E-mail: lokesh.ravi@sjc.ac.in

DOI : http://dx.doi.org/10.13005/bbra/2943

ABSTRACT:

The aim of this study is to construct 3D models of potential drug targets for the Bacterial Kidney Disease (BKD) causing pathogen Renibacterium salmoninarum. The bacterial pathogen Renibacterium salmoninarum was selected for homology modeling studies since there were no known protein structures of the organism reported in the NCBI database. The reported protein sequences were run through DrugBank to pick out drug-targets. Online databases and web tools such as PMDB, UniProt, Drug Bank, and SwissModel were employed in this analysis. An aggregate of 412 protein sequences were identified as potential drug targets and were retrieved from the UniProt. Homology models of the protein sequences were constructed using the SwissModel database for all 412 proteins. These were then refined through a protein blast and Ramachandran plot analysis. Out of the 412 constructed models, 143 models were of reliable quality. These were then submitted to the PMDB database for further reference. To demonstrate the application of these constructed models, protein-ligand docking analysis using Auto Dock Vina was performed. Among the antibiotics that were tested against their known drug targets, trimethoprim demonstrated significant potential for the inhibition of R. salmoninarum’s dihydrofolate reductase protein, with a binding energy of -9.06 Kcal/mol and with the formation of 3 hydrogen bonds. Therefore through protein-ligand docking studies and the construction of 3D models of protein drug targets, Trimethoprim is proposed as a solution to the Bacterial Kidney Disease (BKD) problem in salmonid fishes. Further in-vitro evidences are in demand to prove this hypothesis.

KEYWORDS: Bacterial Kidney Disease; Homology Modelling; Protein Drug Targets; Protein Model Database; Renibacterium salmoninarum

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