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Structure based docking and molecular dynamics studies of Clostridium botulinum using potential natural compounds as drug target

Student name: Ms Arti
Guide: Dr Pallavi Somvanshi
Year of completion: 2018
Host Organisation: International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi
Supervisor (Host Organisation): Dr Dinesh Gupta
Abstract: The emerging cases of food poisoning cases are causing serious threat to human health worldwide. Despite several attempts to control this disease, the endemicity of food poisoning increases yearly. This study involves structure based drug designing against potential therapeutic targets (Uridylate kinase, D- alanine--D-alanine ligase, Diaminopimelate (DAP) epimerase, 1-deoxy-D- xylulose 5-phosphate reductoisomerase, 3-methyl-2-oxobutanoate hydroxymethyltransferase) of Clostridium botulinum ATCC 3502. Homology modeling enables generation of three dimensional models of target proteins using sequence with maximum similarity as template for backbone generation. Many compounds were screened to identify lead molecules capable of inhibiting target proteins. Molecular docking assists in identifying promising candidates for each drug target with highest binding energy to be considered for drug discovery platform. Further, MD simulation was also performed for to study the mobility and conformation of protein–ligand complex at various time intervals.

Keywords: Homology modeling, Molecular docking, MD Simulation