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Online Journal of Bioinformatics©
Volume 21(1): 1-20, 2020.
Homology model drug design for 18kDa antigen in Mycobacterium leprae.
Jayasimha Rayalu D1, Shobha Swarna Latha L1, Ramesh K2, Naidu NV 1, Bhaskhar M3
1Department of Bioinformatics, Global institute of Biotechnology, Himayatnagar, Hyderabad-29, 2Department of Biotechnology, Apex Biosciences, Himayat nagar, Hyderabad-29, 3Department of Zoology, Sri Venkateswara University, Tirupati-517502, A.P. INDIA.
Rayalu JD, Latha SSL, Ramesh K, Naidu NV, Bhaskhar M., Homology model drug design for 18kDa antigen in Mycobacterium leprae. Onl J Bioinform., 21(1): 1-20, 2020. Mycobacterium leprae 18kDa antigen is a small heat shock protein shown to induce immunity to leprosy. We predict structure of 18kDa antigen by construct of a 3D model based on crystal structure and assembly of eukaryotic small heat shock protein (PDB: 1GME) with MODELLER7v7. The structure with least modeller objective function was used to start pico-second‑duration molecular dynamics simulations. We refined the model by molecular dynamic minimization rechecked with ERRAT, WHATCHECK and PROCHECK for reliability. Docking was done with 2-mercaptoethanol and 3-amino-5-methylhexanoic acid inhibitors. We found that 3-amino-5,5-diphenylpentanoic acid had most affinity with 18kDa antigen. However MET-03, ARG-04, ASP-31, ALA-32, TRP-33, ARG-34, GLU-35 ARG-89, GLN-90 LEU-91 and VAL-92 were important determinant residues in binding with ligands. For docking we find that GLU-35 in 18kDa protein domain is an important binding residue.
Key words: 18 kDa antigen, homology modelling, Molecular Dynamics, Docking.