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Online Journal of Bioinformatics ©
Volume 13(2):260-273, 2012
Prediction of crucial water molecules during interaction of curcumin and
demethoxycurcumin at active sites of multiple target proteins
Nitya Singh1, Anil Butle1, Krishna Misra1,2
1Division of Applied Sciences and Indo Russian Centre for Biotechnology [IRCB-, Indian Institute of Information Technology, Allahabad, 2Center for Biomedical Research, SGPGIMS campus, Lucknow, India
Singh N, Butle A, Misra K., Prediction of crucial water molecules during interaction of curcumin and demethoxycurcumin at active sites of multiple target proteins, Onl J Bioinform., 13(2):260-273, 2012. The role of water molecules in binding multiple molecular targets of curcumin and demethoxycurcumin to predict conserved water molecules is described. From CCDC/Astex dataset 272 protein ligand complexes having active sites containing water molecules and structurally cleaned geometries were extracted and screened for targets of curcumin and PDB structures of human origin. Comparative molecular docking simulations were performed with corresponding default ligand of all screened PDBs, curcumin and demethoxycurcumin. Binding patterns and scores in the presence or absence of water molecules during docking simulations revealed that some specific conserved water molecules are not replaced by any ligands. Three Proteins; Map kinase, progesterone and rennin with PDB’IDs 1A9U, 1A28 and 2I4Q respectively, were found to have higher docking scores if water molecules proximal to the active site were included in the molecular docking process. Further docking with all available ligands in PDB for these 3 proteins established the presence of conserved water molecules at their corresponding active sites. Energy profiling of contributing water molecules also established their role and bridging effect in protein ligand interaction. Such findings suggest that the influence of water should be considered while framing efficient computational drug designing strategies which borrow their success on efficient calculations of protein ligand interactions.
Key words: Protein ligand interaction; Molecular docking; Conserved water; Curcumin;Demethoxycurcumin