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OJBTM
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
ABSTRACT
Singh N, Butle A, Misra K., Prediction of crucial water molecules during
interaction of curcumin and demethoxycurcumin
at active sites of multiple target proteins, Online 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