Paper Citing NAMD - Abstract
Munichandrababu, Tirumalasetty; Bhaskar, Baki Vijaya; Ravi, Sahukari; Bhuvaneswar, Cherukupalle; Rajendra, Wudayagiri
Structure based virtual screening of non-steroidal anti-inflammatory drugs (NSAIDs) against RNA-binding motif 6 (RBM6) involved in human lung cancer
MEDICINAL CHEMISTRY RESEARCH, 22:2828-2839, JUN 2013
RNA-binding motif 6 (RBM6) is one of the most potent Lung cancer target proteins in humans. Variations in the expression of two genes such as G15/LUCA15/RBM5 and G16/RBM6/DEF3/NYLU12 show considerable sequence homology to each other in lung cancer cell lines and normal lung tissue. The present study reports construction of basic 3D model of RBM6 protein computationally using Wurst threading server and Modellar 9v7. Further, the developed initial model of the protein was subjected to molecular dynamics simulations using NAMD2.5 software with CHARMM27 force field, TIP 3p model of water, and the energy of structure was minimized with 10,000 steps with integrative time set of 2 ps. The final resolved model reliability was assessed by PROCHECK through Ramachandran plot calculations, Verify3D, and WHATCHECK programs. The Structure Based Virtual Screening was performed with selective 667 NSAIDs drugs from ZINC database against active site of RBM6 using Autodock vina in PyRx Virtual screening tool. The docking results reveal that the compounds ZINC59462883, ZINC59462879, and ZINC 28100170 have -11.2, -10.9, and -10.6 kcal/mol binding affinity, respectively, with RBM6. Through the interaction analysis, it was found that, the binding site residues viz. Ser75, His164, Arg215, Ser216, Arg217, Arg219, Ser279, Glu282, Thr303, and Arg306 were conserved in the interaction of RBM6 with various NSAIDs.
