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Online Journal of Bioinformatics ©
Volume 14(2):213-225, 2013
Virtual inhibitors of L-Type calcium channel
Madhu Sudhana Saddala and A. Usha Rani*
Department of Zoology, DBT-Bioinformatics center, Sri Venkateswara University, Tirupati – 517502, A.P., India.
Saddala MS, Rani U., Virtual inhibitors of L-Type calcium channel, Onl J Bioinform., 14(2):213-225, 2013. Cadmium (Cd) is a toxic metal. Diet, occupation and smoking are the primary routes of exposure in humans which can results in a variety of adverse effects. Cd may allow the entry of excess calcium through voltage-dependent L- type calcium channel (VLCC) which regulates smooth and cardiac muscle contraction. Therefore VLCC could be a potential drug target. Diltiazem (CID 39186) is a vasodilator due to its antagonistic activity on calcium ions on membrane receptors and is a potential blocker of the target protein. VCLC was energy minimized and subjected to molecular dynamic simulations using NAMD 2.9 software with CHARMM27 force field in water The receptor structure was minimized 25,000 steps for 500 ps and simulated 1,000,000 steps for 2ns. 4500 compounds were screened from PubChem database through structure based virtual screening with reference to Diltiazem. The screened compounds were docked into the active site of the protein using Autodock Vina in PyRx Virtual Screening tool. The docking results shows that the compounds CID08830211, CID13650942, CID65739916 and CID65748951 had -9.0, -8.6, -8.4 and -8.2kcal/mol respectively. Through the interaction analysis, it was found that Asp, Thr, Leu, Arg, Tyr, Gln, Pro, Glu, Phe, and His residues of 3LV3 protein were important anchoring residues for the ligands which are main contributors to the blockers interactions.
Keywords: Docking, Diltiazem, H-bond, CCBs, 3LV3, Autodock Vina