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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.
ABSTRACT
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
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