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Online Journal of Bioinformatics ©
Volume 15 (1): 98-105, 2014.
Molecular dynamic simulation docking inhibitors of falcipain - 2
Madhu Sudhana Saddala1, D. kumar Babu1, G. Bhavani1, S. Ayisha2 and A. Usha Rani1*
1Division of Environmental Biology, DBT- Bioinformatics Center, Department of Zoology, Sri Venkateswara University, Tirupati – 517502, A.P., India. 2Department of Microbiology, Sree Vidyanikethan College, Tirupati – 517502, A.P., India.
Saddala MS, Babu DK, Bhavani G, Ayisha S, Usha Rani A., Molecular dynamic simulation docking inhibitors of falcipain – 2, Onl J Bioinform., 15 (1): 98-105, 2014. Falcipain-2 promotes intracellular development of the malaria Plasmodium Spp. parasite and degrades the protein hemoglobin. Inhibition of falcipain-2 prevents parasite maturation and therefore the falcipain 2 protein may be a target for antimalarial drugs. Falcipain-2 was energy minimized and subjected to molecular dynamic simulation using NAMD 2.9 software with CHARMM27 force field in water. The receptor structure was minimized by 25,000 steps for 500 ps and simulated 100,000 steps for 2ns. 15560 compounds were screened from PubChem database through structure based virtual screening referencing Mefloquine. The screened compounds were then docked into the active site of falcipain 2 with Autodock Vina in PyRx Virtual Screening tool. Five compounds CID54578538, CID46233016, CID44361455, CID432301 and CID456309 showed most binding energies of -9.2, -9.1, -8.5, -8.1 and -7.1 kcal/mol respectively. The docking method found these compounds to possess suitable binding energies with falcipain-2 when compared with Mefloquine.
Keywords: Falcipain-2, Virtual screening, Docking, PubChem database and PyMol.