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Online Journal of Bioinformatics ©
Volume 14 (3): 293-301, 2013
In silico inhibitors for falcipain-3 in Plasmodium falciparum.
Madhu Sudhana Saddala, P. Gayathri, J. Obaiah C. Vallamma and A. Usha Rani*
Dept. of Zoology, DBT-Bioinformatics Center, Sri Venkateswara University, Tirupati.
Saddala MS, Gayathri P, Obaiah J,. Vallamma C. Usha Rani A., In silico inhibitors for falcipain-3 in Plasmodium falciparum, Onl J Bioinform., 14 (3): 293-301, 2013. Inhibition of falcipain-3 prevents maturation of Plasmodium falciparum, suggesting that the protein could be a target for antimalarial activity. Falcipain-3 was energy minimized and subjected to molecular dynamics simulations using NAMD 2.9 software with CHARMM27 force field in water and the receptor structure was minimized with 25,000 steps for 500ps and simulated 10,000 steps for 2ns. 2500 compounds were screened from PubChem database through structure based Virtual screening by referencing Mefloquine. The screened compounds were docked into the active site of the protein using Autodock Vina in PyRx Virtual Screening tool. Results showed that CID3000506, CID40468067, CID65330, CID40692 and CID4046 had a highest binding energy of -9.4, -8.9, -8.4, -7.9 and -7.2 kcal/mol, respectively. Lead hit compounds were tested for toxicity and bioavailability with Osiris and Molinspiration online servers. Active site amino acids His18, Asp44, Tyr63, Gln110, Tyr115, Asp168, His196, Glu199, Gly453 and Met434 could play a role in binding and catalytic activity.
KEYWORDS: Falcipain-3, simulations, docking, PubChem database, Autodock Vina