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OJBTM
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.
ABSTRACT
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
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