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OJBTM
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.
ABSTRACT
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.