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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.
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