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OJBTM
Online Journal of Bioinformatics ©
Volume
14 (2): 146-159, 2013
In Silico inhibitors for Plasmodium
falciparum lactate dehydrogenase
Madhu Sudhana Saddala, K. Kranthi Kumar and A.
Usha Rani*
Division of Environmental Biology,
Department of Zoology, DBT Bioinformatics Center, Sri Venkateswara
University, Tirupati
A.P., India.
ABSTRACT
Madhu Sudhana Saddala, K. Kranthi Kumar and A. Usha Rani, In Silico Inhibitors for
Plasmodium falciparum lactate dehydrogenase, Onl J Bioinform.,
14 (2):
146-159, 2013 Dysruption of
receptor sites on Plasmodium falciparum
lactate dehydrogenase (PfLDH)
could inhibit the malarial parasite. We describe Virtual gossypol-like
compounds that might inhibit PfLDH by interacting with amino acids on its receptors.
Multiple sequence alignment of PfLDH with Plasmodium
spp was performed with Clustal
W1.83. A phylogenetic tree was constructed with Tree Viewer 3.0. Protein structure was refined by 2ns molecular
simulation and energy minimization.
Compounds (1997) were then screened Virtually (Autodoc Vina) for similarity with
gossypol from The Zinc database for binding capacity. Docking showed that
sequentially ZINC27313038,
ZINC13759138, ZINC13759183, ZINC13759202, ZINC59648667 and
ZINC11159075 k.cal/mol had most binding
capacity with PfLDH
compared with gossipol. These compounds bind by hydrogen
bonds and hydrophobic interactions and may
inhibit PfLDH
mediated glycolysis The cavity surrounded
by Ile31, Gly99, Asn140, Gly32, Thr101, Gly29 Thr97, Asp53, Met30, Phe52 and
Glu122 may possibly be manipulated to inhibit the parasite.
Keywords: PfLDH,
NAMD, MDSimulation,
Virtual screening, Docking, Zinc database
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