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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.
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