In this study, molecular docking and molecular dynamic simulations were used to generate complexes, determine binding sites, and calculate the binding free energies of different quinoline-based ligands to Plasmodium falciparum lactate dehydrodgenase.  Two binding sites were identified for each ligand, with the cofactor binding site as the primary site. Docking results indicate that in the absence of the cofactor  each ligand was predominantly bound to the vacant cofactor site. In the presence of cofactor, the secondary site was the predominant binding site for each ligand. The average binding energy  of the most stable conformations at the cofactor site was  -6.626 +/- 0.092 kcal/mol. The top conformations at the alternative site had an average binding energy of  -7.378 +/- 0.179 kcal/mol. These results indicate that ligand binding may be competitive with cofactor and that there exists an alternative binding site with equal affinity as the cofactor binding site.

Binding of quinoline-based ligands to <i>Plasmodium falciparum</i> lactate dehydrogenase: A molecular docking study

243rd National Meeting (2012)

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Binding of quinoline-based ligands to Plasmodium falciparum lactate dehydrogenase: A molecular docking study