Exploration and validation of diphosphate-based Plasmodium LytB inhibitors using computational approaches

J Mol Recognit. 2019 Feb;32(2):e2762. doi: 10.1002/jmr.2762. Epub 2018 Sep 7.


LytB or IspH is an indispensable enzyme and a suitable drug target of Plasmodium falciparum that participate in isoprenoid biosynthesis of nonmevalonate pathway (MEP). Recently, we have investigated the structural dynamics of Plasmodium LytB and proposed some novel diphosphate-based inhibitors using molecular modeling and docking studies. Here, we have tried to characterize those previously screened molecules by quantitative structure activity relationships and pharmacophore-based analyses, as well as validated the dynamics of their interactions with LytB protein. Five total compounds having PubChem CID 516, 125696, 165275, 448012, and 9921431 were predicted with significant inhibitory activity by quantitative structure activity relationships and pharmacophore models. Again, the molecular dynamics simulation results showed that these five compounds are able to form stable complexes with the receptor through many direct and water mediated interactions. The binding free energies calculated by Poisson-Boltzmann surface area method resulted within the range between -99.77 and - 43.74 kcal/mol, which favoured their profound inhibitory affinity. Residues of LytB like His41, His74, Ser222, Ser223, and Asn224 in LytB were the main protagonists in contributing the majority of interaction energies to the ligands. Finally, the ADMET, toxicity, and drug-likeness scores also affirm these compounds to be considered for further development of new antimalarial inhibitor in the future.

Keywords: MD simulation; MEP pathway; MM-PBSA; Plasmodium LytB; QSAR; diphosphate; pharmacophore.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antimalarials / chemistry*
  • Antimalarials / pharmacology*
  • Diphosphates
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Plasmodium / drug effects*
  • Plasmodium falciparum
  • Protein Binding


  • Antimalarials
  • Diphosphates