Structure-Based Virtual Screening and Molecular Dynamics Validation of Tryptoline as a Parasite-Selective PfPNP Inhibitor for Antimalarial Development

Abstract

Artemisinin resistance in Plasmodium falciparum has prompted the search for new antimalarial targets. Purine nucleoside phosphorylase (PNP) from P. falciparum offers real promise as a target because the parasite needs purine salvage to survive and lacks adenosine kinase. This study examined whether PfPNP could be selectively targeted through structural comparison and computational drug discovery protocol. BLAST searches with an e-value threshold of 0.001 found no sequence similarity between PfPNP and human PNP. When we compared their 3D structures, we found only 9% sequence identity with an RMSD of 3.08 Å and TM-score of 0.7, indicating they diverge substantially. A key difference emerged in their structure: PfPNP forms a six-unit complex while human PNP forms a three-unit complex, reflecting how differently they've evolved. Screening 326 compounds identified tryptoline as the best lead, showing superior binding efficiency (GLE: -0.638, GLE-SA: -1.500, GLE-IN: -2.326) compared to other candidates. Molecular docking revealed that tryptoline binds through multiple contact points, including aromatic interactions with Tyr160 and electrostatic interactions with Asp206. Molecular dynamics simulation over 100 ns confirmed that tryptoline stays firmly bound, with critical interactions persisting throughout the trajectory. These results support PfPNP as a selective and viable drug target. Cell-based studies and binding assays are needed to validate tryptoline's potential as a new antimalarial.