Computational characterization of a HotDog domain-containing hypothetical protein from the food vacuole of Plasmodium falciparum reveals potential allosteric regulation by antimalarials.

Abstract

Plasmodium falciparum, the causative agent of the most lethal form of human malaria, harbors numerous uncharacterized proteins whose functions remain unexplored yet may be central to its survival and pathogenicity. Among its specialized organelles, food vacuole plays pivotal role in hemoglobin-catabolism, heme-detoxification, nutrient-assimilation and pharmacodynamic-interactions, thereby representing critical therapeutic target. However, numerous food vacuole-associated proteins remain uncharacterized. In this study, multiple bioinformatics tools were employed to comprehensively characterize a hypothetical food vacuole-associated protein, PF11_0364 (designated PfHDDCP). Conserved domain analysis identified HotDog fold, hallmark of acyl-CoA thioesterases, suggesting its possible role in lipid metabolism. 3D structural model of PfHDDCP was generated using I-TASSER and evaluated with PROCHECK and ProSA. Over 90% of residues were located in favored regions of Ramachandran plot, and ProSA Z-score fell within the range typical of native protein structures, indicating good model quality. Domain analysis via NCBI-CDD identified two putative ligand-binding sites in PfHDDCP. Molecular docking using HDOCK and AutoDock predicted that Acetyl-CoA and Acyl Carrier Protein, canonical substrates of thioesterases, bind at Binding-Site 1, which corresponds to the predicted catalytic site. In contrast, antimalarial compounds were predicted to bind at Binding-Site 2, distinct secondary pocket, suggesting possible allosteric site that may interfere with substrate binding. Molecular dynamics simulations performed with Desmond indicated stable PfHDDCP-ligand complexes and ligand-induced conformational changes, supporting model of ligand-mediated functional modulation. Although these results offer preliminary computational insights into structure, function, and druggability of PfHDDCP, they remain predictive and require experimental validation to confirm the proposed enzymatic activity and therapeutic relevance.