Drug target mining and in silico screening of Tibetan plant metabolites for potential alleviation of Oroya fever, a neglected tropical disease

Bartonella bacilliformis is the causative agent of a neglected tropical disease, the Oroya fever or Carrion’s disease. Current treatment options for B. bacilliformis infections are limited, and the emergence of antibiotic-resistant strains underscores the urgent need for novel therapeutic interventions. This study aimed to identify novel inhibitors from Tibetan medicinal plant metabolites against B. bacilliformis, a causative agent of Oroya fever, utilizing a multi-pronged computational approach. We employed pan-genomics and hierarchal subtractive proteomics approach to filter drug targets and then predicted binding affinities of compounds with riboflavin synthase target using AutoDock Vina, DiffDock, and GNINA. The stability of the top inhibitors was confirmed through molecular dynamics (MD) simulations in GROMACS, while MM/GBSA and ADMET profiling assessed pharmacokinetic and toxicity properties. The analysis identified Kaempferol 3-O-gentiobioside, Kaempferol 3-(6''-p-coumarylglucoside)-7-glucoside, and Hirtusneanoside as promising inhibitors. MD simulations demonstrated stable binding with RMSD within 3 Å, and the candidates showed no skin sensitization, AMES mutagenicity, or hepatotoxicity. Physiologically-based pharmacokinetic (PBPK) modeling estimated compound distribution within the human body and revealed slightly higher absorption in pregnant and steatosis conditions, but overall absorption rates were similar across scenarios. Cyclodextrin complexation, particularly with SBE-β-CD indicates potential for enhanced solubility of these ligands. Since Kaempferol 3-O-gentiobioside exhibited off-target effects, the Kaempferol 3-(6''-p-coumarylglucoside)-7-glucoside and Hirtusneanoside are recommended for further investigation. Further testing in laboratory is recommended to explore these leads options for treating Oroya fever.