Computational Screening of Selected Phytochemicals Against Levofloxacin and Metronidazole-Resistant Indonesian H. pylori Strains
Abstract
The incidence of levofloxacin and metronidazole resistance in H. pylori Indonesian strains is increasing. Conventional approaches to antibacterial discovery are often a protracted process. This study uses structure-based virtual screening to quickly discover anti-H. pylori. This study employed homology modeling, docking, ADMET prediction, and molecular dynamics simulation to evaluate phytochemicals against resistant H. pylori gyrA, gyrB, and rdxA structures from Indonesian strains. Three-dimensional structures were constructed from the amino acid sequences gyrA, gyrB, and rdxA of levofloxacin- and metronidazole-resistant H. pylori Indonesian strains. The results of redocking at the binding sites gyrA (0.13 Å), gyrB (0.0024 Å), and rdxA (0.5 Å) obtained a valid RMSD. Curcumin exhibited the lowest average binding scores across gyrA (-154.994 kcal/mol), gyrB (-159.2033 kcal/mol), and rdxA (-166.322 kcal/mol) compared to other compounds and standard therapies, including levofloxacin (-109.1553 and -122.5873 kcal/mol) and metronidazole (-85.6096 kcal/mol). Molecular dynamics simulation results revealed that the curcumin-gyrA complex exhibited comparatively more restrained fluctuation than the other complexes throughout the simulation, as indicated by a consistently low total RMSD value (4-7 Å). Curcumin demonstrated the most favorable computational interaction profile among the evaluated compounds.
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