Antibiotic resistance challenge: evaluating anthraquinones as rifampicin monooxygenase inhibitors through integrated bioinformatics analysis

Abstract

Abstract Objective Antibiotic resistance poses a pressing and crucial global public health challenge, leading to significant clinical and health-related consequences. Substantial evidence highlights the pivotal involvement of rifampicin monooxygenase (RIFMO) in the context of antibiotic resistance. Hence, inhibiting RIFMO could offer potential in the treatment of various infections. Anthraquinones, a group of organic compounds, have shown promise in addressing tuberculosis. This study employed integrated bioinformatics approaches to evaluate the potential inhibitory effects of a selection of anthraquinones on RIFMO. The findings were subsequently compared with those of rifampicin (RIF), serving as a positive control inhibitor. Methods The AutoDock 4.0 tool assessed the binding free energy between 21 anthraquinones and the RIFMO catalytic cleft. The ligands were ranked based on the most favorable scores derived from ΔGbinding. The docking analyses for the highest-ranked anthraquinone and RIF underwent a cross-validation process. This validation procedure utilized the SwissDock server and the Schrödinger Maestro docking software. Molecular dynamics simulations were conducted to scrutinize the stability of the backbone atoms in free RIFMO, RIFMO-RIF, and RIFMO complexed with the top-ranked anthraquinone throughout a 100-ns computer simulation. The Discovery Studio Visualizer tool visualized interactions between RIFMO residues and ligands. An evaluation of the pharmacokinetics and toxicity profiles of the tested compounds was also conducted. Results Five anthraquinones were indicated with ΔGbinding scores less than − 10 kcal/mol. Hypericin emerged as the most potent RIFMO inhibitor, boasting a ΔGbinding score and inhibition constant value of − 12.11 kcal/mol and 798.99 pM, respectively. The agreement across AutoDock 4.0, SwissDock, and Schrödinger Maestro results highlighted hypericin’s notable binding affinity to the RIFMO catalytic cleft. The RIFMO-hypericin complex achieved stability after a 70-ns computer simulation, exhibiting a root-mean-square deviation of 0.55 nm. Oral bioavailability analysis revealed that all anthraquinones except hypericin, sennidin A, and sennidin B may be suitable for oral administration. Furthermore, the carcinogenicity prediction analysis indicated a favorable safety profile for all examined anthraquinones. Conclusion Inhibiting RIFMO, particularly with anthraquinones such as hypericin, holds promise as a potential therapeutic strategy for infectious diseases.