Unveiling the potential of Traditional Chinese Medicines in combating NorA-mediated S. aureus drug resistance. A molecular dynamic study

Abstract

Drug resistance Staphylococcus aureus (S. aureus) is emerging as the most prevalent pathogen in surgical wounds and orthopedic surgeries. NorA is a major drug efflux involved in the drug resistance, reducing intracellular drug concentrations. The current study aimed to find some potential inhibitors derived from Traditional Chinese Medicines (TCM) against NorA using a 500 ns molecular dynamics (MD) simulation. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), free energy, dynamic cross correlation matrix (DCCM) was computed. Three TCM compound; piperine, demethoxycurcumin, and tectorigenin exhibited many hydrogen bonds and hydrophobic contacts in the binding pockets residues, especially with ionizable residues (Arg 98, Glu 222, Asp 307, and Arg 310), forming two different charged regions. RMSD of NorA-piperine complex shows some initial instability at 5.2 Å, followed by an increase to 5.8 Å at 222 ns, and a further rise to 6.1 Å by the end of the 500 ns simulation period. Similarly, the NorA-demethoxycurcumin and NorA-tectorigenin complexes display elevated terminal RMSD of 7.9 Å each. RMSF, Rg, free energy, and binding pockets interactions confirmed the potential activity of piperine, demethoxycurcumin, and tectorigenin against NorA inhibition. In apo state NorA exhibited dispersion within the ranges of −100 to 150 (PC1: 39.97 %) while in complexed with ligands it illustrated significant differences in the motion patterns on PC1 (46.04 % and 27.39 %). The NorA-ligands DCCM displayed predominantly negatively correlated motions, particularly at the terminal resides from 200 to 370 where the pocket binding residues are located. These compounds also demonstrated drug-likeness and fitting best in the binding pocket residues (Asn > 137, Phe > 140, Phe > 303 Asp > 307, Arg > 310, Glu > 222, and Thr > 223). In conclusion, the compounds piperine, demethoxycurcumin, and tectorigenin interact with NorA through hydrogen bonds and hydrophobic contacts, particularly with key ionizable residues, Arg 98, Glu 222, Asp 307, and Arg 310, indicating potential inhibitory activity.