Helichrysum populifolium compounds inhibit MtrCDE efflux pump transport protein for the potential management of gonorrhoea infection

Abstract

The progressive development of resistance in Neisseria gonorrhoeae to almost all available antibiotics has made it crucial to develop novel approaches to tackling multi-drug resistance (MDR). One of the primary causes of antibiotic resistance is the over-expression of the MtrCDE efflux pump protein, making this protein a vital target for fighting against antimicrobial resistance (AMR) in N. gonorrhoeae. This study was aimed at evaluating the potential MtrCDE efflux pump inhibitors (EPIs) and their stability in treating gonorrhoea infection. This is significant because finding novel EPIs would allow for the longer maintenance of antibiotics at therapeutic levels, thereby prolonging the susceptibility of currently available antibiotics. A virtual screening of the selected Helichrysum populifolium compounds (4,5-dicaffeoylquinic acid, apigeninin-7-glucoside, and carvacrol) was conducted to evaluate their potential EPI activity. An integrated computational framework consisting of molecular docking (MD), molecular mechanics generalized born, and surface area solvation (MMGBSA) analysis, molecular dynamics simulations (MDS), and absorption, distribution, metabolism, and excretion (ADME) properties calculations were conducted. Of the tested compounds, 4,5-dicaffeoylquinic acid revealed the highest molecular docking binding energies (−8.8 kcal/mol), equivalent MMGBSA binding free energy (−54.82 kcal/mol), indicative of consistent binding affinity with the MtrD protein, reduced deviations and flexibility (root mean square deviation (RMSD) of 5.65 Å) and, given by root mean square fluctuation (RMSF) of 1.877 Å. Carvacrol revealed a docking score of −6.0 kcal/mol and a MMGBSA computed BFE of −16.69 kcal/mol, demonstrating the lowest binding affinity to the MtrD efflux pump compared to the remaining test compounds. However, the average RMSD (4.45 Å) and RMSF (1.638 Å) of carvacrol-bound MtrD protein showed no significant difference from the unbound MtrD protein, except for the reference compounds, implying consistent MtrD conformation throughout simulations and indicates a desirable feature during drug design. Additionally, carvacrol obeyed the Lipinski rule of five which confirmed the compound’s drug-likeness properties making it the most promising EPI candidate based on its combined attributes of a reasonable binding affinity, sustained stability during MDS, its obedience to the Lipinski rule of five and compliance with drug-likeness criteria. An in vitro validation of the potential EPI activities of H. populifolium compounds confirmed that 4,5-dicaffeoylquinic acid reduced the expulsion of the bis-benzimide dye by MtrCDE pump, while carvacrol showed low accumulation compared to other compounds. While 4,5-dicaffeoylquinic acid demonstrated the highest binding affinity in computational analysis and an EPI activity in vitro, it showed lower stability compared to the other compounds, as indicated in MDS. This leaves carvacrol, as a better EPI candidate for the management of gonorrhoea infection.