Assessing the Inhibitory Potential of Natural Compounds for Targeting the CrtM Proteins in Methicillin-Resistant Staphylococcus aureus through Machine Learning-based QSAR Modeling and Structural Dynamics Analysis.

Introduction: The development of Methicillin-Resistant Staphylococcus aureus (MRSA) presents a significant risk to worldwide health and necessitates the creation of novel antimicrobial approaches. The enzyme dehydrosqualene synthase (CrtM), necessary for the bacterial species Staphylococcus aureus to produce staphyloxanthin, is a viable candidate for medicinal investigation. Blocking CrtM hampers the synthesis of staphyloxanthin, reducing the pathogen's ability to cause disease and making it more vulnerable to both the immune system and conventional antibiotics. This study aimed to target the CrtM protein using in-silico approaches and identified its inhibitors.

Methods: Tanimoto's similarity of 406,621 unique natural compounds collected from the COCONUT database was calculated using the known inhibitor of CrtM, hesperidin. Further, machine learning-based QSAR screening was performed on these natural compounds where two compounds showed promising binding with the CrtM protein (4299376 and 12897366). A binding score of -9.49 kcal/mol was found for 4299376 and 12897366, respectively, via molecular docking; this value was close to that of the control drug, hesperidin, which was -9.55 kcal/mol. Molecular dynamics simulations conducted at 30 ns and with complexes of MM/GBSA demonstrated binding free energies of -14.38 kcal/mol for 12897366 and -42.72 kcal/mol for 4299376, respectively. 4299376 was selected further for 200 ns MD simulation because of its high binding affinity and stability in the RMSD plots.

Results: Additionally, post 200 ns MD analysis and MM/GBSA analysis showed the consistent stability and strong binding of 4299376 with CrtM (RMSD = 0.3 nm and binding free energy of -37.30 kcal/mol). Moreover, the critical residue Gln165 of CrtM was found to have a hydrogen bond with 4299376 in the 0 ns, 100 ns, and 200 ns conformation. Overall, 4299376 performed well in the PCA, free energy landscape, and per-residue decomposition, proving it is an effective CrtM binder. The free energy perturbation (FEP) analysis revealed that as the system progressed from fully bound (λ = 0) to decoupled (λ = 10), the free energy (ΔG) changed from 6.56 kT to -4.38 kT, signifying a reduction in binding free energy and implying an increase in entropy and solvation effects that stabilize the ligand in the decoupled state. This underscores the entropic contribution and solvent interactions as critical determinants in the lowering of binding free energy.

Conclusion: This study concluded that 4299376 exhibits considerable therapeutic potential and could be investigated further for its potential use as an inhibitor against CrtM of S. aureus.