Discovery of natural agents against Staphylococcus aureus based on EIIC by protein modeling, virtual screening and molecular dynamics

In this study, a reasonable 3D structure of enzyme IIC (EIIC) was established using ab initio methods. Curcumin, baicalein and phloretin were screened out from 127,695 natural products based on EIIC protein in Staphylococcus aureus (S. aureus) by using the virtual screening technology. The antibacterial assays results confirmed that these three compounds could inhibit S. aureus cell growth. The results of molecular docking, molecular dynamics and molecular mechanics/generalized born surface area calculation indicated that curcumin, baicalein and phloretin mainly bound to Glu275, His231, and Phe359 of EIIC through hydrogen bonds and van der Waals forces to obstruct the transport of glucose-based carbohydrates, and thereby inhibited the carbohydrate metabolism of S. aureus. The steered molecular dynamics analysis revealed the existence of transfer channel in EIIC and illustrated that curcumin, baicalein and phloretin could dissociate from EIIC when pulling force on them. Furthermore, alanine scanning and hydrogen bond occupancy analyses found that Glu275 played an important role in stabilizing EIIC-baicalein/curcumin/phloretin complexes, and 275Glu@OE1 was a stable hydrogen bond acceptor. Therefore, Glu275 may be a hot spot residue that can maintain the stable binding of agents to EIIC, which may be a direction for the development of new drugs against S. aureus.