Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step in the diaminopimelate (DAP) pathway of bacteria, including the human pathogen methicillin-resistant Staphylococcus aureus (MRSA). The pathway yields essential metabolites required for cell wall and protein synthesis. Accordingly, DHDPS is a promising antibiotic target. However, no potent (i.e. sub-micromolar) DHDPS active site inhibitors have been discovered to date. One factor that has yet to be considered for DHDPS inhibitor design is ‘protein dynamics’ of key active site residues, which occur on timescales amenable to molecular dynamics (MD) simulation. The aim of this study was to characterise the kinetic and thermodynamic events underpinning ligand binding to the active site of DHDPS from MRSA (MRSA-DHDPS) (PDB ID: 3DAQ).

Results of unbiased MD simulations revealed several novel ‘hot spots” of ligand-enzyme interactions in the active site of MRSA-DHDPS. To offer insight into these novel computational findings, MRSA-DHDPS was expressed, purified to homogeneity and characterised in vitro using enzyme kinetics and isothermal titration calorimetry ligand-binding assays. The results show good agreement with in silico studies in terms of thermodynamic binding properties governing substrate and inhibitor binding. However, further studies using surface plasmon resonance are underway to validate the kinetic events observed in our MD simulations. This study has yielded valuable insight into the design of potent inhibitors targeting the active site of bacterial DHDPS.