Lid dynamics and catalytic loop closure in isocitrate lyase inhibitory mechanism

Hafnia alvei, a gram-negative facultative anaerobe under Enterobacteriaceae, is commonly present in the gastrointestinal tract but occasionally isolated from urine, tissue, and catheters. Its morbidity and mortality largely arise from multidrug resistance. This study investigated the proteomics of H. alvei to identify novel drug targets, with isocitrate lyase (ICL) emerging as a promising candidate through subtractive proteomics. ICL, a key enzyme in the glyoxylate cycle, catalyzes the first step and is essential for microorganisms relying on this pathway when the TCA cycle is downregulated. A library of antibacterial compounds, FDA-approved drugs, and reported inhibitors was virtually screened against ICL using molecular docking. Although Lapatinib achieved the highest initial docking score, MD simulations revealed that IBMI-3 and Asinex displayed more favorable predicted binding energies, stronger loop closure, and more favorable binding free energies across all three independent replicates. Three independent 500-ns molecular dynamics simulations were performed for each Apo and ligand-bound system, providing a cumulative sampling time of 1.5 μs per system. This comprises an altogether span of 7.5 μs across all five systems. All complexes remained stable, while significant conformational changes, particularly in the catalytic loop (Lys192, Lys193, Gly195, His196), were observed. These residues facilitated closure of the active site and anchoring of inhibitors. Additionally, terminal residues from the adjacent subunit contributed to lid dynamics, covering the active pocket and blocking ligand release, a phenomenon absent in the ligand-free enzyme. Overall, this research provides an ample opportunity for future clinical and translational studies in circumventing infections caused by H. alvei. provided insights into molecular determinants of binding affinity.