BPS2026 – Allosteric inhibition of matrix metalloproteinase 9 (MMP-9) in silico

Matrix metalloproteinase-9 (MMP-9) is a zinc-dependent endopeptidase with a critical role in extracellular matrix remodeling, inflammation, and neurodegeneration. Overexpression of MMP-9 has been implicated in pathologies including cancer, stroke, and neurotrauma, making it a high-value therapeutic target. Traditional inhibition strategies have focused on the conserved catalytic domain, which contains a Zn 2+ center essential for enzymatic activity; however, they often lack selectivity due to structural conservation among metalloproteinases, particularly matrix metalloproteinase-2 (MMP-2). As a result, there is growing interest in allosteric inhibition as a strategy to selectively modulate MMP-9 activity without the drawbacks of conventional zinc-binding inhibitors. To explore this approach, the web server FTMap was first used to identify putative allosteric hotspots, followed by ligand generation and docking using DOCK 6. A total of 710 new ligands were generated, with a grid score ranging from −69.29 to 88.25 kcal/mol. To assess the stability and binding potential of 157 top-ranked complexes with a grid score cutoff point of −40.10 kcal/mol, molecular dynamics (MD) simulations were performed using AMBER for 250 ns. Average binding free energies were estimated using molecular mechanics-generalized born surface area (MM-GBSA) analysis. Preliminary results show several ligands with favorable binding profiles, characterized by stable interactions and low predicted free energies. Docking against the known allosteric inhibitor JNJ-0966 provided a reference point, supporting the idea that allosteric modulation of MMP-9 is achievable through selective targeting of distal binding pockets. Future work will include extension of MD simulations to 1000 ns for selected top-scoring ligands to further assess stability, followed by comparative binding free energy analyses against JNJ-0966 and the homologous enzyme MMP-2 to evaluate selectivity. This work will serve as a starting point for developing selective MMP-9 inhibitors.