An Integrated Computational Approach to Rationalize the Activity of Non-Zinc-Binding MMP-2 Inhibitors

Antonella Di Pizio,Massimiliano Aschi,Mariangela Agamennone,Eugene A Permyakov

doi:10.1371/journal.pone.0047774

Abstract

Matrix metalloproteinases are a family of Zn-proteases involved in tissue remodeling and in many pathological conditions. Among them MMP-2 is one of the most relevant target in anticancer therapy. Commonly, MMP inhibitors contain a functional group able to bind the zinc ion and responsible for undesired side effects. The discovery of potent and selective MMP inhibitors not bearing a zinc-binding group is arising for some MMP family members and represents a new opportunity to find selective and non toxic inhibitors.In this work we attempted to get more insight on the inhibition process of MMP-2 by two non-zinc-binding inhibitors, applying a general protocol that combines several computational tools (docking, Molecular Dynamics and Quantum Chemical calculations), that all together contribute to rationalize experimental inhibition data. Molecular Dynamics studies showed both structural and mechanical-dynamical effects produced by the ligands not disclosed by docking analysis. Thermodynamic Integration provided relative binding free energies consistent with experimentally observed activity data. Quantum Chemical calculations of the tautomeric equilibrium involving the most active ligand completed the picture of the binding process. Our study highlights the crucial role of the specificity loop and suggests that enthalpic effect predominates over the entropic one.

Highlights

Matrix metalloproteinases (MMPs) are a family of 23 zinc- and calcium-dependent endopeptidases in humans, involved in many processes spanning from connective tissue turnover to cellular signalling [1] in both normal and pathological conditions such as cancer, chronic inflammations, atherosclerosis [2]
– The obtained trajectories were subsequently analyzed by means of Essential Dynamics (ED) in order to extract the significant starting configurations to be used for free energy calculations
– Thermodynamic Integration (TI) calculations were performed at higher temperature (323 K) in order to qualitatively estimate the role of enthalpic and entropic factors

Summary

Introduction

Matrix metalloproteinases (MMPs) are a family of 23 zinc- and calcium-dependent endopeptidases in humans, involved in many processes spanning from connective tissue turnover to cellular signalling [1] in both normal and pathological conditions such as cancer, chronic inflammations, atherosclerosis [2]. The active site, located in the catalytic domain, contains a conserved zinc-binding motif (HExxHxxGxxH) common to all metzincins and responsible for the coordination of the catalytic zinc ion [7], [8], [9] by three histidine residues (His201, His205 and His211), while the conserved glutamate residue (Glu202) plays an essential role for the catalytic activity [10], [11] (Figure 1) Because of their role in many pathological conditions, several MMP inhibitors (MMPIs) have been developed but with no success, as their clinical administration caused severe tendonitislike joint pain, termed ‘‘musculo-skeletal syndrome’’ [12], [13], [14], [15]; this toxicity most probably results from a non specific inhibition of other metallo-enzymes [16], [17]

Methods

Results

Conclusion