Assessing the Interactions\nbetween Snake Venom Metalloproteinases\nand Hydroxamate Inhibitors Using Kinetic and ITC Assays, Molecular\nDynamics Simulations and MM/PBSA-Based Scoring Functions

<i>Bothrops</i> species are the main cause\nof snake bites\nin rural communities of tropical developing countries of Central and\nSouth America. Envenomation by <i>Bothrops</i> snakes is\ncharacterized by prominent local inflammation, hemorrhage and necrosis\nas well as systemic hemostatic disturbances. These pathological effects\nare mainly caused by the major toxins of the viperidae venoms, the\nsnake venom metalloproteinases (SVMPs). Despite the antivenom therapy\nefficiency to block the main toxic effects on bite victims, this treatment\nshows limited efficacy to prevent tissue necrosis. Thus, drug-like\ninhibitors of these toxins have the potential to aid serum therapy\nof accidents inflicted by viper snakes. Broad-spectrum metalloprotease\ninhibitors bearing a hydroxamate zinc-binding group are potential\ncandidates to improve snake bites therapy and could also be used to\nstudy toxin-ligand interactions. Therefore, in this work, we used\nboth docking calculations and molecular dynamics simulations to assess\nthe interactions between six hydroxamate inhibitors and two P–I\nSVMPs selected as models: Atroxlysin-I (hemorrhagic) from Bothrops atrox, and Leucurolysin-a (nonhemorrhagic)\nfrom Bothrops leucurus. We also employed\na large variety of end-point free energy methods in combination with\nentropic terms to produce scoring functions of the relative affinities\nof the inhibitors for the toxins. Then we identified the scoring functions\nthat best correlated with experimental data obtained from kinetic\nactivity assays. In addition, to the characterization of these six\nmolecules as inhibitors of the toxins, this study sheds light on the\nmain enzyme–inhibitor interactions, explaining the broad-spectrum\nbehavior of the inhibitors, and identifies the energetic and entropic\nterms that improve the performance of the scoring functions.