In fact the receptor flexibility, as well as the solvent effect, strongly affects the study of small-big molecule binding. Moreover proteins in solution exist in a manifold of different conformations and the ligand-protein interaction may cause unpredictable conformational rearrangements,,. In this respect dynamical approaches are mandatory. As a matter of fact, although many different docking-based approaches have been applied to handle moving targets and docking software are evolving to account for flexibility, the combined use of docking and molecular dynamics simulations is the most widely used method of investigation. In the present case, the necessity of such a combination of computational tools is even reinforced by the fact that our target macromolecule belongs to a Navitoclax Bcl-2 inhibitor family of flexible enzymes,,, as demonstrated by crystallographic data of MMPs. Moreover they undergo conformational changes upon inhibitor binding, as revealed by previous MD investigations,. Our study has been initiated performing docking calculations for providing reliable initial structures to be used for subsequent MD simulations which incorporate the flexibility of both the ligand and the receptor, and the solvent. Moreover, MD simulations of free ligands in aqueous solution were compared with those of the inhibitor interacting with the active site, to analyze the effect of enzyme-ligand interaction on ligand fluctuation. Computational investigation on the thermodynamics of inhibitor binding is not a simple problem with straightforward receipts. In this study the relative binding free energies have been evaluated through Thermodynamic Integration and compared to the available experimental data for underpinning our analyses and also for identifying plausible dynamical and structural factors determining the activity of both inhibitors. Ligands were manually built in Maestro, exploiting the Built facility. The tautomers for the given input structures were produced by the Tautomerizer tool available in Maestro. The protonation state of the ligands were calculated using the Calculator Plugin of Marvin. Conformational searches applying the Mixed torsional/Low-mode sampling and the automatic setup protocol were carried out on all minimized ligand structures in order to obtain the global minimum geometry of each molecule, as the docking program Glide v 5.7,,, has demonstrated better performances using the global minimum conformation as the ligand starting geometry. Moreover, comparing the diverse conformations of complexed enzymes with the apo form, greater differences concern the S19 loop. In the apo form, the S19 pocket adopts a closed state, while in the complexed forms an open state, differently from what Nutlin-3 abmole described in previous articles,. On the other hand major differences emerged by analysing inter-aromatic interactions which are presumed to play a crucial role, especially in this case, where the binding site is a hydrophobic pocket.