Molecular Docking is an important step of the drug discovery process which aims at calculating the preferred position and shape of one molecule to a second when they are bound to each other. It is possible to identify three phases of Molecular Docking: 1) Ligand Expansion, i.e. unfolding of the ligand molecule; 2) Initial Placement, i.e. placement of the ligand into the protein pocket with rigid roto-translations; 3) Shape Refinement, i.e. rotation of the ligand bonds in order to match the protein pocket. In. our work, we focused on the Ligand Expansion phase and considered a quantum annealing approach to the Molecular Unfolding (MU) problem.