This presentation outlines a low cost use of Molecular Mechanics-Poisson Boltzmann approach (MM-PB) to describe interactions between inhibitors and their macromolecular targets taking account of conformational adaptation upon ligand binding. Computed Gibbs Free energy (Protein-Inhibitor) of complex formation deltaG (enthalpic, entropic and solvation components) for a set of inhibitors (training set) explains their biological activity change and identifies their bioactive bound conformation. The subsequent Pharmacophore (built from the bioactive bound conformation) serves to explore the virtual chemical subspace in the search of new more potent analogues of studied inhibitors. Five case studies related to neglected diseases will be presented.