• force field implementation
• Docking
• 3D-QSAR
• Homology modeling

The aim of this PhD course was to explore a broad overview on the topic of the Structure-Property Relationship (SPR) with a strong emphasis on the pratical aspects. Data in chemical research, and in particular in drug discovery, is varied and oftentimes very complex. In drug discovery one has to make sense of different type of data such as structural, biological, physico-chemical, pharmacological, toxicological and so on, which, ultimately have to be associated to a single molecular structure. In order to sort out these data and extract appropriate information, a number of tools have been devised on computers and workstations in the form of different programs; the reader will find that many of these tools and methods have been used during this PhD course. More in details in Chapter 1 the homology modeling of the adenosine receptors was explored and accompanied to the pharmacophoric analysis and synthesis of new compounds. In Chapter 2 the analysis of the MMP-inhibitor interaction led us to implement the Amber Forcefield, and the following docking analysis allowed the design of new selective inhibitors. The modeling of the activate form of the cannabinoid receptors (Chapter 3) corresponded to an attempt for going away from the homology modeling procedures; together with the goal of obtaining a quantitative model from an automated docking study. In Chapter 4 the study of ligand-estrogen receptor interaction was developed exploring the free energy calculation, while finally in the last Chapter the angiotensin receptor AT1 construction led us to propose a new binding orientation for the non-peptide antagonists, using the 3D-QSAR approach as validation and predictive method.