Isothermal Titration Calorimetry (ITC) plays a central role in the characterization and optimization of lead compounds as viable drug candidates. ITC is the only technique that permits a complete experimental characterization of the binding affinity of a ligand in terms of its thermodynamic components ΔG, ΔH, ΔS and ΔCp. In addition, ITC is ideally suited to characterize coupled processes like protonation/deprotonation reactions. One of the major challenges for ITC has been the analysis of ligands with high binding affinities. This issue becomes a serious problem in drug design, where one of the main goals is to optimize the binding affinities of lead compounds to nanomolar or subnanomolar levels. These binding affinities have been traditionally considered to be beyond the useful range of calorimetric analysis. In this paper we will discuss the implementation of ITC experimental designs aimed at characterizing very high affinity binding processes (Ka＞10⁹ M^-1) and apply them to the characterization of HIV-1 protease inhibitors. We will also discuss the characterization of protonation/deprotonation coupling to the binding reaction.