One of the most important relations in all of chemistry is the free energy relation ∆G = ∆H - T∆S. Tuning the potency of a ligand binding to a protein involves a fine balance between optimizing both entropy and enthalpy. In his review on the role of these two variables, Johns Hopkins's Ernesto Freire makes a very interesting observation; that for a given series of progressively improved set of drugs binding to a given protein, it's the enthalpy that becomes more and more favourable while the entropy pretty much starts out being favourable. Thus, it's enthalpy optimization that's the harder part in drug design.
Freire illustrates his observation by looking at two sets of famous drugs- HIV protease inhibitors and cholesterol-lowering statins. For example if we look at the progression of the protease inhibitors over time starting from about 1995 when we had good but not highly-potent drugs to about 2006 when we had greatly improved drugs, we essentially find the striking fact that while ∆S for drug binding was favourable to begin with in 1995, it's really a great improvement in ∆H that has made the drugs more potent through the years.
Thus Freire concludes that it's improving enthalpy of binding and not entropy that's the hard part in improving potency. The argument is fairly straightforward; favourable entropy depends on desolvation of the drug to get rid of water molecules, as well as displacement of water molecules from the active site by the drug. Both these events are more or less favourable for most drugs as most drugs are reasonably hydrophobic. Thus, high hydrophobicity can by itself confer favourable entropy. But tuning enthalpy is much harder for two reasons; first of all because as Freire notes, it is not possible yet to engineer hydrogen bonds to the tenths of angstroms needed for optimum energetic gain. Secondly, even a slight sub-optimal feature in hydrogen bonding can tip the scales because remember, the hydrogen bonds that the ligand forms with the protein are simply replacing strong hydrogen bonds that were previously formed with the surrounding water. Thus the new hydrogen bonds may not be as strong, and indeed may even be unfavourable with respect to the previous ones. From past discussions, recall that a mere 1.4 kcal/change in free energy from unfavourable hydrogen bonding can lead to a 10-fold loss in binding affinity ("Life is a 3 kcal/mol denizen"). Clearly one has to be careful while designing ligands to form hydrogen bonds. It's perhaps not surprising that hydrophobic effect-induced binding is the main stabilizing factor in both protein folding and ligand design; both man and nature apparently find it much easier to get binding affinity from hydrophobic interactions than polar ones.
These facts are borne out when we see the change in these two thermodynamic variables in the optimization of HIV protease inhibitors over time where, while ∆S is favourable to begin with, ∆H is actually positive and unfavourable at the beginning. Let's also not forget that potency is only the beginning for a ligand that needs to traverse many obstacles in order to be converted into a drug, including ADME-T optimization. Any one of these further modifications can modify the one or both of the thermodynamic variables and change the initially optimized potency.
However, since optimizing enthalpy is both more challenging and more important, Freire prescribes experimentally measuring the two variables as much as possible for every stage of the drug design process starting as early as possible. This can be best accomplished through Isothermal Titration Calorimetry (ITC) which can also shed light on enthalpy-entropy compensation, an important process in the binding of ligands.
Thermodynamic optimization is a tightrope walking act, a prelude to the ultimate juggling game that is drug design. Not only are you trying to balance several variables at once, but some of them are trying to actually pull you down. But simple strategies can quell at least some of these nefarious efforts and reward you with a fine ligand, if not drug.
Reference: E Freire (2008). Do enthalpy and entropy distinguish first in class from best in class? Drug Discovery Today, 13 (19-20), 869-874 DOI: 10.1016/j.drudis.2008.07.005