HIV-1 protease inhibitors: Enthalpic versus entropic optimization of the binding affinity

Existing experimental as well as computational screening methods select pot ential ligands or drug candidates on the basis of binding affinity, Since t he binding affinity is a function of the enthalpy (Delta H) and entropy (De lta S) changes, it is apparent that improved blinding can be achieved in di fferent ways: by optimizing Delta H, Delta S, or a combination of both. How ever, the behavior of enthalpically or entropically optimized inhibitors is fundamentally different, including their response to mutations that may el icit drag resistance. In the design of HIV-I protease inhibitors, high bind ing affinity has usually been achieved by preshaping lead compounds to the geometry of the binding site and by incorporating a high degree of hydropho bicity. The thermodynamic consequence of that approach is that the binding affinity of the resulting inhibitors becomes entropically favorable but ent halpically unfavorable. Specifically, the resulting high binding affinity i s due to an increased solvation entropy (hydrophobic effect) combined with a reduced loss of conformational entropy of the inhibitor upon binding (str uctural rigidity). Here we report that tripeptide inhibitors derived from t he transframe region of Gag-Pol (Glu-Asp-Leu and Glu-Asp-Phe) bind to the H IV-1 protease with a favorable enthalpy change. This behavior is qualitativ ely different from that of known inhibitors and points to new strategies fo r inhibitor design. Since the binding affinities of enthalpically favorable and enthalpically unfavorable inhibitors have opposite temperature depende nce, it is possible to design fast screening protocols that simultaneously select inhibitors on the basis of affinity and enthalpy.