Designing ligands to bind proteins

Abstract

The ability to design drugs (so-called 'rational drug design') has been one of the long-term objectives of chemistry for 50 years. It is an exceptionally difficult problem, and many of its parts lie outside the expertise of chemistry. The much more limited problem - how to design tight-binding ligands (rational ligand design) - would seem to be one that chemistry could solve, but has also proved remarkably recalcitrant. The question is 'Why is it so difficult?' and the answer is 'We still don't entirely know'. This perspective discusses some of the technical issues - potential functions, protein plasticity, enthalpy/entropy compensation, and others - that contribute, and suggests areas where fundamental understanding of protein-ligand interactions falls short of what is needed. It surveys recent technological developments (in particular, isothermal titration calorimetry) that will, hopefully, make now the time for serious progress in this area. It concludes with the calorimetric examination of the association of a series of systematically varied ligands with a model protein. The counterintuitive thermodynamic results observed serve to illustrate that, even in relatively simple systems, understanding protein-ligand association is challenging.

Fig. 1

Association of a benzenesulfonamide with tail (shown as wavy line) to carbonic anhydrase. The tail can make favorable contacts with the surface of the protein.

Fig. 2

Variation in (a) free energy of binding and dissociation constant, (b) enthalpy of binding, and (c) entropy of binding with the number of residues in the tail for benzenesulfonamides with oligoethylene glycol (ArEG_nOMe), oligoglycine (ArGly_nO⁻), and oligosarcosine (ArSar_nO⁻) tails. Linear fits to the data in (b) and (c) are shown. The horizontal dashed line in (c) separates favorable (−TΔS° <0) from unfavorable (−TΔS° >0) entropy of binding. (Reprinted with permission from Krishnamurthy et al. 2006. Copyright 2006 American Chemical Society.)

Fig. 3

The association of para-substituted benzenesulfonamides with oligoethylene glycol (ArEG_nOMe), oligoglycine (ArGly_nO⁻), and oligosarcosine (ArSar_nO⁻) tails with bovine carbonic anhydrase II. (a) EEC plot for the association. The solid lines are linear fits to the datasets and give values for the compensation (from the slopes) as follows: −0·96±0·08 (ArSar_nO⁻), −1·07±0·07 (ArGly_nO⁻), and −1·32±0·09 (ArEG_nOMe); these observations demonstrate perfect compensation between enthalpy and entropy. The dotted vertical line separates favorable (−TΔS°<0) from unfavorable (−TΔS°>0) entropy of binding. (b) A schematic diagram for the association. This schematic diagram represents the catalytic cleft of the enzyme as a cone with the Zn²⁺ co-factor at the apex. The bottom surface (shaded) of the cleft is the ‘hydrophobic wall’ of the enzyme. Ellipses depict the residues of the ligand; the sizes of the ellipses are roughly proportional to the mobility of the individual residues. Benzenesulfonamide ligands with one (white), three (light gray), and five (dark gray) residues in the tail are shown. (Modified with permission from Krishnamurthy et al. 2006. Copyright 2006 American Chemical Society.)