Fragments are frequently evaluated in terms of the number of non-hydrogen atoms, and the lightest element commonly found in drugs is carbon. In a sense, then, a methyl group is the smallest possible fragment. Indeed, molecular modelers often use methyl groups as probes to sample a protein surface, and medicinal chemists fantasize about the “magic methyl” that will give a huge pop in potency. But how much affinity can a methyl group really give you? William Jorgensen and colleagues at Yale attempt to answer this question in a recent issue of J. Med. Chem.
The team analyzed every single paper published in J. Med. Chem. and Bioorg. Med. Chem. Lett. between 2006 and 2011 (ah, the joys of being a grad. student!) This produced a data set of 2145 examples in which researchers had replaced a hydrogen atom with a methyl group and reported dissociation or inhibition constants for both ligands; more than 100 different proteins were represented. Jorgensen and colleagues then plotted the change in free energy (∆∆G) for the hydrogen to methyl replacement.
The result was a roughly Gaussian distribution with a median of 0.0 kcal/mol. In other words, on average, adding a methyl neither improved nor decreased affinity. However, with a standard deviation of 1.0 kcal/mol, it was fairly common to get a 5-fold boost in affinity. But the frequency dropped off quickly from there: a 10-fold improvement occurred about 8% of the time, and the prized 100-fold boosts happened only 0.4% of the time – often enough to gain a persistent foothold in the imagination, but certainly not something you’d want to count on. To yield a 100-fold improvement, each methyl has a group ligand efficiency of 2.7 kcal/mol/atom, which is more than the Kuntz limit!
But higher boosts are possible: in a handful of cases the gain in potency was more than 180-fold, and much of the paper focuses on four of these truly magic methyls. A combination of crystallography and high-level molecular modeling revealed that ideal hydrophobic interactions were responsible for some of the affinity, but in all cases the methyl group also preorganized the conformation of the ligand to optimize interactions with the protein. The authors conclude:
It appears that to reach the 10-fold level, placement of a methyl group in a hydrophobic environment may be adequate; however, to go beyond that, the methyl group also generally needs to induce a propitious conformational change. This is typically achieved by ortho methylation in biaryl systems or by branching at an atom attached to a ring.
Interestingly, these conformational changes make the molecules less flat – more support for including three-dimensional fragments in your collection.