Recent efforts to chart novel classes of molecules beyond the co-called “rule of 5” space have consistently pointed at macrocycles as privileged scaffolds. A lot has been said about their conformation and capacity to hide hydrogen bonds. It is not easy to evaluate the significance of complex conformational ensembles, let alone extract useful rules that might have predictive power. I have been longing for a reductionist approach that could hopefully unambiguously demonstrate the effect of ONE hydrogen bond on lipophilicilty and other drug-like properties in a cyclic molecule. In fact, there is a recent study that does just that. In their J. Med. Chem. paper, Kihlberg and co-workers evaluate a diastereomeric series of T. cruzi growth inhibitors and showcase vastly different solubility, lipophilicity, pKa, and cell permeability for two sets of four stereoisomers. Intriguingly, all it takes is a switch in chirality of one of the stereocenters to improve the chances for intramolecular hydrogen bond and concomitant pKa difference. The authors carefully analyzed the conformations of their 8-membered rings by NMR, considered the differences in chemical shifts, their temperature dependencies, and obtained solid evidence pointing toward the formation of intramolecular hydrogen bond in the trans (not cis) diastereomer shown below. This is a very thought-provoking case as it highlights a fairly small perturbation that results in a substantial difference in properties. While I am impressed with the results, I keep reminding myself that obtaining this sort of data is not trivial and we are unlikely to see easy fixes as there are so many different scaffolds out there. The main reason there is a higher degree of difficulty in macrocycles compared to small molecules is that functional groups are much more interrelated through limited rotation (and the one you see isn’t even a macrocycle… it is a medium-sized model).
amphoteros 