Medicinal chemists talk a lot more about residence time and off rate than they used to. It's become clear that (at least in some cases) a key part of a drug's action is its kinetic behavior, specifically how quickly it leaves its binding site. You'd think that this would correlate well with its potency, but that's not necessarily so. Binding constants are a mix of on- and off-rates, and you can get to the same number by a variety of different means. Only if you're looking at very similar compounds with the same binding modes can you expect the correlation your intuition is telling you about, and even then you don't always get it.
There's a new paper in J. Med. Chem. from a team at Boehringer Ingelheim that takes a detailed look at this effect. The authors are working out the binding to the muscarinic receptor ligand tiotropium, which has been around a long time. (Boehringer's efforts in the muscarinic field have been around a long time, too, come to think of it). Tiotropium binds to the m2 subtype with a Ki of 0.2 nM, and to the m3 subtype with a Ki of 0.1 nM. But the compound has a much slower off rate on the m3 subtype, enough to make it physiologically distinct as an m3 ligand. Tiotropium is better known by its brand name Spiriva, and if its functional selectivity at the m3 receptors in the lungs wasn't pretty tight, it wouldn't be a drug. By carefully modifying its structure and introducing mutations into the receptor, this group hoped to figure out just why it's able to work the way it does.
The static details of tiotropium binding are well worked out - in fact, there's a recent X-ray structure, adding to the list of GPCRs that have been investigated by X-ray crystallography. There are plenty of interactions, as those binding constants would suggest:
The orthosteric binding sites of hM3R and hM2R are virtually identical. The positively charged headgroup of the antimuscarinic agent binds to (in the class of amine receptors highly conserved) Asp3.32 (D1483.32) and is surrounded by an aromatic cage consisting of Y1493.33, W5046.48, Y5076.51, Y5307.39, and Y5347.43. In addition to that, the aromatic substructures of the ligands dig into a hydrophobic region close to W2004.57 and the hydroxy groups, together with the ester groups, are bidentally interacting with N5086.52, forming close to optimal double hydrogen bonds. . .
The similarity of these binding sites was brought home to me personally when I was working on making selective antagonists of these myself. (If you want a real challenge, try differentiating m2 and m4). The authors point out, though, and crucially, that if you want to understand how different compounds bind to these receptors, the static pictures you get from X-ray structures are not enough. Homology modeling helps a good deal, but only if you take its results as indicators of dynamic processes, and not just swapping out residues in a framework.
Doing point-by-point single changes in both the tiotropium structure and the the receptor residues lets you use the kinetic data to your advantage. Such similar compounds should have similar modes of dissociation from the binding site. You can then compare off-rates to the binding constants, looking for the ones that deviate from the expected linear relationship. What they find is that the first event when tiotropium leaves the binding site is the opening of the aromatic cage mentioned above. Mutating any of these residues led to a big effect on the off-rate compared to the effect on the binding constant. Mutations further up along the tunnel leading to the binding site behaved in the same way: pretty much identical Ki values, but enhanced off-rates.
These observations, the paper says with commendable honesty, don't help the medicinal chemists all that much in designing compounds with better kinetics. You can imagine finding a compound that takes better advantage of this binding (maybe), but you can also imagine spending a lot of time trying to do that. The interaction with the asapragine at residue 508 is more useful from a drug design standpoint:
Our data provide evidence that the double hydrogen interaction of N5086.52 with tiotropium has a crucial influence on the off-rates beyond its influence on Ki. Mutation of N5086.52 to alanine accelerates the dissociation of tiotropium more than 1 order of magnitude than suggested by the Ki. Consequently, tiotropium derivatives devoid of the interacting hydroxy group show overproportionally short half-lives. Microsecond MD simulations show that this double hydrogen bonded interaction hinders tiotropium from moving into the exit channel by reducing the frequency of tyrosine-lid opening movements. Taken together, our data show that the interaction with N5086.52 is indeed an essential prerequisite for the development of slowly dissociating muscarinic receptor inverse agonists. This hypothesis is corroborated by the a posteriori observation that the only highly conserved substructure of all long-acting antimuscarinic agents currently in clinical development or already on the market is the hydroxy group.
But the extracellular loops also get into the act. The m2 subtype's nearby loop seems to be more flexible than the one in m3, and there's a lysine in the m3 that probably contributes some electrostatic repulsion to the charged tiotropium as it tries to back out of the protein. That's another effect that's hard to take advantage of, since the charged region of the molecule is a key for binding down in the active site, and messing with it would probably not pay dividends.
But there are some good take-aways from this paper. The authors note that the X-ray structure, while valuable, seems to have large confirmed the data generated by mutagenesis (as well it should). So if you're willing to do lots of point mutations, on both your ligand and your protein, you can (in theory) work some of these fine details out. Molecular dynamics simulations would seem to be of help here, too, also in theory. I'd be interested to hear if people can corroborate that with real-world experience.