G-protein coupled receptors are one of those areas that I used to think I understood, until I understood them better. These things are very far from being on/off light switches mounted in drywall - they have a lot of different signaling mechanisms, and none of them are simple, either.
One of those that's been known for a long time, but remains quite murky, is allosteric modulation. There are many compounds known that clearly are not binding at the actual ligand site in some types of GPCR, but (equally clearly) can affect their signaling by binding to them somewhere else. So receptors have allosteric sites - but what do they do? And what ligands naturally bind to them (if any)? And by what mechanism does that binding modulate the downstream signaling, and are there effects that we can take advantage of as medicinal chemists? Open questions, all of them.
There's a new paper in Nature that tries to make sense of this, and trying by what might be the most difficult way possible: through computational modeling. Not all that long ago, this might well have been a fool's errand. But we're learning a lot about the details of GPCR structure from the recent X-ray work, and we're also able to handle a lot more computational load than we used to. That's particularly true if we are David Shaw and the D. E. Shaw company, part of the not-all-that-roomy Venn diagram intersection of quantitative Wall Street traders and computational chemists. Shaw has the resources to put together some serious hardware and software, and a team of people to make sure that the processing units get frequent exercise.
They're looking at the muscarinic M2 receptor, an old friend of mine for which I produced I-know-not-how-many antagonist candidates about twenty years ago. The allosteric region is up near the surface of the receptor, about 15A from the acetylcholine binding site, and it looks like all the compounds that bind up there do so via cation/pi interactions with aromatic residues in the protein. (That holds true for compounds as diverse as gallamine, alcuronium, and strychnine), and the one shown in the figure. This is very much in line with SAR and mutagenesis results over the years, but there are some key differences. Many people had thought that the aromatic groups of the ligands the receptors must have been interacting, but this doesn't seem to be the case. There also don't seem to be any interactions between the positively charged parts of the ligands and anionic residues on nearby loops of the protein (which is a rationale I remember from my days in the muscarinic field).
The simulations suggest that the two sites are very much in communication with each other. The width and conformation of the extracellular vestibule space can change according to what allosteric ligand occupies it, and this affects whether the effect on regular ligand binding is positive or negative, and to what degree. There can also, in some cases, be direct electrostatic interactions between the two ligands, for the larger allosteric compounds. I was very glad to see that the Shaw group's simulations suggested some experiments: one set with modified ligands, which would be predicted to affect the receptor in defined ways, and another set with point mutations in the receptor, which would be predicted to change the activities of the known ligands. These experiments were carried out by co-authors at Monash University in Australia, and (gratifyingly) seem to confirm the model. Too many computational papers (and to be fair, too many non-computational papers) don't get quite to the "We made some predictions and put our ideas to the test" stage, and I'm glad this one does.