Steering library bias toward A2A adenosine receptor ligand discovery
The A2A adenosine receptor is an important GPCR, well-known for binding caffeine. Adenosine receptors are emerging as relevant drug targets for a variety of disorders including Parkinson's disease, and there is interest in discovering new ligands that bind to them. Among adenosine receptor subtypes, the A2A receptor is one of the few GPCRs whose crystal structure is available. Thus the A2A is amenable to structure-based design efforts, and virtual screening is an especially attractive endeavor in this regard.
In the present report, a team of researchers from NIH and UCSF led by Brian Shoichet, John Irwin and Kenneth Jacobson use virtual screening to discover new ligands for the A2A. There are several points to note here. The authors use the ZINC library of drug like molecules to dock about a million and a half compounds into the binding pocket of the A2A crystal structure. They pick the best-scored 500 (0.035% of the total) ligands and investigate their fit in the binding site. Using criteria like electrostatic and VdW complementarity and novelty of chemotype, they finally select 20 of these 500 hits and test them in assays. Out of these 20, 7 inhibited binding by more than 40% at 20 μM concentration, thus constituting a hit rate of 35%. While the compounds formed the same kinds of interactions as some other A2A ligands, they were also relatively diverse in structure. The ligands were also tested in aggregation-based screens to determine that their activity was not a spurious artifact of aggregation-based inhibition.
This is a pretty good hit rate. Generally virtual screening campaigns are lucky to have a hit rate of a few percent. Curiously, the authors also found a similarly high hit rate during a past VS campaign against the well-known β2 adrenergic receptor. What could be responsible for this high hit rate against GPCRs? The reasons are interesting. One reason could be that GPCRs are very well adapted to bind small molecules in compact pockets, enclosing them and forming many kinds of productive interactions. But more intriguingly, as the authors have noted earlier, there is "biogenic bias" in favor of certain target-specific chemotypes in commercial libraries that are screened, both during VS as well as HTS. This in turn reflects the biases of medicinal chemists in picking and synthesizing certain kinds of chemotypes based on the importance of drug targets and past successes in hitting these targets. GPCRs clearly are enormously important, and GPCR-friendly ligand chemotypes thus constitute a large part of screening libraries. These chemotypes are much more prevalent than those for kinases or ion channels for instance.
This observation has both positive and negative implications. The positive implication is that one is likely to keep finding high hit rates for GPCRs using VS. However, the negative implication is that one is also going to be constrained by biogenic bias, and this might preclude finding more diverse and entirely novel subtypes. Thus, while VS campaigns for GPCRs might find a good number of hits, the novelty of these hits might not always be satisfying. One other quite intriguing point emerging in this study is that the kind of hits found (agonist, inverse agonist, antagonist etc.) reflects the ligand which the target structure used for VS is co-crystallized with. Thus the A2A houses an antagonist in the binding site, leading to a preponderance of antagonists in the top docking hits. Indeed, agonists ranked abysmally low in the list.
GPCR ligand discovery is one of the most important goals in drug discovery. This and other similar studies demonstrate that, with all its caveats, VS can be productively used to mine for new GPCR drugs.
Carlsson, J., Yoo, L., Gao, Z., Irwin, J., Shoichet, B., & Jacobson, K. (2010). Structure-Based Discovery of A2A Adenosine Receptor Ligands Journal of Medicinal Chemistry DOI: 10.1021/jm100240h