The story actually starts a decade ago, with a collaboration between Astex and the Institute of Cancer Research. The two organizations were interested in PKB (also known as Akt1), which has a central role in the PI3K signaling cascade. Virtual, biochemical, and crystallographic screens identified small fragments such as substituted pyrazoles and 7-azaindole (which astute readers will recognize as the starting point for vemurafenib) that bind to the so-called hinge region of PKB. Structure-guided fragment-growing ultimately led to compound 2.
This compound, while potent against PKB, was unselective against the related protein kinase A (PKA), so further crystallographically-enabled medicinal chemistry led to CCT128930, with 30-fold selectivity against PKA. This compound had limited oral bioavailability, so further optimization led to compound 3.
In 2005, Astex partnered this program with AstraZeneca, which is presumably where the current paper picks up. Although compound 3 had good pharmacokinetics and was selective against PKA, it inhibited the kinase ROCK2, which regulates blood pressure; it was also a modest hERG inhibitor. Extensive SAR explorations around the hinge-binding element, the amine, and the aromatic group were not productive, but substitution off the benzylic position was tolerated. Adding a basic substituent dramatically reduced hERG binding, but at the cost of oral bioavailability. However, adding a variety of neutral, polar substituents led ultimately to AZD5363, which has no detectable hERG inhibition, good selectivity against ROCK2, and improved solubility and cell activity.
This paper nicely illustrates some of the challenges in drug discovery: high-affinity molecules were obtained relatively quickly, but these still required a huge amount of effort to achieve selectivity, oral bioavailability, and other properties. Indeed, only three heavy atoms differentiate compound 3 from AZD5363, but it took a heroic effort to get there.
Finally, it is worth noting that this research was done at Alderley Park, which attendees of Fragments 2009 will remember fondly. Sadly, AstraZeneca has announced that they will be closing this site. There are many very talented scientists there, and Practical Fragments wishes all of them the best of luck.