The three members of the Pim family of serine/threonine kinases help cancer cells proliferate and survive, and are thus interesting as potential anti-cancer targets. Structurally the kinases are also intriguing because they have a proline residue in the “hinge” region of the purine binding site, differentiating them from the other 500+ kinases in the human genome. Two recent papers describe different fragment-screening approaches against Pim-1: one case rediscovers fragments of a previously reported compound and the other identifies a new series of potent inhibitors unlike other reported kinase inhibitors.
In the first paper, published in Acta Cryst. Section D, researchers from Bayer Schering Pharma AG performed a crystallographic screen of just 36 fragments against Pim-1. Despite the small library size, a dozen of the fragments produced interpretable electron density, although only 4 of these showed activity better than 10 mM. Fragment 3, with an IC50 of 130 micromolar in an enzymatic assay, was the most potent. Interestingly, a close analog of this cinnamic acid fragment was also part of a Pim-2 inhibitor previously identified through HTS by a group from Boehringer Ingelheim. The Bayer folks synthesized this molecule (compound 1), confirmed that it is also potent against Pim-1, and found that, crystallographically, it overlays beautifully with the fragment.
The second paper, published in Bioorg. Med. Chem. Lett., describes how researchers at Genzyme used a fragment-based approach to develop potent Pim-1 inhibitors. The researchers used SPR to screen a library of about 1800 fragments at 75 micromolar concentration and then used a biochemical assay to characterize the active molecules. Benzofuran-2-carboxylic acids such as compound 10 (below) were particularly interesting: not only did they have high ligand efficiencies, they don’t look anything like typical kinase inhibitors. X-ray crystallography revealed that the bromine atom is binding in a hydrophobic pocket, while the acid is making hydrogen bond contacts with the catalytic lysine and other residues. A related fragment with comparable potency had a methoxy substituent in the 7-position, and by transforming this into a positively charged moiety the researchers were able to improve the potency to low nanomolar with a dramatic increase in ligand efficiency.
has recently acquired Genzyme. Practical Fragments wishes all the folks in Massachusetts well during the integration.