Better properties from fragments: c-Abl kinase activators

Last year we described the discovery of asciminib, an allosteric inhibitor of the kinase BCR-Abl that binds in the enzyme’s myristoyl-binding pocket. As we also highlighted nearly a decade ago, molecules that bind in this pocket can either inhibit or activate the enzyme. Although inhibitors have the most obvious therapeutic potential as anti-cancer agents, activators of the ubiquitously expressed c-Abl protein could potentially treat chemotherapy-induced neutropenia. In a recent J. Med. Chem. paper, Sophie Bertrand and coworkers at GlaxoSmithKline describe their efforts in this area.

The researchers started with a high-throughput screen of 1.3 million compounds. Among the hits was fragment-sized compound 2, which showed good binding and activation in biochemical assays but only modest activity in cells. Building off the left side of the molecule improved biochemical potency, but cell activity still lagged. SAR studies on the dichlorophenyl moiety suggested that this hydrophobic group was probably optimal, and a crystal structure of an analog bound to the enzyme confirmed this. Replacing the central thiazole with other aromatic rings also did little to improve cell activity.

The researchers acknowledge “that the chemistry strategy was largely pursuing compounds with rather poor physical properties,” notably low solubility, high lipophilicity, and high aromatic character. As co-author Robert Young has noted previously, physical properties matter. Happily, a fragment screen identified compound 28.

Adding the acetyl group from the HTS hit generated compound 29, with improved activity compared to the fragment. Moreover, this molecule had better solubility and permeability compared to the more lipohilic, thiazole-containing compound 2. Compound 29 also showed significantly improved activation of c-Abl in a cellular assay. Crystallography revealed that it bound in a similar fashion as compound 2, but with a twisted, more “three-dimensional” shape.

Further optimization, in part informed by previous work done on the thiazole series, ultimately led to compound 52, the most active compound synthesized. Another molecule in the pyrazoline series showed good pharmacokinetic properties in mice. Unfortunately, in vivo efficacy studies had to be halted early due to unexpected (and not clearly understood) toxicity.

This paper nicely illustrates several points. First, the power of fragment-assisted drug discovery, in which information from both HTS and FBLD is combined for lead optimization. Second, the inherently fuzzy line between FBLD and other discovery approaches: had compound 28 been tested in the HTS collection, it likely would have been a hit. Third, the importance of physicochemical properties. And finally, the inadequacy of potency and physicochemical properties alone to produce a developable compound. You can optimize your molecule to the best of your ability but still be sideswiped by nasty surprises such as toxicity. It is helpful to be clever in drug discovery, but you need to be lucky too.