Fragments vs MKK3: modeling all the way to low nanomolar

The mitogen-activated protein kinase (MAPK) signaling pathway is a rich source of targets, particularly for inflammation. Within this cascade the p38 kinases have been heavily studied, but many of the inhibitors that entered the clinic derailed for various reasons, including efficacy. Thus, some groups have sought to block the pathway upstream of p38. A paper just published online in Bioorg. Med. Chem. Lett. by Steve Swann and colleagues at Takeda describes some of their efforts to accomplish this.

The researchers focused on MKK3 and to a lesser degree the related MKK6, both of which phosphorylate and activate p38. They began by screening their 11,012 fragments in a biochemical assay at 100 µM each. Hits were prioritized by estimating the IC₅₀ values and thus approximate ligand efficiency (LE) and lipophilic ligand efficiency values (LLE) for each compound that inhibited >30%. Of these, 93 gave LE ≥ 0.35 kcal/mol per heavy atom and LLE ≥ 4. (Incidentally, this seems like a perfectly reasonable use of metrics to triage a large number of compounds, and the speed and simplicity is a good counterargument to more complicated proposals.) Some hits were tested using full dose-response curves to determine actual IC₅₀ values and surface plasmon resonance assays to determine K_d values; compound 1 was particularly compelling.

Readers may recall that Takeda found this very same fragment as an inhibitor of BTK (a kinase in an unrelated pathway), and they used the compound/BTK crystal structure along with the published crystal structure of MKK6 to develop a binding model. In their pursuit of MKK3/6 inhibitors, the Takeda team performed biochemical screens of available related compounds. This led to compound 2, which modeling predicted would bind in a similar fashion. The binding model also suggested the possibility of picking up a hydrogen bond to a lysine residue, leading to the more potent compound 3. Further optimization led to compounds 4 and 6, both with low nanomolar potency against MKK3 and low micromolar or high nanomolar cell-based activity. Profiling these against a dozen other kinases within the p38 signaling pathway revealed good selectivity against all except MKK6.

This is a nice, concise paper that illustrates how modeling, even without direct structural information, can be used to advance a fragment to low nanomolar inhibitors, albeit in a well-studied class of targets. It is also another illustration that the same fragment can be used to develop completely different series. And finally, these molecules look promising as chemical probes and possibly drug leads; it will be fun to watch as more data are disclosed.