Figure 2.

Strategy for development of a p38α mitogen-activated protein kinase (MAPK) inhibitor. (A) The p38α MAPK inhibitor MW01-2-069A-SRM was developed using a structure-assisted and computational modeling design strategy, along with consideration of compound molecular properties. The inhibitor is based on a 3-amino-6-phenyl pyridazine scaffold (MW01-3-183WH) found in other central nervous system (CNS)-active compounds [46,68]. A pyridinyl pharmacophore characteristic of many p38 MAPK inhibitors was added to the scaffold. Modeling forecasted that MW01-2-069A-SRM could be accommodated by the p38α MAPK structure. The smaller Thr106 gatekeeper residue allowed the phenyl ring of the compound to occupy a hydrophobic pocket while the nitrogen of the pyridine ring could make a critical H-bond interaction with the amide bond between Met109 and Gly110. These interactions are important for selectivity and affinity for the p38α MAPK isoform. MW01-2-069A-SRM was a p38α MAPK inhibitor, with an IC50 of approximately 0.8 μM, and was relatively selective for p38α MAPK; at 20 μM, the compound showed complete inhibition of p38α MAPK, partial inhibition of p38β MAPK, and no inhibition of p38δ MAPK, p38γ MAPK, or 40 other protein kinases [41]. (B) Validation of the design approach and modeling of predicted interactions was done by testing analogs that did not show the predicted interactions with the kinase. For example, the scaffold compound MW01-3-183WH, which lacks the pyridine ring, is inactive. The inactive analog MW01-4-199SRM has a pyridine nitrogen in a different structural orientation, which should compromise activity due to distance constraints and altered electronegativity. Another inactive analog, MW01-6-189WH, has an identical composition to MW01-2-069A-SRM, but has its pyridine ring in a different position on the pyridazine scaffold. These data show that the pyridine pharmacophore must be introduced adjacent to the phenyl group in the molecular context of the scaffold, as found in MW01-2-069A-SRM, to produce a p38α MAPK inhibitor with good affinity and selectivity.

Borders et al. BMC Neuroscience 2008 9(Suppl 2):S12   doi:10.1186/1471-2202-9-S2-S12