Structural Bioinformatics-Based Prediction of Exceptional Selectivity of p38 MAP Kinase Inhibitor PH-797804

Abstract

PH-797804 is a diarylpyridinone inhibitor of p38alpha mitogen-activated protein (MAP) kinase derived from a racemic mixture as the more potent atropisomer (aS), first proposed by molecular modeling and subsequently confirmed by experiments. On the basis of structural comparison with a different biaryl pyrazole template and supported by dozens of high-resolution crystal structures of p38alpha inhibitor complexes, PH-797804 is predicted to possess a high level of specificity across the broad human kinase genome. We used a structural bioinformatics approach to identify two selectivity elements encoded by the TXXXG sequence motif on the p38alpha kinase hinge: (i) Thr106 that serves as the gatekeeper to the buried hydrophobic pocket occupied by 2,4-difluorophenyl of PH-797804 and (ii) the bidentate hydrogen bonds formed by the pyridinone moiety with the kinase hinge requiring an induced 180 degrees rotation of the Met109-Gly110 peptide bond. The peptide flip occurs in p38alpha kinase due to the critical glycine residue marked by its conformational flexibility. Kinome-wide sequence mining revealed rare presentation of the selectivity motif. Corroboratively, PH-797804 exhibited exceptionally high specificity against MAP kinases and the related kinases. No cross-reactivity was observed in large panels of kinase screens (selectivity ratio of >500-fold). In cellular assays, PH-797804 demonstrated superior potency and selectivity consistent with the biochemical measurements. PH-797804 has met safety criteria in human phase I studies and is under clinical development for several inflammatory conditions. Understanding the rationale for selectivity at the molecular level helps elucidate the biological function and design of specific p38alpha kinase inhibitors.

Apoptosis Signal-regulating Kinase 1 (ASK1)-p38 Pathway-dependent Cytoplasmic Translocation of the Orphan Nuclear Receptor NR4A2 Is Required for Oxidative Stress-induced Necrosis

“…1I). We further examined the requirement of p38 for H 2 O 2 -induced HeLa cell death by using another p38 inhibitor, PH797804, whose high potency and selectivity has been established (19). As shown in Fig.…”

Anti-Inflammatory Properties of a NovelN-Phenyl Pyridinone Inhibitor of p38 Mitogen-Activated Protein Kinase: Preclinical-to-Clinical Translation

“…3A). Although PH-797804 was shown to inhibit cellular p38 kinase activity as assessed by either MK-2 immune complex kinase assay or p38 kinase-dependent phosphorylation of HSP27, no inhibitory effect was observed on either the JNK pathway (c-Jun phosphorylation) or ERK pathway (ERK phosphorylation) in U937 cells at concentrations up to 1 M (Xing et al, 2009).…”

“…Binding potency is primarily driven through two key interactions: 1) engagement of the active site adjacent hydrophobic pocket by the 2,4-difluorophenyl moiety and 2) the formation of a bidentate H-bond between the PH-797804 pyridinone and the M109-G110 peptide backbone in the kinase crossover region (Xing et al, 2009). The relative uniqueness across the human kinome of the large hydrophobic pocket gatekeeper residue (T106) in p38␣ kinase coupled with the induced peptide backbone flip at G110 required for bidentate H-bond formation are key structural features driving kinase selectivity for PH-797804 (Xing et al, 2009). The p38␣ kinase isoform-restricted expression in monocytes, U937 cells, and RASF coupled with the high selectivity observed with PH-797804 suggests that the biological activity observed with this compound is driven through modulation of p38␣ in these cells.…”

“…The selectivity of PH-797804 against the JNK2 kinase (binding K i ratio Ͼ50,000-fold) is significantly greater than that observed for the p38 kinase inhibitor SB203580 (16-fold binding K i ratio; data not shown). In addition to the kinases noted above, PH-797804 was profiled against approximately 65 kinase and nucleotide binding proteins, and no cross-reactivity was observed (selectivity ratio Ͼ500-fold; Table 2) (Xing et al, 2009).…”

Complementing ultrafast shape recognition with an optical isomerism descriptor

“…Furthermore, the USR:OptIso was tested on two pairs of isomers of recently published kinase inhibitors (2 and 3 in Fig. 5) [31,32]. The first 12 descriptors of USR have identical values, while the optical isomerism descriptor reduces the similarity score from 1 to 0.705 for compound 2 and from 1 to 0.650 for compound 3.…”