Kinase selectivity

MAPK cascades are composed of three cytoplasmic kinases, the MAPKKK, MAPKK, and MAPK, that are regulated by phosphorylation (Fig. 1) [1, 2]. The MAPKKK, also called MEKK for MEK kinase, is a serine/threonine kinase. Selective activation of MAPKKKs by upstream cellular stimuli results in the phosphorylation of MAPKK, also called MEK for MAP/ERK kinase by the MAPKKK. MAPKKK members are structurally diverse and are differentially regulated by specific upstream stimuli. The MAPKK is phosphorylated by the MAPKKK on two specific serine/ threonine residues in its activation loop. The MAPKK family members are dual specificity kinases capable of phosphorylating critical threonine and tyrosine residues in the activation loop of the MAPKs. MAPKKs have the fewest members in the MAPK signaling module. MAPKs are a family of serine/threonine kinases that upon activation by their respective MAPKKs, are capable of phosphorylating cytoplasmic substrates as well as... 

GMCSF)-stimulated STAT5 phosphorylation assay in TF1 cells. The kinase selectivity of these compounds was reproduced functionally in a JAK3-dri-ven, IL-2-stimulated STAT5 phosphorylation assay in HT2 cells. Both examples demonstrated favorable iv pharmacokinetics in Sprague-Dawley rats [42]. 

In addition, 2-aryl pyridyl indazoles have been reported in the patent literature [25]. For example, compound 13 is reported to inhibit AKT-1 (IC50 < 0.18 pM). No kinase selectivity data were presented. 

Compound 14 (IC50 = 0.30 pM against AKT-1) is representative of a series of pyridopyrizine AKT inhibitors [26], This compound inhibited AKT-mediated phosphorylation of GSK3fi in IGF-1-stimulated MCF-7 cells (IC50 = 0.5 pM). No kinase selectivity data were reported. 

Figure 3.6 Protein kinases. Selected amino acid residues within proteins are targets for kinases, (a) Tyrosine kinase reaction, (b) Serine/threonine kinase...

In addition to the preceding kinase inhibitors, a number of patents describe compounds that are claimed to be active against PKB (e.g., diamino tri-azines, diaminopyrimidines or 5-aminocarbonylindazoles) [1,144]. Although in general no kinase inhibitory data are provided in these patents, the diverse chemical scaffolds covered in these specifications may represent promising new chemotypes for the future generation of PKB kinase-selective inhibitors. 

Keywords Src Src family kinases Kinase selectivity Structure-based design Mechanism-based design... 

Card, A., Caldwell, C., Min, H., et al. (2009) High-throughput biochemical kinase selectivity assays panel development and screening applications. J Biomol Screen 14(1), 31-42. 

Sciabola, S., Stanton, R. V., Wittkopp, S., et al. (2008) Predicting kinase selectivity profiles using Free-Wilson QSAR analysis. J Chem Inform Model 48(9), 1851-1867. 

Fig. 16.1. Progress of two rounds of Chk1 targeted libraries. Cpd-1 is the original HTS hit with a broad kinase inhibition profile and based on which the first round library was designed and synthesized. 1808-1 is the best hit from the first round targeted library with improved kinase selectivity profile, based on which the second round library was designed and synthesized. 1819-1 is the best lead with improved potency, kinase selectivity, and solubility. Co-crystal structures of Chkl kinase domain and corresponding lead compounds were solved and extensively utilized in structure-based singleton and library designs. For details of the X-ray co-Crystal structures, please refer to the publications from Ming and et al (4a) and Foloppe and et al for details (4b).

Fig. 16.6. Objectives of the first round library. The main goal is to explore the protein pocket probed by the right-hand side of Cpd-1 to improve kinase selectivity and further build SAR knowledge. The single aryl-aryl bond was replaced by three bonds containing an amide group with more flexibility. A registered combinatorial synthesis protocol (LJ0194) was used for this library and a 2x44 plate format was planned before the design of the library.

Fig. 16.9. Top hits from the first targeted library. One can see that a fairly diverse set of small amines are all tolerated by the binding pocket but with a significant reduction in potency when compared with the initial HTS hit Cpd-1 (5 nM). On the other hand, the top hit 1808-1 shows significant improvement in kinase selectivity and improved solubility (see data given in Fig. 16.1).

Top hits from the second round library. One compound 1819-1 (0.5 nM) shows significant improvement over tif d 1808-1 (300 nM) in terms of Chk1 inhibition results. More data show (see Fig. 16.1) that it is even more potent th th initial hit Cpd-1 (5 nM) while having a much improved kinase selectivity profile and better solubility. 

Two rounds of targeted libraries (2x44 and 2x88) were designed, synthesized, and assayed within 6 months. This effort led to a new lead matter 1819-1 with improved potency ( 10 folds), kinase selectivity (>100 folds), and better solubility ( 1 log unit or 10 folds) when compared with the original HTS hit Cpd-1. The extensive SAR information spanned by those 264... 

Fig. 2.9 The transformation of a tyrosine kinase-selective inhibitor 38 into a CDK-selective template (39 and 40) was achieved by adjusting the template substitution pattern.

The kinase superfamily consists of numerous kinases that have a common folding pattern. Therefore, it is generally difficult to improve the target kinase selectivity with respect to all the other kinases at the same time. However, protein kinases play various important roles in the human body, and they are also very attractive targets for drug discovery. We believe that this approach should be useful for the more systematic and efficient development of highly specific kinase inhibitors. 

To illustrate the use of the target family landscape for understanding kinase selectivity profiles, Naumann and Matter used a series of 86 2,6,9-substituted purines. These selective CDK inhibitors bind to the kinase ATP binding site [46]. A detailed comparison with experimental selectivity profiles showed good agreement with the chemometric analysis. 

Kinases, selective and Nonselective Inhibitors of Mitochondria Topics in Chemical Biology Cysteine Proteases and Cysteine Protease Inhibitors Protein-Protein Interactions, Tools to Study DNA Damage, Sensing of... 

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