Ten things you should know about protein kinases: IUPHAR Review 14

Abstract

Many human malignancies are associated with aberrant regulation of protein or lipid kinases due to mutations, chromosomal rearrangements and/or gene amplification. Protein and lipid kinases represent an important target class for treating human disorders. This review focus on 'the 10 things you should know about protein kinases and their inhibitors', including a short introduction on the history of protein kinases and their inhibitors and ending with a perspective on kinase drug discovery. Although the '10 things' have been, to a certain extent, chosen arbitrarily, they cover in a comprehensive way the past and present efforts in kinase drug discovery and summarize the status quo of the current kinase inhibitors as well as knowledge about kinase structure and binding modes. Besides describing the potentials of protein kinase inhibitors as drugs, this review also focus on their limitations, particularly on how to circumvent emerging resistance against kinase inhibitors in oncological indications.

Figure 1

(A) Reversible phosphorylation and (B) kinase drug discovery. For explanation, see text. DualPase, dual-specificity phosphatases; DualPK, dual-specificity kinases; PI, phosphatidylinositol; PIP, phosphatidylinositolphosphate; PI3K, phosphatidylinositol kinases; STPase, Ser/Thr-specific phosphatases; STPK, Ser/Thr-specific kinases; TPK, Tyr-specific kinases.

Figure 2

Kinase (inactive), pseudokinase and atypical kinase conformational states. Various examples of the positions and forms of structural elements in different kinases. The same colour scheme as in Figure 2 is used. Panels (A)–(C) show the inactive states of three kinases, with only those structural elements where there are large shifts compared with the active state coloured. (A) Inactive conformation of Hck: C-helix out and closed A-loop (PDB entry 1HCK). (B) Inactive conformation of Abl1 kinase: Collapsed P-loop and closed A-loop with DFG-motif out (PDB entry 1IEP). (C) Inactive conformation of c-Met: C-helix out and yet another conformation of the A-loop (PDB entry 3CCN). Panels (D) and (E) show the structures of the pseudokinases JAK2 (PDB entry 4FVR), where the HRD sequence motif is not conserved, and MLKL (PDB entry 4MWI), where both the DFG and HRD sequence motifs are not conserved respectively. Panel (F) shows the structure of the atypical kinase, haspin (PDB entry 2VUW).

Figure 3

The active conformation of protein kinases. Front (A) and side views (B) of a typical active kinase conformation displaying the ternary complex of the insulin receptor (InsR), ATP and peptide substrate (pdb 1ir3). The helices and β-sheets forming the canonical kinase fold are labelled, as well as important secondary structure elements which are shown colour coded. (C) The ATP-site pharmacophore: The hydrophobic channel, the sugar pocket, the hinge and the hydrophobic back-pocket are the major pharmacophores. (D) Close-up of the active ATP site of the InsR. For explanations, see text. The two Mg²⁺ ions are in magenta.

Figure 4

Representative binding modes of the four classes of kinase inhibitors. Representative binding modes of the four classes of kinase inhibitors with ligand in blue sticks and key polar interactions shown as red dotted lines: (A) gefitinib bound to EGFR (type 1, pdb 2ity); (B) vemurafenib bound to B-Raf (type 1.5, pdb 3og7); (C) imatinib bound to ABL (type 2, pdb 1iep); and (D) afatinib bound covalently to EGFR (pdb 4g5j). Activation states of helix-C and the DFG-motif are annotated.

Figure 5

Clinically relevant resistance mutations of MEK1, ABL1 and ALK. (A) MEK1 and MEK2 mapped onto pdb 3eqc. The majority of the mutations cluster at the interface with the autoinhibitory N-terminal helix (top left in this view). (B) ABL mapped onto pdb 1iep. The imatinib-resistant mutants are spread all over the kinase domain; however, the most resistant against imatinib is the gatekeeper mutant T315I in the hinge (green) and the mutations located in the P-loop (red). (C) ALK mapped onto pdb 2xp2. Crizotinib-resistant mutations. The most resistant mutation is L1196M in the hinge (green) region.

Figure 6

Allosteric pockets. Examples of allosteric ligands mapped onto an active kinase conformation, comprising the myristate site of ABL (pdb 3k5v), the PIF pocket in PDK1 (3hrf), the substrate site in CHK1 (pdb 3f9n), the DEF (docking site for ERK) site in p38 (pdb 3new) and the allosteric back-pocket in MEK1 (DFG-in, pdb 1s9j, green), Akt1 (DFG-out, pdb 3o96, magenta) and FAK (DFG-out, pdb 4ebw, blue).

Figure 7

(A) Major issues in kinase drug discovery. (B) Pie chart showing the percentage distribution of clinically relevant driver mutations in lung adenocarcinoma [adapted from with high costs ‘Chipping away at the lung cancer genome’ by Pao and Hutchinson (2012)]. (C) Selectivity of selected approved protein kinase inhibitors as determined by the DiscoverX KinomeScan. The human kinome is represented as circular phylogenetic tree without the atypical protein kinases and results are reported as a map (Treespot), which allows visualizing compound interactions across the human kinome panel. AZD6244 (selumetinib) is an allosteric MEK inhibitor which displays the same selectivity as trametinib. Data are taken from http://www.discoverx.com/tools-resources/interaction-maps.