Developing irreversible inhibitors of the protein kinase cysteinome

Abstract

Protein kinases are a large family of approximately 530 highly conserved enzymes that transfer a γ-phosphate group from ATP to a variety of amino acid residues, such as tyrosine, serine, and threonine, that serves as a ubiquitous mechanism for cellular signal transduction. The clinical success of a number of kinase-directed drugs and the frequent observation of disease causing mutations in protein kinases suggest that a large number of kinases may represent therapeutically relevant targets. To date, the majority of clinical and preclinical kinase inhibitors are ATP competitive, noncovalent inhibitors that achieve selectivity through recognition of unique features of particular protein kinases. Recently, there has been renewed interest in the development of irreversible inhibitors that form covalent bonds with cysteine or other nucleophilic residues in the ATP-binding pocket. Irreversible kinase inhibitors have a number of potential advantages including prolonged pharmacodynamics, suitability for rational design, high potency, and ability to validate pharmacological specificity through mutation of the reactive cysteine residue. Here, we review recent efforts to develop cysteine-targeted irreversible protein kinase inhibitors and discuss their modes of recognizing the ATP-binding pocket and their biological activity profiles. In addition, we provided an informatics assessment of the potential "kinase cysteinome" and discuss strategies for the efficient development of new covalent inhibitors.

Fig. 1

Electrophiles used in irreversible kinase inhibitors.

Fig. 2

Representative chemical structures of reported irreversible protein kinase inhibitors

Figure 3

Representative binding modes of irreversible protein kinase inhibitors A. ERK(PDB: 2E14), B. EGFR(PDB: 2JIV), C. BMX(Modeling based PDB: 3SXS), D.EGFR(PDB: 3IKA), E. VEGFR(modeling based PDB: 1VR2), F. RSK2(Modeling based PDB: 2QR7), G. BTK(Modeling based PDB:3GEN), H. KIT( Modeling based PDB:1T46), I. JNK(PDB:3V6S), J. FGFR(PDB:2FGI), K. NEK2(Modeling based PDB: 2JAV), L.GSK3-β (Modeling based PDB:1I09)

Figure 4

Representative positions of accessible cysteines in the active site, 1YVJ – kinase domain used for depiction (cyan = staurosporine). The various colored circles indicate relative positions of Cys residues depicted on top of 1YVJ. Red = hinge region, Yellow = gatekeeper and neighboring residues, Blue = glycine loop closer to the ATP-site, Mauve = flexible region of glycine loop, Green = activation loop (DFG-area), Orange = roof region

Fig. 5

Distribution of the cysteinome in the kinome tree. Red dots represent kinases that have been proven to be targeted irreversibly by small molecule inhibitors.

Fig. 6

Schematic representation of reversible PKI scaffold base approach to develop irreversible inhibitors

Figure 7

Schematic representation of flowchart for profiling data based approach