Kinase drug discovery 20 years after imatinib: progress and future directions

Abstract

Protein kinases regulate nearly all aspects of cell life, and alterations in their expression, or mutations in their genes, cause cancer and other diseases. Here, we review the remarkable progress made over the past 20 years in improving the potency and specificity of small-molecule inhibitors of protein and lipid kinases, resulting in the approval of more than 70 new drugs since imatinib was approved in 2001. These compounds have had a significant impact on the way in which we now treat cancers and non-cancerous conditions. We discuss how the challenge of drug resistance to kinase inhibitors is being met and the future of kinase drug discovery.

Fig. 1. Timeline depicting important events in the development and approval of kinase inhibitors over the past 20 years since imatinib was approved for treatment of CML in 2001.

Events involving tyrosine kinases are in pink boxes, those involving serine/threonine-specific protein kinases are in blue boxes and those involving phosphatidylinositol 3-kinases (PI3Ks) are in grey boxes. BTK, Bruton’s tyrosine kinase; CML, chronic myeloid leukaemia; CLL, chronic lymphocytic leukaemia; EGFR, epidermal growth factor receptor; FGFR, fibroblast growth factor receptor; GIST, gastrointestinal tumour; NTRK, neurotrophic receptor tyrosine kinase; TKI, tyrosine kinase inhibitor.

Fig. 2. Mutations in the classical MAP kinase cascade cause cancer.

The classical mitogen-activated protein (MAP) kinase cascade is frequently hyperactivated in lung and other cancers owing to the overexpression or mutation of receptor tyrosine kinases, such as the epidermal growth factor receptor (EGFR), ALK and MET, and more downstream effectors that are most commonly RAS and BRAF. Examples of drugs that target the EGFR (gefitinib, erlotinib and osimertinib), ALK (crizotinib, brigatinib and alectinib) and MET (capmatinib and tepotinib) are highlighted in red. The three approved inhibitors of BRAF and the four approved inhibitors of MEK1 and MEK2 are also shown.

Fig. 3. Mechanisms that can cause drug resistance.

Drug resistance occurs primarily through four main mechanisms. Acquired drug resistance mutations most commonly affect the binding of the drug to its target. Acquired oncogenic amplifications or rearrangements can activate downstream signalling to bypass inhibition of the drug target. Mutations in downstream effectors can activate signalling pathways despite effective inhibition of an upstream kinase target. State transformation can lead to kinase inhibitor insensitivity.

Fig. 4. Chemical structures of first-generation, second-generation and third-generation EGFR inhibitors.

Epidermal growth factor receptor (EGFR) kinase inhibitors are a key example of the theme of next-generation agent development to continuously improve drug properties. First-generation inhibitors, gefitinib and erlotinib, have an anilinoquinazoline core backbone structure and bind reversibly in competition with ATP to potently inhibit EGFR catalytic activity. Second-generation inhibitors, afatinib and dacomitinib, share the quinazoline core structure, but contain a covalent warhead that enables irreversible binding and which increases potency but also toxicity. Afatinib and dacomitinib also did not overcome the common acquired resistance mutation EGFR^T790M, which led to the development of the third-generation inhibitors osimertinib and olmutinib. To overcome the high affinity of EGFR-T790M for ATP, these inhibitors contain a covalent warhead. They also contain a pyrimidine core backbone that is structurally distinct from the quinazoline-based structures to optimize selective binding within the catalytic domain that harbours the EGFR-T790M alteration.

Fig. 5. Binding modes for first-generation, second-generation and third-generation EGFR inhibitors.

X-ray crystal structures highlighting the binding modes for first-generation, second-generation and third-generation EGFR inhibitors, showing key residues in the kinase domain. Highlighted is the gatekeeper Thr790, which when mutated to Met is a frequent cause of drug resistance to first-generation and second-generation inhibitors, and Leu858, which when mutated to Arg is a frequent cause of EGFR activation. Exon 19, deletion of which also causes activation, is included for orientation. a | Crystal structure of the wild-type kinase domain of the EGFR in complex with gefitinib (green) (Protein Data Bank (PDB) identifier 2ITY). b | Crystal structure of the wild-type kinase domain of the EGFR in complex with afatinib (green). Afatinib forms a covalent bond with Cys797 of the EGFR (PDB identifier 4G5J). c | Crystal structure of the EGFR-T790M mutant in complex with osimertinib (green), which also forms a covalent bond with Cys797. The Thr790Met mutation changes the conformation of the ATP-binding pocket, which increases affinity for ATP (PDB identifier 6JX4).