Biochemical Mechanisms of Resistance to Small-Molecule Protein Kinase Inhibitors

Abstract

Protein kinases have emerged as one of the most frequently targeted families of proteins in drug discovery. While the development of small-molecule inhibitors that have the potency and selectivity necessary to be effective cancer drugs is still a formidable challenge, there have been several notable successes in this area over the last decade. However, in the course of the clinical use of these inhibitors, it has become apparent that drug resistance is a recurring problem. Because kinase inhibitors act by targeting a specific kinase or set of kinases, there is a strong selective pressure for the development of mutations that hinder drug binding but preserve the catalytic activity of these enzymes. To date, resistance mutations to clinically-approved kinase inhibitors have been identified in a number of kinases. This review will highlight recent work that has been performed to understand how mutations in the kinase catalytic domain confer drug resistance. In addition, recent experimental efforts to predict potential sites of clinical drug resistance will be discussed. KeywordsDFG motif; Gatekeeper residue; Hydrogen bond; IC 50 ; Imatinib; K d ; P-loop; Protein kinase Reversible protein phosphorylation cascades represent a central theme in cellular signal transduction. Protein kinases are the single family of enzymes that catalyze the transfer of the γ-phosphate group from adenosine 5'-triphosphate (ATP) to a target protein, and thus are key regulators of these phosphorylation pathways (1). Due to the central role that these enzymes play in cellular behavior, it is not surprising that misregulated protein kinase activity contributes to a number of diseases including cancer, inflammation and diabetes (2). Currently, there are dozens of small-molecule protein kinase inhibitors undergoing clinical evaluation, with eleven approved for clinical use (3,4).The catalytic domains of protein kinases are bi-lobal with a smaller N-terminal lobe comprised mainly of β-strands and a larger α-helical C-terminal lobe (Figure 1, top left panel) (5,6). These lobes are joined by a segment known as the hinge region, which outlines a narrow hydrophobic cleft where ATP binds. The adenine ring of ATP makes key hydrogen-bonding contacts with the amide backbone of the hinge region. The α-and β-phosphate groups of ATP are aligned for catalysis via an interaction with a divalent magnesium ion and a conserved catalytic lysine (7,8). Protein substrates bind in an extended conformation along a shallow groove on the Clobe, which allows the residue that will be phosphorylated to accept the γ-phosphate of ATP. Adjacent to the ATP-binding cleft is a 20-30 residue long activation loop that increases the catalytic activity of most kinases when phosphorylated (9). The activation loop contains the highly conserved Asp-Phe-Gly (DFG) motif, the conformation of which is directly coupled to * Corresponding author. Department of Chemistry, University of Washington, Seattle, WA, 98195, Phone: 206-543-1653, maly@chem.washington.edu. NIH Public Access...

Effect of dihydropyrrol and maleimide derivatives on the state of the liver and colon in normal rats and those with colorectal carcinogenesis induced by dimethylhydrazine

“…Але та незначна кількість препаратів, які на сьогодні є апробовани-ми [8,9], мають низку недоліків, серед яких індивідуальна гіперчутливість, виникнення резистентності через мутації генів рецепторів-мішеней як наслідок високої молекулярної специфічності препарату, органоспецифічна токсичність, зумовлена функціонуванням ре-цептора, що блокується [5,8,10].…”

Epithelial Tissue Hyperplasia Induced by the RAF Inhibitor PF-04880594 Is Attenuated by a Clinically Well-Tolerated Dose of the MEK Inhibitor PD-0325901

“…First, clinical development of vemurafenib revealed that a large number of patients with BRAFV600E mutation had primary or acquired resistance to the RAF inhibitor. Acquired resistance does not seem to develop as a result of mutation of "gatekeeper" residues in BRAF itself, as occurs in resistance to BCR-ABL and EGFR inhibitors (5), but from activation of other proteins in the same or parallel signaling pathways (6). Two of the most common resistance mechanisms involve mutation in the NRAS gene and upregulation of PDGFRb expression (7).…”

Structural and Biochemical Basis for Intracellular Kinase Inhibition by Src-specific Peptidic Macrocycles

“…The nitrophenylalanine occupies the adenine-binding pocket, but does not mimic the adenine hydrogen bonding pattern observed for MC4 and most ATP-competitive kinase inhibitors (Krishnamurty and Maly, 2010). When compared to the positioning of the pyrazine group in MC4b, the nitrophenylalanine building block does not bind as deeply into the pocket (Fig.…”

“…Rather, our structural and biochemical data indicate that MC25 resides 6.7 Å angstroms from Thr338 and that its affinity for Src derives from additional electrostatic interaction between the nitrophenyl group and catalytic Lys295, thereby explaining how MC25 binding is not perturbed by the T338I mutation. This shallow positioning in the nucleotide binding site and interaction with Lys295 are unusual, as most small molecule kinase inhibitors make a characteristic set of hydrophobic and hydrogen bond interactions that mimic the adenine ring of ATP (Krishnamurty and Maly, 2010). An exception are inhibitors like the 5′-fluorosulfonylbenzoate derivatives of the pan-SFK inhibitor PP1 that covalently attach to the catalytic lysine (Gushwa et al, 2012).…”