A rationale for the design of an inhibitor of tyrosyl kinase

Small molecule substrate phosphorylation site inhibitors of protein kinases: approaches and challenges

Protein kinases are important mediators of cellular communication and attractive drug targets for many diseases. Although success has been achieved with developing ATP-competitive kinase inhibitors, the disadvantages of ATP-competitive inhibitors have led to increased interest in targeting sites outside of the ATP binding pocket. Kinase inhibitors with substrate-competitive, ATP-noncompetitive binding modes are promising due to the possibility of increased selectivity and better agreement between biochemical and in vitro potency. However, the difficulty of identifying these types of inhibitors has resulted in significantly fewer small molecule substrate phosphorylation site inhibitors being reported compared to ATP-competitive inhibitors. This review surveys reported substrate phosphorylation site inhibitors and methods that can be applied to the discovery of such inhibitors, including a discussion of the challenges inherent to these screening methods.

Substrate activity screening with kinases: discovery of small-molecule substrate-competitive c-Src inhibitors

Substrate-competitive kinase inhibitors represent a promising class of kinase inhibitors, however, there is no methodology to selectively identify this type of inhibitor. Substrate activity screening was applied to tyrosine kinases. By using this methodology, the first small-molecule substrates for any protein kinase were discovered, as well as the first substrate-competitive inhibitors of c-Src with activity in both biochemical and cellular assays. Characterization of the lead inhibitor demonstrates that substrate-competitive kinase inhibitors possess unique properties, including cellular efficacy that matches biochemical potency and synergy with ATP-competitive inhibitors.

The chemical biology of protein phosphorylation

The explosion of scientific interest in protein kinase-mediated signaling networks has led to the infusion of new chemical methods and their applications related to the analysis of phosphorylation pathways. We highlight some of these chemical biology approaches across three areas. First, we discuss the development of chemical tools to modulate the activity of protein kinases to explore kinase mechanisms and their contributions to phosphorylation events and cellular processes. Second, we describe chemical techniques developed in the past few years to dissect the structural and functional effects of phosphate modifications at specific sites in proteins. Third, we cover newly developed molecular imaging approaches to elucidate the spatiotemporal aspects of phosphorylation cascades in live cells. Exciting advances in our understanding of protein phosphorylation have been obtained with these chemical biology approaches, but continuing opportunities for technological innovation remain.

A computational study of the phosphorylation mechanism of the insulin receptor tyrosine kinase

Although various groups have studied the phosphorylation mechanism of the insulin receptor tyrosine kinase (IRK), an unanimous picture has not yet emerged. In this work, we performed a computational study to gain further insights. We first built a structural model of the reactant complex with the guide of several crystal structures and previous computational studies of the cyclic AMP-dependent protein kinase. We then optimized the structure by performing geometry optimization using a quantum mechanical model containing nearly 300 atoms. A reaction path was then traced between the reactant and the product by using a multiple coordinate-driven method. The calculations mapped out a sequence of structural changes depicting the conversion of the reactant to the product. Analysis of the structural changes revealed the formation of a dissociative transition state and the involvement of a proton transfer from the hydroxyl group of the tyrosyl residue of the peptide substrate to a conserved aspartate in the active site of the enzyme. The proton transfer began well before the transition state was reached and finished only shortly before the product was completely formed. In addition, the formation of a hydrogen bonding network among Arg1136, Asp1132, the gamma-phosphate of ATP, and the tyrosine residue of the substrate appeared to hold the latter two in a near-attack position for reaction. The model estimated a reaction barrier of 14 kcal/mol, semiquantitatively in accord with experiment.

ATP-phosphopeptide conjugates as inhibitors of Src tyrosine kinases

A number of Src SH2 domain inhibitors enhance the kinase catalytic activity by switching the closed inactive to the open active conformation. ATP-phosphopeptide conjugates were designed and synthesized as Src tyrosine kinase inhibitors based on a tetrapeptide sequence pTyr-Glu-Glu-Ile (pYEEI) and ATP to block the SH2 domain signaling and substrate phosphorylation by ATP, respectively. In general, ATP-phosphopeptide conjugates with optimal linkers such as compounds 5 and 7 (K(i) = 1.7-2.6 microM) showed higher binding affinities to the ATP-binding site relative to the other ATP-phosphopeptide conjugates having short or long linkers, 1-4 and 6, (K(i) = 10.1-16.1 microM) and ATP (K(m) = 74 microM). These ATP-phosphopeptide conjugates may serve as novel templates for designing protein tyrosine kinase inhibitors to block SH2 mediated protein-protein interactions and to counter the activation of enzyme that resulted from the SH2 inhibition.

Designing bisubstrate analog inhibitors for protein kinases

Protein kinases play critical roles in signal transduction pathways by transmitting extracellular signals across the cell membrane to distant locations in the cytoplasm and the nucleus. The development of protein kinase inhibitors has been hindered by the broad overlapping substrate specificities exhibited by these enzymes. The design of bisubstrate analog inhibitors could provide for the enhancement of specificity and potency in protein kinase inhibition. Bisubstrate analog inhibitors form a special group of protein kinase inhibitors that mimic two natural substrates/ligands and that simultaneously associate with two regions of given kinases. Most bisubstrate analogs have been designed to mimic the phosphate donor (ATP) and the acceptor components (Ser-, Thr-, or Tyr-containing peptides). Recent studies have emphasized the importance of maintaining a specific distance between these two components to achieve potent inhibition. In this review, we present a discussion of the methods for designing protein kinase inhibitors by mechanism-based approaches. Emphasis is given to bivalent approaches, with an interpretation of what has been learned from more and less successful examples. Future challenges in this area are also highlighted.

Molecular rulers: an assessment of distance and spatial relationships of Src tyrosine kinase Sh2 and active site regions

The three-dimensional structures of the inactive conformations of Hck and Src, members of the Src protein-tyrosine kinase family, have recently been described. In both cases, the catalytic domain lies on the opposite face of the enzyme from the SH2 and SH3 domains. The active conformation of these enzymes has not yet been described. Given the known role of the SH2 and SH3 domains in promoting substrate binding, enzyme activation likely reorients the relative spatial arrangement between the SH2/SH3 domains and the active site region. We describe herein a series of "molecular rulers" and their use in assessing the topological and spatial relationships of the SH2 and active site regions of the Src protein-tyrosine kinase. These synthetic compounds contain sequences that are active site-directed (-Glu-Glu-Ile-Ile-(F(5))Phe-, where (F(5))Phe is pentafluorophenylalanine) and SH2-directed (-Tyr(P)-Glu-Glu-Ile-Glu-), separated by a sequence of variable length. The most potent bivalent compound, acetyl-Glu-Glu-Leu-Leu-(F(5))Phe-(GABA)(3)-Tyr(P)-Glu-Glu-Ile-Glu-amide (where GABA is gamma-aminobutyric acid), displays a >120-fold enhancement in inhibitory potency relative to the simple monovalent active site-directed species, acetyl-Glu-Glu-Leu-Leu-(F(5))Phe-amide. The short linker length (3 GABA residues) between the active site- and SH2-directed peptide fragments suggests that the corresponding domains on the Src kinase can assume a nearly contiguous spatial arrangement in the active form of the enzyme.

Molecular approaches to receptors as targets for drug discovery

Many receptors have been selected as viable drug discovery targets. One particular class of receptors that have received much interest and so far relatively good success are the receptor protein tyrosine kinases (RPTKs). Typically, RPTKs are activated following the binding of the peptide growth factor ligand to its receptor. The RPTKs play crucial roles in signal transduction pathways that regulate a number of cellular functions, such as cell differentiation and proliferation, both under normal physiological conditions as well as in a variety of pathological disorders. A variety of different tumour types have been shown to have dysfunctional RPTKs, either as a result of excess production of the growth factor, the receptor or both, or via mutations in the RPTKs structure. Irrespective of the cause, this leads to the over-activity of the particular RPTK system and in turn to the aberrant and inappropriate cellular signalling within the tumour cell. RPTKs are attractive targets in the search for therapeutic agents, not only against cancers but also against many other disease indications. Although an ever-increasing number of RPTKs have been selected as viable molecular targets for drug discovery programmes, four examples will be covered in this article. These are the epidermal growth factor receptor (EGF-R), platelet-derived growth factor receptor (PDGF-R), fibroblast growth factor receptor (FGR-R) and vascular endothelial growth factor receptor (VEGF-R), with the main emphasis of interest being on their role in oncology.

Development of inhibitors for protein tyrosine kinases

In the last 5 years, through combinatorial chemistry, high-throughput screening, computational chemistry, and traditional medicinal chemistry, numerous inhibitors for various protein tyrosine kinases (PTKs) have been developed. The majority of these compounds are small molecules that compete at the ATP binding site of the catalytic domain of the enzymes. Some compounds such as pseudosubstrate-based peptide inhibitor binds to the peptide/protein substrate site of the catalytic domain. Some inhibitors, primarily monoclonal antibodies, bind to the extracellular domain of receptor tyrosine kinases. Some of these inhibitors are highly potent and selective. Several are currently undergoing clinical trials for a number of diseases such as cancer.

Kinetic analysis of the cyclin-dependent kinase-activating kinase (Cak1p) from budding yeast

Cak1p, the Cyclin-dependent kinase-activating kinase from budding yeast, is an unusual protein kinase that lacks many of the highly conserved motifs observed among members of the protein kinase superfamily. Cak1p phosphorylates and activates Cdc28p, the major cyclin-dependent kinase (CDK) in yeast, and is thereby required for passage through the yeast cell cycle. In this paper, we explore the kinetics of CDK phosphorylation by Cak1p, and we examine the role of the catalytic step in the reaction mechanism. Cak1p proceeds by a sequential reaction mechanism, binding to both ATP and CDK2 with reasonable affinities, exhibiting K(d) values of 7.2 and 0.6 microm, respectively. Interestingly, these values are approximately the same as the K(M) values, indicating that the binding of substrates is fast with respect to catalysis and that the most likely reaction mechanism is rapid equilibrium random. Cak1p is a slow enzyme, with a catalytic rate of only 4.3 min(-)(1). The absence of a burst phase indicates that product release is not rate-limiting. This result, and a solvent isotope effect, suggests that a catalytic step is rate-limiting.

Probing the catalytic mechanism of the insulin receptor kinase with a tetrafluorotyrosine-containing peptide substrate

The interaction of a synthetic tetrafluorotyrosyl peptide substrate with the activated tyrosine kinase domain of the insulin receptor was studied by steady-state kinetics and x-ray crystallography. The pH-rate profiles indicate that the neutral phenol, rather than the chemically more reactive phenoxide ion, is required for enzyme-catalyzed phosphorylation. The pK(a) of the tetrafluorotyrosyl hydroxyl is elevated 2 pH units on the enzyme compared with solution, whereas the phenoxide anion species behaves as a weak competitive inhibitor of the tyrosine kinase. A structure of the binary enzyme-substrate complex shows the tetrafluorotyrosyl OH group at hydrogen bonding distances from the side chains of Asp(1132) and Arg(1136), consistent with elevation of the pK(a). These findings strongly support a reaction mechanism favoring a dissociative transition state.

Protein tyrosine kinases: structure, substrate specificity, and drug discovery

Protein tyrosine kinases (PTKs) play a crucial role in many cell regulatory processes. It is therefore not surprising to see that functional perturbation of PTKs results in many diseases. Despite the diverse primary structure organization of various PTKs, the catalytic or kinase domains of various PTKs as well as that of Ser/Thr kinases are generally conserved. The high resolution crystal structure of a few PTKs has been solved in the last few years. In contrast to the well-defined linear peptide substrate motifs recognized by specific Ser/Thr kinases, the identification of specific substrate motifs for PTK has been slow. It is not until recently that through the use of combinatorial peptide library methods that specific recognition motifs for specific PTKs have begun to emerge. Efficient and specific peptide substrates for some PTKs with Km at the mid microM range have been identified. Based on these peptide substrates, relatively potent (IC50 at the low microM range) and highly selective pseudosubstrate-based peptide inhibitors have been developed. There has been enormous effort in the development of PTK inhibitors for diseases such as cancer, psoriasis, and osteoporosis. Several new high-throughput PTK assay technologies have recently been described. Small molecules against specific PTK have been developed. Most of them are competitive inhibitors at the ATP binding site. Some of these inhibitors have already been in clinical trial.

A cellular reporter assay to monitor insulin receptor kinase activity based on STAT 5-dependent luciferase gene expression

A highly sensitive method for determination of insulin receptor (IR) kinase activity in whole cells, which is based on a STAT5 (signal transducer and activator of transcription 5)-dependent reporter gene assay, has been developed. We show in Rat1 fibroblasts stably overexpressing the human IR (Rat1-HIR-cl5) an insulin-dependent direct association and phosphorylation of STAT5b by IR kinase. Rat1-HIR cells transfected with a luciferase gene reporter construct under control of a STAT5-inducible promoter showed insulin-mediated induction of STAT5-dependent luciferase activity, with peak activities around 8 h of insulin treatment over a wide dose range. Transient STAT5b but not STAT5a cotransfection significantly enhanced reporter gene activity, yielding up to a fivefold induction. Addition of the IR kinase inhibitor tyrphostin AG1024 down-regulated luciferase induction in a dose-dependent manner. This is the first assay allowing determination of IR kinase activity in intact cells in a 24-well culture and a microtiter format. Kinetics of this cellular response, sensitivity range, and signal amplitude make it well suited for automation and offer the potential for establishing high-throughput screening systems for both insulin mimetic substances and IR kinase antagonists in a simple nonradioactive assay.

Implications for Src kinases in hematopoiesis: signal transduction therapeutics

Signal transduction therapeutics is now the dominant theme of drug discovery, and its most immediate impact will be in cancer therapeutics. Blood cell proliferation, differentiation, and activation are controlled by cytokines, whose receptors contain tyrosine kinase catalytic domains or recruit cytosolic tyrosine kinases. Among the most important cytosolic protein tyrosine kinases are the Src and Jak families. Receptor or cytosolic protein tyrosine kinases activate a similar set of intracellular signaling molecules. In blood cells, excessive tyrosine kinase activity is associated with either cancer or autoreactive diseases. Therefore, tyrosine kinases and their substrates serve as excellent candidates for drug intervention. Herceptin has been approved for use in breast cancer. Other agents, such as SU101 and CGP 57418B, are well into phase I-III trials. Newer, more selective tyrosine kinase inhibitors are being evaluated for future use in the treatment of hematologic and solid tumors as well as a wide range of inflammatory or autoimmune diseases.

Nonphosphorylatable tyrosine surrogates. Implications for protein kinase inhibitor design

Tyrosine-specific protein kinases are known to utilize short synthetic tyrosine-containing peptides as substrates and, as a consequence, a number of inhibitory peptides have been prepared by replacing the tyrosine moiety in these peptides with a nonphosphorylatable phenylalanine residue. Unfortunately, the inhibitory efficacy of these phenylalanine-based peptides is often disappointing. These results demonstrate the need for nonphosphorylatable tyrosine surrogates that enhance enzyme affinity. As a consequence, we prepared nearly two dozen different phenethylamine derivatives, attached them to the C terminus of an active site-directed peptide (Glu-Glu-Leu-Leu), and examined their effectiveness as inhibitors of pp60(c-)src. Three derivatives exhibit enhanced inhibitory activity (relative to phenethylamine), including para-substituted sulfonamide and guanidino analogs as well as a pentafluoro-containing species. The para-sulfonamide derivative was selected for further study and was found to function as a competitive inhibitor versus variable peptide substrate and as a noncompetitive inhibitor versus variable ATP. In short, the enhanced inhibitory activity of the sulfonamide derivative is not due to the association of this moiety with the ATP binding site. Furthermore, peptides containing the para-guanidino and pentafluoro derivatives of phenylalanine were prepared. These species also display enhanced inhibitory activity toward pp60(c-)src relative to the corresponding phenylalanine-based peptide.

The role of the catalytic base in the protein tyrosine kinase Csk

A potential distinguishing feature between protein tyrosine kinases and homologous serine/threonine kinases is the function of the catalytic base in these enzymes. In this study, we show that a peptide containing the unnatural amino acid trifluorotyrosine shows remarkably similar efficiency as a substrate of the tyrosine kinase Csk (C-terminal Src kinase) compared with the corresponding tyrosine-containing peptide despite a 4-unit change in the phenolic pKa. These results argue against the importance of early tyrosine deprotonation by a catalytic base in Csk. To further explore the role of the proposed catalytic base, the Csk mutant protein D314E was produced. This mutant displayed a significant reduction in kcat (approximately 10(4)) but relatively little effect on substrate Km values compared with wild-type Csk. Examination of the thio effect (kcat-ATP/kcat-adenosine 5'-O-(thiotriphosphate)) for D314E Csk led to the suggestion that a role of aspartate 314 may be to enhance the reactivity of the gamma-phosphate of ATP toward electrophilic attack. These results may have significant impact on protein tyrosine kinase inhibitor design.

Epidermal growth factor receptor tyrosine kinase. Investigation of catalytic mechanism, structure-based searching and discovery of a potent inhibitor

Inhibition of tyrosine kinases is a possible approach for the treatment of cancer. We have investigated the catalytic mechanism of the epidermal growth factor receptor tyrosine kinase (EGF-RTK) in order to obtain information for use in structure-based searching for inhibitors. Initial rate studies imply that EGF-RTK forms a ternary complex together with ATP and peptide substrate. Investigation of pH and temperature dependence suggests that the kinase reaction requires the ionised form of a carboxylate (pK = 6.3) and the protonated form of another group (pK = 9.1). These characteristics are consistent with a mechanism where the carboxylate of Asp813(pK = 6.3) facilitates deprotonation of the tyrosyl hydroxyl of the peptide substrate, activating it as a nucleophile to attack the gamma-phosphorus of ATP which interacts with a protonated enzyme side-chain (pK = 9.1), possibly the guanidinium group of Arg817. This proposed catalytic mechanism was used to define a query when searching for inhibitors in a database of predicted three-dimensional structures. The procedure involved searching for compounds that mimic the ATP gamma-phosphate, tyrosyl hydroxyl and the tyrosyl aromatic ring, all of which seem to interact strongly with the enzyme during catalysis. This search allowed identification of inhibitors of EGF-RTK which were used to define queries for two-dimensional searching of a larger database, leading to the discovery of 4-(3-chloroanilino)quinazoline (CAQ) which is a potent inhibitor (Ki = 16 nM) of the enzyme. The compound is believed to be the first representative from a new structural class of anilinoquinazoline tyrosine kinase inhibitors. It follows competitive kinetics with respect to ATP and noncompetitive kinetics when the peptide is varied, implying that it functions as an analogue of ATP. CAQ is a novel and potent lead in the search for tyrosine kinase inhibitors as potential agents for the treatment of cancer.

Design of a potent peptide inhibitor of the epidermal growth factor receptor tyrosine kinase utilizing sequences based on the natural phosphorylation sites of phospholipase C-gamma 1

Peptides that possess primary sequences identical to segments surrounding the natural phosphorylation sites of phospholipase C-gamma 1 (i.e., tyrosines 472, 771, 783, and 1284) have been synthesized and evaluated with respect to substrate kinetics for the epidermal growth factor receptor tyrosine kinase. A peptide that was based on tyrosine 472 was the superior substrate in terms of lowest Km value at 37 microM and had the following amino acid sequence: Lys-His-Lys-Lys-Leu-Ala-Glu-Gly-Ser-Ala-Tyr472-Glu-Glu-Val. This peptide sequence was used as a foundation to make amino acid substitutions and/or chemical modifications directed toward the synthesis of a potent peptide inhibitor. As a result, a nine amino acid peptide was synthesized having a K(i) of 10 microM.

Inhibition of the epidermal growth factor receptor tyrosine kinase activity by leflunomide

The active metabolite of leflunomide, A77 1726 inhibits the proliferation of a variety of mammalian cell lines in culture. Epidermal growth factor (EGF)-dependent proliferation is inhibited by A77 1726 at an effective dose of 30-40 microM. A77 1726 appears to directly inhibit the EGF receptor tyrosine-specific kinase activity both in intact cells and purified EGF receptors at the same effective dose. These data suggest that leflunomide inhibits cellular proliferation by the inhibition of tyrosine-specific kinase activities.