Catalytic subunit of cyclic AMP-dependent protein kinase: structure and dynamics of the active site cleft.

The catalytic subunit of cyclic AMP-dependent protein kinase serves as a structural template for the entire family of Ser, Thr, and Tyr specific protein kinases. We review here the dynamics of the active catalytic subunit. These dynamics correlate with an opening and closing of the active site cleft, and are considered to be a requirement for catalysis. The motions, described by a set of several crystal structures, reveal a very fluid active site cleft. This active site cleft with its dynamic opening and closing is a prime target for protein kinase inhibitors.     

Structural aspects of protein kinase control-role of conformational flexibility

Protein kinases catalyze the phosphotransfer reaction fundamental to most signaling and regulatory processes in the eukaryotic cell. Absolute control of individual protein kinase activity is, therefore, of utmost importance to signaling fidelity in the cell. Mechanisms for activity modulation, including complete and reversible inactivation, have been shown by crystal structures of many active and inactive protein kinases. The structures of inactivated kinases, compared with those of active and catalytically competent kinases such as the protein kinase A catalytic subunit, highlight recurring structural alterations among a set of elements of the catalytic kinase core. These 'activity modulation sites' apparently comprise the principal evolved mechanisms for control of enzyme activity in the catalytic domain. In combination, they enable diverse physiological regulatory mechanisms operative for most protein kinases. Identification and characterization of these sites should impact strategies for discovery and design of target-specific therapeutic drugs as the range of structural variations for specific kinases becomes known. The principle site, the ATP-binding pocket, is the target of many physiological regulators and also most experimental or therapeutic inhibitors, which typically block it in a competitive or allosteric fashion. Co-crystallization studies with protein kinase A and other kinases have revealed binding features of several classes of protein kinase inhibitors. Ligand-induced structural changes are common and tend to optimize buried surface areas. The ability to optimize binding energies arising from the hydrophobic effect creates a logarithmic dependence of binding energy on buried surface areas. Exceptions to this rule arise for specific inhibitor classes, and possibly also as artifacts of structure determination.     

Interleukin 1 alpha activates two forms of p54 alpha mitogen-activated protein kinase in rabbit liver

We have identified in rabbits two hepatic forms of T669 peptide kinases that are very strongly activated after systemic injection with the inflammatory cytokine interleukin 1 (IL-1). The T669 peptide contains a major phosphorylation site of the epidermal growth factor receptor, threonine 699 and is a substrate for mitogen-activated protein (MAP) kinases. The kinases were purified to homogeneity and corresponded to 50- and 55-kD proteins on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Amino acid sequencing of 12 tryptic peptides of both kinases identified them as p54 MAP kinase alpha. This kinase belongs to the novel family of stress-activated protein kinases. This is the first evidence of IL-1 activating a specific protein kinase in vivo.     

Modulation of protein kinase signaling by protein phosphatases and inhibitors

Protein tyrosine phosphatases (PTPs) form a large family of enzymes that serve as key regulatory components in signal transduction pathways. Defective or inappropriate regulation of PTP activity leads to aberrant tyrosine phosphorylation, which contributes to the development of many human diseases. In addition to controlling the phosphorylation states of protein kinase substrates, PTPs can also directly modulate protein kinase activity. Evidence suggests that PTPs can exert both positive and negative effects on a signaling pathway. Thus, further understanding of the fundamental role of protein tyrosine phosphorylation in complex and critical signal transduction pathways requires detailed studies of both the kinases and the phosphatases. In this review, we first summarize our current understanding of PTP structure and function. We then discuss the molecular basis of PTP substrate specificity, focusing primarily on mitogen-activated protein (MAP) kinase phosphatase 3. We demonstrate that the MAP kinase phosphatases display exquisite substrate specificity requiring extensive protein-protein interactions for precise down-regulation of MAP kinase activity. We also highlight our recent progress in developing small molecule PTP1B inhibitors. Using a novel combinatorial approach that is designed to target both the active site and a unique peripheral site in PTP1B, we have obtained a PTP1B inhibitor with 2.4 nM affinity and orders of magnitude selectivity against a panel of PTPs. Currently, some of the compounds are being evaluated in both cell and animal models to further define the role of PTP1B in insulin signaling.     

Viral and host-cell protein kinases: enticing antiviral targets and relevance of nucleoside, and viral thymidine, kinases.

Numerous targets are known for development of antiviral agents, and some significant successes have been achieved with nucleoside analogues. These are "activated" by phosphorylation by viral and/or host-cell nucleoside kinases, the final target being principally the viral polymerase. With latency of herpes viruses, the viral thymidine kinase may be the ultimate target. Less attention has been devoted to viral protein kinases as antiviral targets, largely because 5 years ago, these the study of such enzymes was considered "still in its infancy." In the interim, identification of viral and host-cell protein kinases involved in viral gene expression, and viral replication, has made impressive advances. In conjunction with current progress in development of specific inhibitors of cellular protein kinases, and the differences in sequence motifs between these and the viral enzymes, the latter are indeed attractive targets, as are also some host-cell protein kinases. Examples include, amongst others, the essential protein kinases of vaccinia virus; the nonsegmented negative-strand RNA viruses, all essentially dependent on host-cell kinases, e.g., protein kinase CK-II (casein kinase-II), for which good inhibitors, such as halogenated benzimidazoles and benzotriazoles, are known; herpes viruses, with emphasis on human cytomegalovirus, the UL97 gene of which codes for a protein kinase that, like viral thymidine kinases, "activates," by phosphorylation, a nonpeptide antiviral acyclonucleoside ganciclovir, an analogue of the antiherpes aciclovir. The latter, in turn, is active against animal cytomegaloviruses following phosphorylation by the products of their UL97 gene homologues. Attention is also directed to the antiviral activity of the cyclic phosphate of ganciclovir, a structural analogue of the second messenger cyclic GMP.     

Designing specific protein kinase inhibitors: insights from computer simulations and comparative sequence/structure analysis

Protein kinases are important targets for designing therapeutic drugs. We describe here a computational approach to extend the usefulness of a single protein-inhibitor structure in aiding the design of protein kinase inhibitors. This approach is based on using sensitivity analysis to identify the most significant functional groups of a lead compound in accounting for binding affinity and on using comparative sequence/structure analysis to examine whether these functional groups would present specificity. A sensitivity analysis study is similar to genetic or chemical modification experiments in which specific features of a lead compound are modified to examine whether they affect properties such as binding affinity. In this study, the binding affinity was estimated by using an implicit-solvent model in which the electrostatic contributions were obtained by solving the Poisson equation, and the hydrophobic effects were accounted for by using surface-area-dependent terms. The comparative sequence/structure analysis involves the study of the amino acid distributions of a large number of protein kinases (384 in this study) near the ligand-binding sites. This analysis provides useful guiding principles for designing specific inhibitors targeted towards a particular kinase. Here, we illustrate the utility of these computational approaches by applying them to identify the determinants of the recognition between the protein kinase A and two of its inhibitors. One inhibitor, balanol, binds to the ATP-binding pocket. The other, protein kinase inhibitor, binds to the substrate-binding site. These analyses have helped to construct pharmacophore models for mining new drug leads from small-molecule libraries and for suggesting how a lead compound or a peptide inhibitor may be modified to generate selective inhibitors.     

Protein kinases as targets for anticancer agents: from inhibitors to useful drugs

Many components of mitogenic signaling pathways in normal and neoplastic cells have been identified, including the large family of protein kinases, which function as components of signal transduction pathways, playing a central role in diverse biological processes, such as control of cell growth, metabolism, differentiation, and apoptosis. The development of selective protein kinase inhibitors that can block or modulate diseases caused by abnormalities in these signaling pathways is widely considered a promising approach for drug development. Because of their deregulation in human cancers, protein kinases, such as Bcr-Abl, those in the epidermal growth factor-receptor (HER) family, the cell cycle regulating kinases such as the cyclin-dependent kinases, as well as the vascular endothelial growth factor-receptor kinases involved in the neo-vascularization of tumors, are among the protein kinases considered as prime targets for the development of selective inhibitors. These drug-discovery efforts have generated inhibitors and low-molecular weight therapeutics directed against the ATP-binding site of various protein kinases that are in various stages of development (up to Phase II/III clinical trials). Three examples of inhibitors of protein kinases are reviewed, including low-molecular weight compounds targeting the cell cycle kinases; a potent and selective inhibitor of the HER1/HER2 receptor tyrosine kinase, the pyrollopyrimidine PKI166; and the 2-phenyl-aminopyrimidine STI571 (Glivec(R), Gleevec) a targeted drug therapy directed toward Bcr-Abl, the key player in chronic leukemia (CML). Some members of the HER family of receptor tyrosine kinases, in particular HER1 and HER2, have been found to be overexpressed in a variety of human tumors, suggesting that inhibition of HER signaling would be a viable antiproliferative strategy. The pyrrolo-pyrimidine PKI166 was developed as an HER1/HER2 inhibitor with potent in vitro antiproliferative and in vivo antitumor activity. Based upon its clear association with disease, the Bcr-Abl tyrosine kinase in CML represents the ideal target to validate the clinical utility of protein kinase inhibitors as therapeutic agents. In a preclinical model, STI571 (Glivec(R), Gleevec) showed potent in vitro and in vivo antitumor activity that was selective for Abl, c-Kit, and the platelet-derived growth factor-receptor. Phase I/II studies demonstrated that STI571 is well tolerated, and that it showed promising hematological and cytogenetic responses in CML and clinical responses in the c-Kit-driven gastrointestinal tumors.     

Death-associated protein kinase (DAPK) family modulators: Current and future therapeutic outcomes

Serine/threonine kinases (STKs) represent the majority of discovered kinases to date even though a few Food and Drug Administration approved STKs inhibitors are reported. The third millennium came with the discovery of an important group of STKs that reshaped our understanding of several biological signaling pathways. This family was named death-associated protein kinase family (DAPK family). DAPKs comprise five members (DAPK1, DAPK2, DAPK3, DRAK1, and DRAK2) and belong to the calcium/calmodulin-dependent kinases domain. As time goes on, the list of biological functions of this family is constantly updated. The most extensively studied member is DAPK1 (based on the publications number and Protein Data Bank reported crystal structures) that plays fundamental biological roles depending on the cellular context. DAPK1 regulates apoptosis, autophagy, contributes to the pathogenesis of Alzheimer's disease, acts as a tumor suppressor, inhibits metastasis, mediates the body responses to viral infections, and regulates the synaptic plasticity and depression. For their biological roles, several DAPKs’ modulators have been reported for treatment of many diseases as well as acting as probe compounds to facilitate the understanding of the biological functions elicited by this family. Despite that, the number of reported modulators is still limited and more research needs to be conducted on the discovery of novel strategies to activate or inhibit this family. In this report, we aim at drawing more attention to this family by reviewing the recent updates regarding the structure, biological roles, and regulation of this family. In addition, the small-molecule modulators of this family are reviewed in details with their potential therapeutic outcomes evaluated to help medicinal chemists develop more potent and selective possible drug candidates.     

Cloning and characterization of microbial activated Aedes aegypti MEK4 (AaMEK4): influences of noncatalytic domains on enzymatic activity

Protein kinases are known to be involved in a number of signal transduction cascades. Both the stress‐activated Jun N‐terminal kinase (JNK) and mitogen‐activated protein kinase (MAPK) p38 pathways have been shown to correlate with the insect immune response to microbial infection. MAP kinase kinase 4 (MEK4) is an upstream kinase of JNK and p38 kinase. The cDNA of AaMEK4 was cloned and characterized. AaMEK4 was activated by microbial lysates of Gram‐positive, Gram‐negative bacteria and yeast. The conserved lysine (K₁₁₂) and the putative phosphorylation sites (S₂₃₈ and T₂₄₂) were shown to be important for kinase activity by site‐directed mutagenesis. A common MAPK docking site (MAPK_dsA) was found and in addition, a new nearby docking site, MAPK_dsB, was identified in the N‐terminal noncatalytic domain of AaMEK4. MAPK_dsB was shown to be a unique element in the MEK4 family. In this study, both MAPK_dsA and _dsB were demonstrated to be important to AaMEK4 enzymatic activity for the downstream protein kinase, Aap38.     

ATP site-directed competitive and irreversible inhibitors of protein kinases

Several tyrosine and serine/threonine protein kinases have emerged in the last few years as attractive targets in the search for new therapeutic agents being applicable in many different disease indications. Initially, inhibition of these protein kinases by ATP site-directed inhibitors was considered less prone to success, but medicinal chemists from both academia and industry have been able to impart potency and selectivity to a limited number of scaffolds by modulating and fine-tuning the interactions of the modified template with the ATP binding site of the selected kinase. The chemical templates that have been used in the synthesis of ATP site-directed protein kinase inhibitors are reviewed with emphasis on the kinase inhibitors that have entered or are about to enter clinical trials. Examples have been selected to illustrate how structure-based design approaches and new methods to increase compound diversity have had an impact on this area of research.     

Protein kinases CK1 and CK2 as new targets for neurodegenerative diseases

Following the discovery of the human kinome, protein kinases have become the second most important group of drug targets as they can be modulated by small ligand molecules. Moreover, orally active protein kinase inhibitors have recently reached the market and there are many more in clinical trials. The lack of treatments for neurodegenerative diseases has increased human and financial efforts in the search for new therapeutic targets that could provide new effective drug candidates. The importance of kinases in the molecular pathway of neuronal survival is under study, but different key pathways have been described. New roles for the old casein kinases 1 and 2, currently known as protein kinases CK1 and CK2, have recently been discovered in the molecular pathology of different neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases and amyotrophic lateral sclerosis. The search for specific inhibitors of these enzymes has become an important challenge for the treatment of these devastating diseases. The role of these two kinases in the molecular pathology of different neurodegenerative diseases together with different chemical families that are able to more or less specifically inhibit CK1 and CK2 are discussed in this review. © 2010 Wiley Periodicals, Inc. Med Res Rev 31:924‐954, 2011     

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.     

Protein tyrosine kinase signaling diversity and susceptibility to targeted kinase inhibitors.

Protein kinases, including tyrosine kinases, are one of the largest classes of proteins implicated in cancer development and progression. Recent discovery of selective therapies targeting tyrosine kinase receptor signaling has provided encouraging clinical results. Clinical trials with anti-EGFR, anti-ErbB2/Her2, anti-Bcr-Abl and others have demonstrated the clinical utility of tyrosine kinases as therapeutic targets and as surrogate markers to guide the selection of patients susceptible to respond to treatment. This success has been tempered in part because resistance to targeted therapies is now documented to occur in experimental models and in patients, which hampers therapeutic efficacy. Mechanisms of resistance include cell heterogeneity in target expression, mutations in target's encoding genes, and compensatory signaling mechanisms. This paper provides a brief overview on the diversity of tyrosine kinase signaling and the impact on cancer cell response to targeted tyrosine kinase inhibitors.     

Strategies toward the design of novel and selective protein tyrosine kinase inhibitors.

Protein tyrosine kinases play a fundamental role in signal transduction pathways. Deregulated tyrosine kinase activity has been observed in many proliferative diseases (e.g., cancer, psoriasis, restenosis, etc.). Tyrosine kinases are, therefore, attractive targets for the design of new therapeutic agents against cancer. We have built up a pharmacophore model of the ATP-binding site of the epidermal growth factor receptor (EGFR) kinase and used it for the rational design of kinase inhibitors. Several examples of the successful use of this model are presented in this review. Amongst these, 4-substituted-pyrrolo[2,3-d]pyrimidines, a new class of highly potent and selective inhibitors of the EGFR kinase, have been identified and further optimized. The most active derivatives inhibited the EGFR tyrosine kinase with IC50 values between 1 and 5 nM. In EGF-dependent cellular systems, tyrosine phosphorylation, as well as c-fos mRNA expression, was inhibited with similar IC50 values. Further successful application of this pharmacophore model led to the identification and optimization of phenylamino-pyrazolo[4,3-d]pyrimidines and substituted isoflavones and quinolones, other classes of potent, selective, and ATP competitive EGFR kinase inhibitors with IC50 values in the low nanomolar range. Structure-activity relationships of both classes are discussed.     

Pharmacological Assessment Defines Leishmania donovani Casein Kinase 1 as a Drug Target and Reveals Important Functions in Parasite Viability and Intracellular Infection

Protein kinase inhibitors have emerged as new drugs in various therapeutic areas, including leishmaniasis, an important parasitic disease. Members of the Leishmania casein kinase 1 (CK1) family represent promising therapeutic targets. Leishmania casein kinase 1 isoform 2 (CK1.2) has been identified as an exokinase capable of phosphorylating host proteins, thus exerting a potential immune-suppressive action on infected host cells. Moreover, its inhibition reduces promastigote growth. Despite these important properties, its requirement for intracellular infection and its chemical validation as a therapeutic target in the disease-relevant amastigote stage remain to be established. In this study, we used a multidisciplinary approach combining bioinformatics, biochemical, and pharmacological analyses with a macrophage infection assay to characterize and define Leishmania CK1.2 as a valid drug target. We show that recombinant and transgenic Leishmania CK1.2 (i) can phosphorylate CK1-specific substrates, (ii) is sensitive to temperature, and (iii) is susceptible to CK1-specific inhibitors. CK1.2 is constitutively expressed at both the promastigote insect stage and the vertebrate amastigote stage. We further demonstrated that reduction of CK1 activity by specific inhibitors, such as D4476, blocks promastigote growth, strongly compromises axenic amastigote viability, and decreases the number of intracellular Leishmania donovani and L. amazonensis amastigotes in infected macrophages. These results underline the potential role of CK1 kinases in intracellular survival. The identification of differences in structure and inhibition profiles compared to those of mammalian CK1 kinases opens new opportunities for Leishmania CK1.2 antileishmanial drug development. Our report provides the first chemical validation of Leishmania CK1 protein kinases, required for amastigote intracellular survival, as therapeutic targets.