Showing papers on "Kinome published in 2006"

The dictyostelium kinome--analysis of the protein kinases from a simple model organism.

Abstract: Dictyostelium discoideum is a widely studied model organism with both unicellular and multicellular forms in its developmental cycle. The Dictyostelium genome encodes 285 predicted protein kinases, similar to the count of the much more advanced Drosophila. It contains members of most kinase classes shared by fungi and metazoans, as well as many previously thought to be metazoan specific, indicating that they have been secondarily lost from the fungal lineage. This includes the entire tyrosine kinase–like (TKL) group, which is expanded in Dictyostelium and includes several novel receptor kinases. Dictyostelium lacks tyrosine kinase group kinases, and most tyrosine phosphorylation appears to be mediated by TKL kinases. About half of Dictyostelium kinases occur in subfamilies not present in yeast or metazoa, suggesting that protein kinases have played key roles in the adaptation of Dictyostelium to its habitat. This study offers insights into kinase evolution and provides a focus for signaling analysis in this system.

The Rice Kinase Database. A Phylogenomic Database for the Rice Kinome

Abstract: The rice (Oryza sativa) genome contains 1,429 protein kinases, the vast majority of which have unknown functions. We created a phylogenomic database (http://rkd.ucdavis.edu) to facilitate functional analysis of this large gene family. Sequence and genomic data, including gene expression data and protein-protein interaction maps, can be displayed for each selected kinase in the context of a phylogenetic tree allowing for comparative analysis both within and between large kinase subfamilies. Interaction maps are easily accessed through links and displayed using Cytoscape, an open source software platform. Chromosomal distribution of all rice kinases can also be explored via an interactive interface.

Probing the human kinome for kinases involved in pancreatic cancer cell survival and gemcitabine resistance

Abstract: Except for gemcitabine, chemotherapeutic agents are ineffective with pancreatic adenocarcinoma because this cancer is resistant to apoptosis induction. Involvement of specific kinases in such resistance is likely. We developed a systematic strategy to screen the human kinome and select kinases whose inhibition in pancreatic cancer cells can increase 1) spontaneous apoptosis or 2) gemcitabine-induced apoptosis. The pancreatic adenocarcinoma cell line MiaPaCa-2 was transfected with 645 pairs of siRNAs directed to all human kinases. The same experiment was conducted in cells treated with 150 μM gemcitabine. Apoptosis was measured after 2 days and the results were normalized for cell viability. A panel of 56 kinases whose inhibition increased spontaneous apoptosis by at least 50% was established. Ten of them gave similar results on Panc1 and BxPC3 pancreatic adenocarcinoma cell lines. A panel of 83 kinases whose inhibition increased gemcitabine-induced apoptosis by 50% or more was also established. Twelve kin...

Protein kinase CK2: a newcomer in the 'druggable kinome'.

Abstract: The acronym CK2 (derived from the misnomer ‘casein kinase’ 2) denotes one of the most pleiotropic members of the eukaryotic protein kinase superfamily, characterized by an acidic consensus sequence in which a carboxylic acid (or pre-phosphorylated) side chain at position n + 3 relative to the target serine/threonine residue plays a crucial role. The latest repertoire of CK2 substrates includes approx. 300 proteins, but the analysis of available phosphopeptide databases from different sources suggests that CK2 alone may be responsible for the generation of a much larger proportion (10–20%) of the eukaryotic phosphoproteome. Although for the time being CK2 is not included among protein kinases whose inhibitors are in clinical practice or in advanced clinical trials, evidence is accumulating that elevated CK2 constitutive activity co-operates to induce a number of pathological conditions, including cancer, infectious diseases, neurodegeneration and cardiovascular pathologies. The development and usage of cell-permeant, selective inhibitors discloses a scenario whereby CK2 plays a global anti-apoptotic role, which under special circumstances may lead to untimely and pathogenic cell survival.

RNAi-based screening of the human kinome identifies Akt-cooperating kinases: a new approach to designing efficacious multitargeted kinase inhibitors.

Abstract: Tumors comprise genetically heterogeneous cell populations, whose growth and survival depend on multiple signaling pathways. This has spurred the development of multitargeted therapies, including small molecules that can inhibit multiple kinases. A major challenge in designing such molecules is to determine which kinases to inhibit in each cancer to maximize efficacy and therapeutic index. We describe an approach to this problem implementing RNA interference technology. In order to identify Akt-cooperating kinases, we screened a library of kinase-directed small interfering RNAs (siRNAs) for enhanced cancer cell killing in the presence of Akt inhibitor A-443654. siRNAs targeting casein kinase I gamma 3 (CSNK1G3) or the inositol polyphosphate multikinase (IPMK) significantly enhanced A-443654-mediated cell killing, and caused decreases in Akt Ser-473 and ribosomal protein S6 phosphorylation. Small molecules targeting CSNK1G3 and/or IPMK in addition to Akt may thus exhibit increased efficacy and have the potential for improved therapeutic index.

Computational proteomics of biomolecular interactions in the sequence and structure space of the tyrosine kinome: deciphering the molecular basis of the kinase inhibitors selectivity.

Abstract: Understanding and predicting the molecular basis of protein kinases specificity against existing therapeutic agents remains highly challenging and deciphering this complexity presents an important problem in discovery and development of effective cancer drugs. We explore a recently introduced computational approach for in silico profiling of the tyrosine kinases binding specificity with a class of the pyrido-[2,3-d]pyrimidine kinase inhibitors. Computational proteomics analysis of the ligand–protein interactions using parallel simulated tempering with an ensemble of the tyrosine kinases crystal structures reveals an important molecular determinant of the kinase specificity. The pyrido-[2,3-d]pyrimidine inhibitors are capable of dynamically interacting with both active and inactive forms of the tyrosine kinases, accommodating structurally different kinase conformations with a similar binding affinity. Conformational tolerance of the protein tyrosine kinases binding with the pyrido[2,3-d]pyrimidine inhibitors provides the molecular basis for the broad spectrum of potent activities and agrees with the experimental inhibition profiles. The analysis of the pyrido[2,3-d]pyrimidine sensitivities against a number of clinically relevant ABL kinase mutants suggests an important role of conformational adaptability of multitargeted kinase inhibitors in developing drug resistance mechanisms. The presented computational approach may be useful in complementing proteomics technologies to characterize activity signatures of small molecules against a large number of potential kinase targets. Proteins 2007. © 2006 Wiley-Liss, Inc.

Protein Tyrosine Kinases as Targets for Cancer and Other Indications

Abstract: The identification and characterization of the members of individual signal transduction cascades, and advances in understanding how these signals are integrated in normal and pathological conditions have provided new strategies for therapeutic intervention. Rapid progress has occurred in last few years in the development of inhibitors that target protein tyrosine kinases (PTKs), enzymes that transfer the γ-phosphate group of adenosine triphosphate (ATP) to the hydroxyl group of tyrosine residues on target proteins. Although PTKs represent a small percentage of the total number of kinases in the “kinome,” 90 of 518, a disproportional number of inhibitors currently in clinical trials are directed against them; e.g., more than 20 different tyrosine kinases are being evaluated as potential targets in oncology. There are a number of reasons why tyrosine kinases have been considered to be good targets. Epistatically, PTKs are located upstream and downstream of tumor suppressor genes or oncogenes and have been demonstrated to play central roles in apoptosis, proliferation, invasion, and differentiation (1). Aberrant activation of tyrosine kinases, owing to mutation or overexpression, is sufficient for them to become transforming in cellular and animal models. The majority of targets are receptor protein tyrosine kinases (RPTKs), as deregulating mutations of over half of the known RPTKs have been associated with different human malignancies; see Table 1 for examples. Finally, and equally as important as the epidemiological and biochemical data, the prevalence of PTKs as targets is because of the fact that they are considered druggable.

Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases

Abstract: Motivation: According to the models of divergent molecular evolution, the evolvability of new protein function may depend on the induction of new phenotypic traits by a small number of mutations of the binding site residues. Evolutionary relationships between protein kinases are often employed to infer inhibitor binding profiles from sequence analysis. However, protein kinases binding profiles may display inhibitor selectivity within a given kinase subfamily, while exhibiting cross-activity between kinases that are phylogenetically remote from the prime target. The emerging insights into kinase function and evolution combined with a rapidly growing number of publically available crystal structures of protein kinases complexes have motivated structural bioinformatics analysis of sequence--structure relationships in determining the binding function of protein tyrosine kinases. Results:In silico profiling of Imatinib mesylate and PD-173955 kinase inhibitors with protein tyrosine kinases is conducted on kinome scale by using evolutionary analysis and fingerprinting inhibitor--protein interactions with the panel of all publically available protein tyrosine kinases crystal structures. We have found that sequence plasticity of the binding site residues alone may not be sufficient to enable protein tyrosine kinases to readily evolve novel binding activities with inhibitors. While evolutionary signal derived solely from the tyrosine kinase sequence conservation can not be readily translated into the ligand binding phenotype, the proposed structural bioinformatics analysis can discriminate a functionally relevant kinase binding signal from a simple phylogenetic relationship. The results of this work reveal that protein conformational diversity is intimately linked with sequence plasticity of the binding site residues in achieving functional adaptability of protein kinases towards specific drug binding. This study offers a plausible molecular rationale to the experimental binding profiles of the studied kinase inhibitors and provides a theoretical basis for constructing functionally relevant kinase binding trees. Contact: gverkhiv@ucsd.edu Supplementary information: The supplementary material contains the details of the phylogenetic analysis of protein tyrosine kinases, including phylogenetic dendrograms of protein tyrosine kinases based on sequence alignments of the kinases catalytic domain and evolutionary conservation profiles of the binding site residues. This section provides a more detailed description of the Monte Carlo binding simulations, including energetic model and simulated tempering technique generalized for ligand--protein binding dynamics with the multiple protein tyrosine kinase structures.

All pathways to cancer apoptosis meeting in Thiruvananthapuram (India).

Abstract: An extensive amount of research in the past three decades has revealed many pathways of cell death. Although ‘apoptosis’ is the term used for most types of cell death, the pathways that lead to it are not always the same. The list of agents that mediate apoptosis is constantly growing. Because cancer is a hyperproliferative disorder, apoptosis of cancer cells and not of normal cells is a critical issue. Both physiologic and pharmacologic inducers of apoptosis have been identified. At an international conference held in Kerala, India, scientists discussed how apoptosis occurs, what mediates it, what pharmacologic agents induce it, how it is genetically regulated, and its role in tumorigenesis and cancer. It is said that multiple pathways can lead to enlightenment. What better place to discuss this than Thirvananthapuram (Trivandrum), Kerala. Created by Parsuram, the legendary Brahmin ‘protector,’ Kerala, the southernmost state in India, sits where the Indian Ocean and Arabian Sea meet, where Vasco de Gama landed in search of spices, where St. Thomas landed in search of enlightenment, where the world’s second oldest mosque is located, and where one of the world’s oldest synagogues is located. The purpose of 31⁄2-day conference that convened on December 18, 2005 was to bring together laboratory and clinical scientists to share current knowledge and future strategies for promoting the death of cancer cells. The participants included over 450 physicians and researchers from 16 different countries worldwide. The format of the meeting was daily major symposia, parallel minisymposia, and poster sessions. Dr. Abdul Kalam, the President of India and an aerospace engineer, inaugurated the meeting and reminded the importance of stem cell cloning and nontoxic drugs in cancer treatment and the role of patient databases and genomics in cancer care. The conference began with a keynote speech delivered by Dr. John Mendelsohn (Houston, TX, USA). He enlightened the audience by describing the journey that led to the discovery of Erbitux, a monoclonal antibody against epidermal growth factor receptor (EGFR). Major highlight of Dr. Mendelsohn’s talk was that although this antibody induces apoptosis of EGFR-overexpressing tumor cells in the laboratory, its effect on tumor cells in patients was not mediated through EGFR but through antibody-dependent cell-mediated cytotoxicity. Erbitux when combined with chemotherapeutic agents is effective in some patients with colorectal cancer. Another interesting revelation was that this antibody induces antitumor response in patients that is unrelated to the level of EGFR expression in tumor cells. In a plenary lecture, Dr. Bharat Aggarwal (Houston, TX, USA), explained the connection between inflammation and cancer. A common molecule in these two processes is the tumor necrosis factor (TNF). He pointed out that natural products could serve as good drugs for treatment of both inflammation and cancer. One such product is curcumin, which exhibits a blocking effect on the TNF. Curcumin is being tested in early clinical trials in patients with multiple myeloma, breast cancer, and pancreatic cancer. Dr. S Krishna (Banglore, India) delineated the Notch oncogenic signaling pathway in human epithelial neoplasms. His group has identified deregulated Notch signaling in cervical cancer. The midmorning session began with a speech by Dr. Premkumar Reddy (Philadelphia, PA, USA), who discussed the human kinome. Eucaryotic and atypical protein kinases of the human kinome constitute more than 500 proteins mostly belonging to tyrosine kinases or serine/threonine kinases. Many of these kinases are either mutated, constitutively active, or overexpressed in human cancers. The best example of such an agent is imatinib, the inhibitor of Bcr-Abl tyrosine kinase, he pointed out. Dr. Raj Puri (Bethesda, MD, USA) discussed early laboratory, preclinical, and animal model studies that were conducted with an immunotoxin composed of IL-13 and a mutated form of Pseudomonas exotoxin. These preclinical results were translated into phase I/II investigations in patients with solid tumors. Dr. Kapil Mehta (Houston, TX, USA) discussed the implications of elevated tissue transglutaminase expression in the development of drug resistance and metastatic phenotypes in tumor cells. Cell Death and Differentiation (2006), 1–2 & 2006 Nature Publishing Group All rights reserved 1350-9047/06 $30.00

Developments in cancer management by innovative genomics. 2006 report of the National Cancer Consortium

Abstract: Research on developing molecular diagnostics for hereditary cancers resulted in establishing diagnostic services for familiar polyposis and non-polyposis patients (mutation determination of APC, MYH, STK11, SMAD4, MLH1, MSH2). In familiar testicular cancers the role of gr/gr gene on Y chromosome was identified. Molecular diagnostic tool was established to monitor the progression of follicular lymphoma using Bcl-2/IgH fusion sequences. Molecular diagnostic tools were developed to monitor circulating endothelial precursor cells (CEP) as well and the technique was tested in lung cancer patients. In malignant melanoma we have tested several potential novel markers among which ryanodine receptor seems to be a promising one, while the functional P2X7 receptor may serve as a therapeutic target. We have determined the tyrosine kinase "kinome" profile of HER-2-amplified breast cancers. Furthermore, the "kinome" profile was found to be characteristic for head and neck cancers of various anatomical location. Based on previous studies on the anti-migratory and antimetastatic potential of low-molecular-weight heparins, we have identified short heparin-derived oligosaccharides with maintained antimetastatic- but non-anticoagulant potentials. Pharmacogenomic studies on the role of polymorphism of the serine-hydroxymethyl-transferase (SHMT) gene in the efficacy of 5-FU and FOLFIRI protocols of colorectal cancer patients revealed a significant effect resulting in altered overall survival as well.

Intracellular Signaling in Cancer

Abstract: Cancer genes that encode protein kinases are the most commonly mutated class of genes to be causally linked to the progressive outgrowth of malignant neoplasms. Protein kinases operate as important molecular switches that impinge, directly or indirectly, upon an integrated signaling circuitry that often becomes genetically reprogrammed, through successive mutations, to transmit many of the growth-stimulating and survival signals that govern the transformation of normal human cells into a cancerous cell mass. Of the 291 genes recently included in a comprehensive catalog of known human cancer genes, 9.3% (27 distinct genes) encode kinase domain sequences. This number far exceeds a random prediction of 6.3 genes (2%) and reinforces the hypothesis that a vast majority of human cancer cells carry genetic defects in the growth-signaling circuitry that enable these cells to grow autonomously and evade cellular senescence and death. First, we provide a general overview of a prototypical growth-signaling circuit and a detailed analysis of the canonical Ras/Raf/MEK/ERK pathway, because it has a central role in cancer cell signaling. This analysis is followed by a discussion of each of the kinases known to be mutated in cancer; we will describe the domain organization and normal function(s) of the protein, its oncogenic alterations in cancer and how this alters its activity, and identify the tumor/cancer types in which these changes are most common. Keywords: Cancer Gene; Chromosomal Translocation; Human Kinome; Kinase Domain; Neoplasm

Protein Kinases: Physiological Roles in Cell Signalling

Abstract: By catalysing reversible phosphorylation of their substrates, protein kinases play pleiotropic roles in cells and act as predominant arbiters in the coordination of cellular responses to their environment Despite large variation in biological functions between kinases, there is great structural conservation across the human kinome Besides structural aspects, substrate specificity relies on dynamic factors such as concentration, activity and localisation This article discusses these fundamental aspects of protein kinases as related to cellular signalling while also taking note of the less commonly discussed members of the class such as pseudokinases and ectokinases The complexity of signalling networks is demonstrated by a discussion on the crosstalk involved between the metabolic and signal transduction pathways By having roles in such processes as cell growth, proliferation and death, protein kinases are at the centre of the regulation of the cell and therefore also at the heart of many human diseases when dysregulated Key Concepts Protein kinases are enzymes that catalyse the phosphorylation of a protein substrate Reversible phosphorylation is a key feature of cellular signalling There are some highly conserved structural motifs across the human kinome despite great differences in biological functions Activation of a kinase is dependent upon assembly of the regulatory spine Structural and dynamic factors contribute to substrate selectivity Kinases are present both within the cell and in extracellular spaces (ectokinases) Crosstalk with other post-translational modifications and between other pathways makes protein kinases participants in nearly every physiological process Keywords: protein kinase; pseudokinase; signal transduction; kinome; metabolism; phosphorylation; post-translational modification