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Molecular Pharmacology Apr 2022Protein kinase A (PKA) is a holoenzyme consisting of a regulatory (R)-subunit dimer and two catalytic (C)-subunits. There are two major families of C-subunits, C and C,... (Review)
Review
Protein kinase A (PKA) is a holoenzyme consisting of a regulatory (R)-subunit dimer and two catalytic (C)-subunits. There are two major families of C-subunits, C and C, and four functionally nonredundant R-subunits (RI, RI, RII, RII). In addition to binding to and being regulated by the R-subunits, the C-subunits are regulated by two tail regions that each wrap around the N- and C-lobes of the kinase core. Although the C-terminal (Ct-) tail is classified as an intrinsically disordered region (IDR), the N-terminal (Nt-) tail is dominated by a strong helix that is flanked by short IDRs. In contrast to the Ct-tail, which is a conserved and highly regulated feature of all PKA, PKG, and protein kinase C protein kinase group (AGC) kinases, the Nt-tail has evolved more recently and is highly variable in vertebrates. Surprisingly and in contrast to the kinase core and the Ct-tail, the entire Nt-tail is not conserved in nonmammalian PKAs. In particular, in humans, C actually represents a large family of C-subunits that are highly variable in their Nt-tail and also expressed in a highly tissue-specific manner. Although we know so much about the C1-subunit, we know almost nothing about these C isoforms wherein C2 is highly expressed in lymphocytes, and C3 and C4 isoforms account for ∼50% of PKA signaling in brain. Based on recent disease mutations, the C proteins appear to be functionally important and nonredundant with the C isoforms. Imaging in retina also supports nonredundant roles for C as well as isoform-specific localization to mitochondria. This represents a new frontier in PKA signaling. SIGNIFICANCE STATEMENT: How tails and adjacent domains regulate each protein kinase is a fundamental challenge for the biological community. Here we highlight how the N- and C-terminal tails of PKA (Nt-tails/Ct-tails) affect the structure and regulate the function of the kinase core and show the combinatorial variations that are introduced into the Nt-tail of the C- and C-subunits in contrast to the Ct-tail, which is conserved across the entire AGC subfamily of protein kinases.
Topics: Animals; Cyclic AMP-Dependent Protein Kinase RIalpha Subunit; Cyclic AMP-Dependent Protein Kinases; Humans; Protein Isoforms; Protein Kinases; Signal Transduction
PubMed: 34330820
DOI: 10.1124/molpharm.121.000315 -
Nature Reviews. Drug Discovery Jun 2017Kinome-wide profiling platforms have comprehensively identified the relevant kinases that are targeted by numerous protein kinase inhibitors. However, recent projects... (Review)
Review
Kinome-wide profiling platforms have comprehensively identified the relevant kinases that are targeted by numerous protein kinase inhibitors. However, recent projects have begun to discover non-kinase targets of kinase inhibitors. These non-kinase targets can contribute to the desired or undesired activities of inhibitors, or act as silent bystanders. As a full awareness of a drug's mechanism of action is crucial for the interpretation of results and for successful preclinical and clinical drug development, these discoveries highlight the importance of understanding the pharmacology of kinase inhibitors beyond the kinome. In this Review, I discuss kinase inhibitors for which non-kinase targets have been identified and the application of emerging techniques to validate drug-target engagement in intact cells.
Topics: Animals; Drug Design; Drug Evaluation, Preclinical; Humans; Molecular Targeted Therapy; Protein Kinase Inhibitors; Protein Kinases
PubMed: 28280261
DOI: 10.1038/nrd.2016.266 -
Journal of Proteomics Mar 2022Protein kinases regulate almost all biological processes including cell proliferation, differentiation, apoptosis, and gene expression. Dysregulation of protein... (Review)
Review
Protein kinases regulate almost all biological processes including cell proliferation, differentiation, apoptosis, and gene expression. Dysregulation of protein phosphorylation caused by abnormal activity and expression of protein kinases results in the onset of various diseases such as cancer and metabolic syndromes. The activities of a large number of protein kinases are regulated by phosphorylation. Therefore, analysis of the phosphorylation status of protein kinases is important for elucidation of biological phenomena and the pathogenesis of diseases. To investigate protein phosphorylation, phosphate-binding tag molecule "Phos-tag" was developed. In addition, various techniques and tools using Phos-tag such as Phos-tag SDS-PAGE, have been developed for analysis and profiling of protein phosphorylation. Here, we describe the methods and analytical techniques that use Phos-tag for investigation of protein kinase phosphorylation and the applications of phosphorylation analysis. SIGNIFICANCE: Protein kinases play pivotal roles in regulating many biological processes and pathogenesis of diseases. Determination of phosphorylation status of protein kinases can provide the essential information for their activation. This review provides analytical techniques for analysis of phosphorylation status of protein kinases by Phos-tag SDS-PAGE. We believe that this review would help readers to study in kinomics research.
Topics: Electrophoresis, Polyacrylamide Gel; Phosphoproteins; Phosphorylation; Protein Kinases; Pyridines
PubMed: 35065289
DOI: 10.1016/j.jprot.2022.104485 -
Advances in Experimental Medicine and... 2019This chapter focuses on protein kinases that transfer the phosphate group of ATP to the hydroxyl group of a substrate protein. Five hundred eighteen human protein... (Review)
Review
This chapter focuses on protein kinases that transfer the phosphate group of ATP to the hydroxyl group of a substrate protein. Five hundred eighteen human protein kinases are classified into serine/threonine kinases and tyrosine kinases and individually or synergistically transduce physiologic stimuli into cell to promote cell proliferation or apoptosis, etc. Protein kinases are identified as drug targets because dysfunction of kinases leads to severe diseases such as cancers and autoimmune diseases. A large number of the crystal structures of the protein kinase inhibitor complex are available in Protein Data Bank and facilitated the drug discovery targeting protein kinases. The protein kinase inhibitors are classified into categories, Type-I, Type-II, Type-III, Type-IV, and Type-V, and as a separate class, covalent-type inhibitors. In any type, a protein kinase inhibitor bound to the allosteric region is advantageous in terms of selectivity compared to the traditional ATP-competitive one. In the following sections, the successful and promising examples of the partially or fully allosteric protein kinase inhibitors are illustrated in the following pages.
Topics: Adenosine Triphosphate; Drug Design; Drug Discovery; Enzyme Activation; Humans; Protein Binding; Protein Kinase Inhibitors; Protein Kinases
PubMed: 31707699
DOI: 10.1007/978-981-13-8719-7_3 -
Journal of Biochemistry Apr 2019Accumulating information on eukaryotic protein phosphorylation implies a large and complicated phospho-signalling network in various cellular processes. Although a large... (Review)
Review
Accumulating information on eukaryotic protein phosphorylation implies a large and complicated phospho-signalling network in various cellular processes. Although a large number of protein phosphorylation sites have been detected, their physiological consequences and the linkage between each phosphorylation site and the responsible protein kinase remain largely unexplored. To understand kinase-oriented phospho-signalling pathways, we have developed novel substrate screening technologies. In this review, we described the in vitro and in vivo screening methods named kinase-interacting substrate screening analysis and kinase-oriented substrate screening analysis, respectively.
Topics: Animals; Humans; Phosphoproteins; Protein Kinases; Proteomics; Signal Transduction
PubMed: 30590682
DOI: 10.1093/jb/mvy115 -
European Journal of Medicinal Chemistry May 2024The continued growth of data from biological screening and medicinal chemistry provides opportunities for data-driven experimental design and decision making in... (Review)
Review
The continued growth of data from biological screening and medicinal chemistry provides opportunities for data-driven experimental design and decision making in early-phase drug discovery. Approaches adopted from data science help to integrate internal and public domain data and extract knowledge from historical in-house data. Protein kinase (PK) drug discovery is an exemplary area where large amounts of data are accumulating, providing a valuable knowledge base for discovery projects. Herein, the evolution of PK drug discovery and development of small molecular PK inhibitors (PKIs) is reviewed, highlighting milestone developments in the field and discussing exemplary studies providing a basis for increasing data orientation of PK discovery efforts.
Topics: Drug Discovery; Protein Kinase Inhibitors; Humans; Protein Kinases; Molecular Structure
PubMed: 38636127
DOI: 10.1016/j.ejmech.2024.116413 -
IUBMB Life Apr 2023Protein phosphorylation is a fundamental element of cell signaling. First discovered as a biochemical switch in glycogen metabolism, we now know that this...
Protein phosphorylation is a fundamental element of cell signaling. First discovered as a biochemical switch in glycogen metabolism, we now know that this posttranslational modification permeates all aspects of cellular behavior. In humans, over 540 protein kinases attach phosphate to acceptor amino acids, whereas around 160 phosphoprotein phosphatases remove phosphate to terminate signaling. Aberrant phosphorylation underlies disease, and kinase inhibitor drugs are increasingly used clinically as targeted therapies. Specificity in protein phosphorylation is achieved in part because kinases and phosphatases are spatially organized inside cells. A prototypic example is compartmentalization of the cyclic adenosine 3',5'-monophosphate (cAMP)-dependent protein kinase A through association with A-kinase anchoring proteins. This configuration creates autonomous signaling islands where the anchored kinase is constrained in proximity to activators, effectors, and selected substates. This article primarily focuses on A kinase anchoring protein (AKAP) signaling in the heart with an emphasis on anchoring proteins that spatiotemporally coordinate excitation-contraction coupling and hypertrophic responses.
Topics: Humans; Phosphorylation; A Kinase Anchor Proteins; Cyclic AMP-Dependent Protein Kinases; Signal Transduction; Protein Kinases
PubMed: 36177749
DOI: 10.1002/iub.2677 -
Nature Reviews. Drug Discovery Jul 2019Pseudokinases are members of the protein kinase superfamily but signal primarily through noncatalytic mechanisms. Many pseudokinases contribute to the pathologies of... (Review)
Review
Pseudokinases are members of the protein kinase superfamily but signal primarily through noncatalytic mechanisms. Many pseudokinases contribute to the pathologies of human diseases, yet they remain largely unexplored as drug targets owing to challenges associated with modulation of their biological functions. Our understanding of the structure and physiological roles of pseudokinases has improved substantially over the past decade, revealing intriguing similarities between pseudokinases and their catalytically active counterparts. Pseudokinases often adopt conformations that are analogous to those seen in catalytically active kinases and, in some cases, can also bind metal cations and/or nucleotides. Several clinically approved kinase inhibitors have been shown to influence the noncatalytic functions of active kinases, providing hope that similar properties in pseudokinases could be pharmacologically regulated. In this Review, we discuss known roles of pseudokinases in disease, their unique structural features and the progress that has been made towards developing pseudokinase-directed therapeutics.
Topics: Animals; Binding Sites; Humans; Molecular Conformation; Molecular Structure; Molecular Targeted Therapy; Protein Binding; Protein Kinase Inhibitors; Protein Kinases; Small Molecule Libraries
PubMed: 30850748
DOI: 10.1038/s41573-019-0018-3 -
Trends in Endocrinology and Metabolism:... Dec 2018The discovery of liver kinase B1 (LKB1) as an upstream kinase for AMP-activated protein kinase (AMPK) led to the identification of several related kinases that also rely... (Review)
Review
The discovery of liver kinase B1 (LKB1) as an upstream kinase for AMP-activated protein kinase (AMPK) led to the identification of several related kinases that also rely on LKB1 for their catalytic activity. Among these, the salt-inducible kinases (SIKs) have emerged as key regulators of metabolism. Unlike AMPK, SIKs do not respond to nucleotides, but their function is regulated by extracellular signals, such as hormones, through complex LKB1-independent mechanisms. While AMPK acts on multiple targets, including metabolic enzymes, to maintain cellular ATP levels, SIKs primarily regulate gene expression, by acting on transcriptional regulators, such as the cAMP response element-binding protein-regulated transcription coactivators and class IIa histone deacetylases. This review describes the development of research on SIKs, from their discovery to the most recent findings on metabolic regulation.
Topics: AMP-Activated Protein Kinase Kinases; AMP-Activated Protein Kinases; Animals; Energy Metabolism; Gluconeogenesis; Humans; Protein Serine-Threonine Kinases
PubMed: 30385008
DOI: 10.1016/j.tem.2018.09.007 -
International Journal of Molecular... Oct 2018Activated by AMP-dependent and -independent mechanisms, AMP-activated protein kinase (AMPK) plays a central role in the regulation of cellular bioenergetics and cellular... (Review)
Review
Activated by AMP-dependent and -independent mechanisms, AMP-activated protein kinase (AMPK) plays a central role in the regulation of cellular bioenergetics and cellular survival. AMPK regulates a diverse set of signaling networks that converge to epigenetically mediate transcriptional events. Reversible histone and DNA modifications, such as acetylation and methylation, result in structural chromatin alterations that influence transcriptional machinery access to genomic regulatory elements. The orchestration of these epigenetic events differentiates physiological from pathophysiological phenotypes. AMPK phosphorylation of histones, DNA methyltransferases and histone post-translational modifiers establish AMPK as a key player in epigenetic regulation. This review focuses on the role of AMPK as a mediator of cellular survival through its regulation of chromatin remodeling and the implications this has for health and disease.
Topics: AMP-Activated Protein Kinase Kinases; Animals; Chromatin Assembly and Disassembly; DNA Methylation; Epigenesis, Genetic; Histone Code; Humans; Protein Kinases
PubMed: 30347687
DOI: 10.3390/ijms19103238