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Kinase

A kinase is an enzyme that catalyzes the transfer of a phosphate group from a high-energy donor molecule, such as adenosine triphosphate (ATP), to a specific substrate, thereby modifying its function or activity.^[1] This phosphorylation reaction is a reversible post-translational modification essential for regulating diverse cellular processes, including signal transduction, metabolism, cell cycle progression, and gene expression.^[2] Kinases are ubiquitous across all domains of life and encompass a broad range of types, such as protein kinases, lipid kinases, and carbohydrate kinases, each targeting distinct biomolecules.^[3] Protein kinases, which phosphorylate proteins primarily on serine, threonine, or tyrosine residues, form the largest and most extensively studied subclass, accounting for approximately 2% of the genes in the human genome with around 500 such enzymes identified.^[4] These enzymes function within intricate signaling networks, often as part of cascades where one kinase activates another, amplifying signals from extracellular cues like hormones or growth factors to elicit intracellular responses such as proliferation, differentiation, or apoptosis.^[5] Dysregulation of protein kinase activity, through mutations or overexpression, disrupts these pathways and contributes to pathological conditions, including cancers, cardiovascular diseases, and immune disorders.^[6] Given their central role in cellular regulation, kinases have emerged as prime therapeutic targets, particularly in oncology, where small-molecule inhibitors can selectively block aberrant kinase signaling to halt tumor growth.^[7] As of October 2025, the U.S. Food and Drug Administration has approved 94 small-molecule protein kinase inhibitors, many of which target specific kinases like tyrosine kinases involved in oncogenesis, demonstrating the clinical success and ongoing expansion of kinase-targeted therapies.^[8]

Fundamentals

Definition and Catalytic Mechanism

Kinases constitute a large superfamily of enzymes within the Enzyme Commission class EC 2.7, known as phosphotransferases, which catalyze the transfer of phosphorus-containing groups from donor molecules such as adenosine triphosphate (ATP) or guanosine triphosphate (GTP) to diverse acceptor substrates, including proteins, lipids, nucleotides, and carbohydrates.^[9] This superfamily encompasses hundreds of distinct enzymes essential for metabolic and regulatory processes across organisms.^[10] The core catalytic mechanism of kinases involves the nucleophilic attack by the substrate's acceptor group on the γ-phosphate of ATP, facilitated by the enzyme's active site, which positions the reactants and stabilizes the transition state. The general reaction can be represented as:

\text{R-OH (substrate)} + \text{ATP} \xrightarrow{\text{kinase, Mg}^{2+}} \text{R-OPO}_3^{2-} + \text{ADP}

where R-OH denotes the hydroxyl or other nucleophilic group on the substrate, and the phosphate transfer occurs via an inline associative or dissociative mechanism, often involving two magnesium ions to coordinate the phosphates and neutralize charges.^[2] In this process, the enzyme lowers the activation energy by aligning the substrate and ATP, enabling the cleavage of the phosphoanhydride bond and formation of a new phosphoester bond. Structural features, such as conserved aspartate residues in the active site, further coordinate the magnesium and promote phosphoryl transfer.^[11] Kinases facilitate various types of phosphorylation depending on the acceptor atom: O-phosphorylation, the most common form, occurs on oxygen atoms (e.g., in serine, threonine, or tyrosine residues of proteins); N-phosphorylation targets nitrogen atoms (e.g., in histidine or arginine); while less prevalent forms include S-phosphorylation on sulfur (e.g., cysteine) and C-phosphorylation on carbon atoms in certain metabolites.^[12] The energy for these reactions derives from the hydrolysis of ATP's high-energy γ-β phosphoanhydride bond, which releases approximately -30.5 kJ/mol under standard conditions, rendering the phosphorylation thermodynamically favorable and effectively irreversible in cellular environments due to the subsequent utilization or hydrolysis of the products.^[13] From an evolutionary perspective, kinases are ancient enzymes conserved across all three domains of life—Bacteria, Archaea, and Eukarya—reflecting their emergence early in cellular evolution to enable phosphate-based energy transfer and regulation.^[14] This ubiquity highlights their indispensable role in fundamental biochemical pathways predating eukaryotic complexity.

Structural Diversity

Kinases exhibit a highly conserved catalytic domain characterized by a bilobal architecture, consisting of an N-terminal lobe primarily responsible for nucleotide binding and a larger C-terminal lobe involved in substrate recognition and binding. This bilobal fold creates a deep cleft at the interface where ATP and the substrate interact, enabling the phosphotransfer reaction. Key structural motifs within this domain include the P-loop (G-x-G-x-x-G), a glycine-rich sequence in the N-lobe that coordinates the phosphate groups of ATP, and the HRD motif in the catalytic loop of the C-lobe, which positions the aspartate residue for proton abstraction during catalysis.^[15]^[16] The activation segment, often referred to as the activation loop, plays a crucial role in regulating kinase activity through dynamic conformational changes. In the inactive state, this loop is typically disordered, obstructing the active site and preventing substrate access. Phosphorylation within the activation loop induces a rigid, ordered conformation that repositions catalytic residues and opens the substrate-binding site, thereby activating the enzyme. This phosphorylation-dependent switch is a widespread regulatory mechanism across kinase families.^[17] Structural variations exist among kinase families, distinguishing conventional eukaryotic protein kinases (ePKs), which adhere closely to the canonical bilobal fold, from atypical kinases (aPKs) that deviate in sequence and sometimes structure while retaining catalytic function. For instance, Rio kinases, an aPK family, lack certain ePK-specific subdomains like the activation loop but maintain a core kinase fold adapted for roles in ribosome biogenesis. Additionally, kinases can be classified by localization: soluble forms predominate in the cytosol, while membrane-associated variants often feature lipid-binding domains or transmembrane segments that anchor them to cellular membranes, influencing their substrate specificity and regulation.^[18]^[19]^[20] Many kinases possess allosteric sites—distinct from the ATP-binding pocket—that serve as regulatory hotspots for inhibitors or activators, allowing fine-tuned control without competing with substrates. These sites often involve hydrophobic pockets or interfaces between lobes, enabling type III or IV inhibitors to induce inactive conformations selectively. Crystal structures, such as that of protein kinase A (PKA), the prototypical kinase, provide foundational insights into these features; the PKA catalytic subunit (PDB: 1ATP) exemplifies the active bilobal conformation with bound ATP and substrate peptide, serving as a model for comparative analysis across the kinome.^[21]

Historical Development

Early Discoveries

The term "kinase" derives from the Greek word kinesis, meaning "movement," and was initially applied to enzymes that phosphorylate carbohydrates, thereby "activating" them for metabolic flux in processes like glycolysis and muscle contraction. The first kinase identified was hexokinase, discovered in 1927 by Otto Meyerhof in extracts of baker's yeast (Saccharomyces cerevisiae), where it catalyzes the ATP-dependent phosphorylation of glucose to glucose-6-phosphate as the committed step of glycolysis.^[22] This finding built on earlier studies of fermentation and provided key evidence for the Embden-Meyerhof-Parnas pathway of glucose breakdown.^[23] A major advance occurred in 1955 when Edmond H. Fischer and Edwin G. Krebs identified the first protein kinase, phosphorylase kinase, in rabbit skeletal muscle extracts during investigations of glycogen metabolism. This enzyme transfers a phosphate group from ATP to glycogen phosphorylase b, converting it to the active phosphorylase a form that promotes glycogenolysis.^[24] Their work demonstrated protein phosphorylation as a regulatory mechanism and was pivotal in revealing the enzymatic basis for the conversion, earning Fischer and Krebs the 1992 Nobel Prize in Physiology or Medicine.^[25] Early characterization relied on techniques like radioisotope labeling with ^{32}P, introduced in biochemical research in the mid-1940s, which allowed sensitive detection of phosphate incorporation into proteins and substrates.^[26] During the 1960s and 1970s, research expanded to recognize phosphorylation as a reversible post-translational modification, with the parallel discovery of protein phosphatases that remove phosphate groups. A landmark was the 1968 identification of cAMP-dependent protein kinase (PKA) by Donal A. Walsh in Edwin G. Krebs' laboratory, which phosphorylates various substrates in response to cyclic AMP signaling and regulates diverse cellular processes like hormone action.^[27] This enzyme, initially termed "kinase kinase" for its activation of phosphorylase kinase, exemplified kinase cascades and broadened the view of kinases beyond carbohydrate metabolism to protein regulation.^[28] The advent of ^{32}P labeling further enabled quantitative assays of kinase activity, facilitating these insights into dynamic signaling.^[29]

Key Advances in Classification and Research

In the late 20th century, advances in genomic sequencing enabled the systematic cataloging of the human kinome, revealing approximately 518 protein kinase genes, including both active enzymes and pseudokinases, which are catalytically inactive homologs lacking key residues for phosphate transfer but retaining regulatory roles.^[30] This comprehensive mapping, building on earlier enzymatic isolations like hexokinase in the 1920s, highlighted the kinome's diversity and underscored the need for refined taxonomy. Concurrently, Hanks and Hunter proposed a foundational classification of eukaryotic protein kinases (ePKs) based on conserved sequence motifs in the catalytic domain, organizing them into nine major groups such as AGC, CAMK, and CMGC, which facilitated phylogenetic analysis and identification of subfamilies.^[31] Pseudokinases, comprising about 10% of the kinome, were explicitly incorporated into this framework as evolutionary remnants with allosteric functions, expanding the understanding beyond active catalysts.^[30] Technological breakthroughs in structural biology and functional genomics further propelled kinase research. The 1991 X-ray crystal structure of the protein kinase A (PKA) catalytic subunit at 2.7 Å resolution provided the first atomic view of a kinase domain, revealing a bilobal architecture with an active cleft for ATP and substrate binding, which served as a template for modeling other kinases and rational inhibitor design.^[32] High-throughput screening (HTS) assays, emerging in the 1990s and maturing by the early 2000s, accelerated inhibitor discovery by testing thousands of compounds against kinase activity, leading to seminal hits like the BCR-ABL inhibitor imatinib and enabling kinome-wide selectivity profiling.^[33] Similarly, kinome-wide small interfering RNA (siRNA) knockdown screens, first demonstrated around 2008-2010, allowed systematic perturbation of the entire kinome to uncover essential kinases in cellular processes, such as IRAK4 and GAK in hypoxic adaptation.^[34] By the 2020s, cryo-electron microscopy (cryo-EM) advanced kinase structural studies, resolving large complexes intractable to X-ray crystallography, such as the 2025 structures of human NAD kinase tetramers at 3.2 Å, illuminating nucleotide-binding mechanisms in non-protein kinases, and CRAF/MEK1/14-3-3 assemblies revealing autoinhibitory conformations.^[35]^[36] CRISPR-based kinome editing emerged as a powerful tool for functional validation, with genome-wide screens from 2020-2025 identifying critical dependencies like PLK1 in glioblastoma survival and MINK1 in drug resistance, enabling precise knockouts across the kinome.^[37]^[38] AI-driven models, such as Phosformer-ST (2024), improved prediction of kinase-substrate interactions by integrating sequence motifs and phosphorylation data, achieving over 90% accuracy in benchmarking against experimental datasets.^[39] The Kinase.com database received updates in 2025, incorporating AlphaFold-predicted structures for underexplored atypical and non-protein kinases like lipid and nucleotide kinases, enhancing classification of underrepresented families and revealing evolutionary expansions.^[40] These developments addressed prior gaps in non-protein kinase taxonomy, integrating atypical enzymes into broader kinome frameworks for comprehensive research.^[41]

Classification by Substrate Specificity

Protein Kinases

Protein kinases represent the largest and most extensively studied class of kinases, comprising approximately 518 genes in the human genome, which accounts for about 2% of all protein-coding genes.^[42] These enzymes catalyze the transfer of the γ-phosphate group from ATP to specific amino acid residues on target proteins, primarily serine (Ser), threonine (Thr), tyrosine (Tyr), or histidine (His), thereby modulating protein function, localization, and interactions in cellular signaling.^[43] Unlike other kinase classes, protein kinases focus exclusively on amino acid phosphorylation to regulate diverse processes such as cell growth, differentiation, and response to environmental cues.^[44] Protein kinases are classified into a hierarchical system of groups, families, and subfamilies based on sequence similarity, structure, and function, with seven major groups identified in the human kinome: AGC (including protein kinase A [PKA], protein kinase G [PKG], and protein kinase C [PKC] families), CAMK (calcium/calmodulin-dependent protein kinases), CK1 (casein kinase 1), CMGC (encompassing cyclin-dependent kinases [CDKs], mitogen-activated protein kinases [MAPKs], glycogen synthase kinase 3 [GSK3], and CDK-like kinases), TK (tyrosine kinases), TKL (tyrosine kinase-like), and others such as STE (sterile kinases).^[45] This classification reflects evolutionary conservation and functional specialization, with AGC kinases often involved in cyclic nucleotide signaling, CAMK in calcium-mediated responses, CMGC in cell cycle and stress signaling, and TK/TKL in tyrosine-specific phosphorylation events.^[46] Prominent examples within the CMGC group include cyclin-dependent kinases (CDKs), which orchestrate cell cycle progression by phosphorylating substrates that control DNA replication and mitosis; key members such as CDK1 drives G2/M transition, while CDK4 and CDK6 initiate G1/S phase in complex with cyclin D.^[47] Mitogen-activated protein kinases (MAPKs), also in the CMGC group, form multi-tiered cascades—typically involving MAPK kinase kinases (MAP3Ks), MAPK kinases (MAP2Ks), and MAPKs—that propagate signals from extracellular stimuli like growth factors or stresses; the ERK pathway (extracellular signal-regulated kinase) promotes proliferation, the JNK pathway (c-Jun N-terminal kinase) mediates apoptosis and inflammation, and the p38 pathway responds to environmental stresses such as UV radiation or cytokines.^[48] Tyrosine kinases (TKs) are subdivided into receptor tyrosine kinases (RTKs), which are transmembrane proteins activated by ligand binding, and non-receptor tyrosine kinases (NRTKs), which operate intracellularly; EGFR (epidermal growth factor receptor), an RTK, exemplifies growth factor signaling by dimerizing upon EGF binding to autophosphorylate and activate downstream pathways like RAS-MAPK, while Src, a prototypical NRTK, integrates signals from integrins and G-protein-coupled receptors to regulate adhesion and motility.^[49]^[50] Specificity in protein kinase-substrate interactions is enhanced by dual-specificity mechanisms, where some kinases (e.g., certain MAP2Ks) phosphorylate both tyrosine and threonine/serine residues in activation loops, and by docking interactions, such as D-motifs on substrates that bind to complementary grooves on kinase domains to ensure efficient and selective phosphorylation.^[51] These regulatory features underscore the precision of protein kinase signaling in maintaining cellular homeostasis.^[52]

Lipid Kinases

Lipid kinases are a subclass of enzymes that catalyze the transfer of a phosphate group from ATP to hydroxyl groups on lipid headgroups or backbones, thereby modulating lipid signaling and membrane properties. These kinases play pivotal roles in cellular processes such as membrane trafficking, signal transduction, and cytoskeletal dynamics, with phosphoinositide signaling being a central pathway where they generate bioactive lipids like phosphatidylinositol phosphates that recruit effector proteins to membranes.^[53]^[54] Phosphatidylinositol kinases (PIKs), particularly the phosphoinositide 3-kinases (PI3Ks), are among the most studied lipid kinases, classified into three main classes based on structure and substrate specificity. Class I PI3Ks, which include isoforms like PI3Kα, phosphorylate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂) at the 3-position of the inositol ring to produce phosphatidylinositol 3,4,5-trisphosphate (PIP₃), a key second messenger in pathways such as insulin signaling where PI3Kα activation promotes glucose uptake and cell growth via downstream Akt activation. In contrast, Class II PI3Ks generate phosphatidylinositol 3-phosphate (PI(3)P) and phosphatidylinositol 3,4-bisphosphate (PI(3,4)P₂), contributing to clathrin-mediated endocytosis and vesicle trafficking by regulating membrane curvature and protein recruitment. Class III PI3Ks, exemplified by VPS34, primarily produce PI(3)P to nucleate autophagy initiation complexes on membranes and facilitate endosomal sorting during endocytosis, ensuring cellular homeostasis under stress.^[55]^[56]^[57]^[58] Sphingosine kinases (SphKs), including SphK1 and SphK2, phosphorylate sphingosine to form sphingosine-1-phosphate (S1P), a bioactive lipid that influences membrane fluidity and acts as an extracellular signaling molecule via G protein-coupled receptors (S1PRs). SphK1 predominantly localizes to the cytosol and promotes cell survival and migration by elevating S1P levels, which activate S1PRs to trigger pathways like ERK and Rho GTPase signaling in processes such as wound healing and immune cell chemotaxis. SphK2, often nuclear or mitochondrial, has contrasting effects, enhancing apoptosis under certain conditions while also contributing to S1P production that supports cell proliferation; dysregulation of both isoforms is linked to pathological migration in diseases like cancer, with S1PRs serving as therapeutic targets through antagonists that block pro-survival signals.^[59]^[60] Other notable lipid kinases include diacylglycerol kinases (DAGKs), which attenuate protein kinase C (PKC) signaling by phosphorylating diacylglycerol (DAG) to phosphatidic acid (PA), thereby terminating DAG-mediated activation of PKC in pathways involving T-cell receptor signaling and synaptic plasticity. Ceramide kinases (CerKs) phosphorylate ceramide to ceramide-1-phosphate (C1P), which can promote cell survival but also contribute to apoptosis when ceramide levels rise, as C1P influences calcium homeostasis and mitochondrial function during stress-induced cell death.^[61]^[62] Recent studies from the 2020s highlight lipid kinases' involvement in neurodegeneration, where dysregulated PI3K signaling impairs neuronal survival in Alzheimer's disease by altering PIP₃-mediated Akt protection against amyloid-β toxicity, while SphK1/S1P axis disruptions exacerbate α-synuclein aggregation in Parkinson's disease models. DAGKs, particularly isoforms like DGKβ, influence synaptic spine maintenance, and their inhibition may mitigate neuroinflammatory damage, whereas CerK modulation of ceramide levels affects microglial activation and neuronal apoptosis in tauopathies. These findings underscore lipid kinases as emerging targets for neuroprotective therapies.^[63]^[64]^[65]^[66]

Nucleotide and Carbohydrate Kinases

Nucleotide kinases constitute a class of enzymes that phosphorylate nucleosides and nucleotides, ensuring the maintenance of intracellular nucleotide pools critical for DNA and RNA biosynthesis. These kinases participate in both de novo and salvage pathways, recycling nucleobases and nucleosides to support nucleic acid synthesis and cellular proliferation. By catalyzing the transfer of phosphate groups from ATP or other donors, they prevent nucleotide imbalances that could impair replication and transcription processes.^[67] A key example is adenylate kinase (AK), a ubiquitous enzyme with multiple isozymes (AK1–AK9) distributed across cellular compartments such as the cytosol, mitochondria, and nucleus. AK maintains the equilibrium of adenine nucleotides through the reversible reaction:

$2 \ADP \rightleftharpoons \AMP + \ATP

This interconversion facilitates rapid phosphate transfer, supporting energy homeostasis and buffering ATP levels during metabolic stress; the total amount of ATP in the human body is approximately 250 g, which is recycled at a rate equivalent to the body weight (about 50-70 kg for an average adult) per day via such mechanisms.^[68]^[69] AK's role extends to signaling AMP to metabolic sensors like AMP-activated protein kinase, linking energy status to broader cellular responses.^[68] Nucleoside kinases exemplify the salvage pathway's efficiency in nucleotide metabolism. Thymidine kinase 1 (TK1), a cytosolic enzyme upregulated during the S-phase of the cell cycle, phosphorylates thymidine to deoxythymidine monophosphate (dTMP), which is subsequently converted to deoxythymidine triphosphate (dTTP) for nuclear DNA synthesis and repair. In contrast, thymidine kinase 2 (TK2), localized to the mitochondria, performs an analogous phosphorylation to sustain mitochondrial DNA replication independently of the cell cycle. Deficiencies in TK2 are associated with neuromuscular disorders due to impaired mitochondrial nucleotide supply.^[70] UMP-CMP kinase (UMPK), also known as cytidylate kinase, exhibits dual specificity by phosphorylating uridine monophosphate (UMP) and cytidine monophosphate (CMP) to their diphosphate forms, contributing to pyrimidine nucleotide pools for RNA and DNA production. In antiviral contexts, UMPK activates nucleoside analogs—such as those used against herpesviruses—by phosphorylating them into active diphosphates, enhancing their incorporation into viral genomes and inhibiting replication.^[71] Carbohydrate kinases phosphorylate monosaccharides, enabling their integration into central metabolic routes like glycolysis and the pentose phosphate pathway (PPP), where they support energy generation and biosynthetic precursor production. These enzymes typically utilize ATP as the phosphate donor, activating sugars for downstream catabolism or anabolism while preventing their diffusion across membranes.^[72] Hexokinases (isoforms HK1–HK4) initiate glucose metabolism by catalyzing its phosphorylation to glucose-6-phosphate (G6P):

\text{Glucose} + \ATP \rightarrow \text{G6P} + \ADP

This irreversible step commits glucose to glycolysis or diversion to the PPP, where G6P is oxidized to generate NADPH and ribose-5-phosphate for nucleotide synthesis. HK isoforms differ in tissue distribution and regulatory properties; for example, HK2 is inducible in proliferating cells, underscoring its role in metabolic adaptation.^[72] Phosphofructokinase (PFK), particularly the muscle isoform PFK-M, serves as a major regulatory kinase in glycolysis, phosphorylating fructose-6-phosphate to fructose-1,6-bisphosphate and committing the pathway to ATP production. As the rate-limiting enzyme, PFK integrates signals from energy status (e.g., ATP inhibition, AMP activation) to modulate glycolytic flux.^[73] Galactokinase handles dietary galactose by phosphorylating it to galactose-1-phosphate in the Leloir pathway, primarily in the liver. This product is then converted via uridylyltransferase to glucose-1-phosphate, which enters glycolysis or glycogen synthesis after isomerization to G6P, thus linking galactose catabolism to glucose metabolism. Defects in galactokinase lead to galactosemia variants with cataract risks due to accumulated intermediates.^[74] Beyond these, riboflavin kinase (RFK) phosphorylates riboflavin (vitamin B2) to flavin mononucleotide (FMN), the rate-limiting step in flavin adenine dinucleotide (FAD) biosynthesis. FAD serves as a cofactor for numerous flavoproteins involved in oxidation-reduction reactions, including those in the electron transport chain and fatty acid metabolism. RFK's activity ensures adequate flavin availability for mitochondrial bioenergetics.^[75] Collectively, nucleotide and carbohydrate kinases integrate metabolism by sustaining nucleotide pools for nucleic acid assembly and channeling phosphorylated sugars into the PPP for ribose-5-phosphate and NADPH generation, which are vital for reductive biosynthesis and antioxidant defense during DNA/RNA production. This coordination underscores their indispensable roles in cellular growth and response to metabolic demands.^[67]^[72]

Regulation and Cellular Roles

Mechanisms of Activation and Inhibition

Kinases are primarily regulated through dynamic mechanisms that control their catalytic activity, ensuring precise spatiotemporal signaling in cells. Activation often involves phosphorylation events, particularly on the activation loop (A-loop) within the kinase domain, which repositions key residues to stabilize the active conformation and enhance substrate binding affinity. For instance, in many protein kinases, trans-phosphorylation by upstream kinases on threonine or tyrosine residues in the A-loop induces a conformational shift from an inactive, disordered state to an active, ordered structure, thereby increasing catalytic efficiency by orders of magnitude. This process is conserved across eukaryotic kinases and is essential for signal amplification in pathways like receptor tyrosine kinase (RTK) signaling.30002-5) Scaffold proteins further facilitate kinase activation by assembling multi-kinase cascades, promoting efficient phosphorylation while preventing off-target interactions. These scaffolds, such as KSR in the MAPK/ERK pathway, tether kinases in proximity, enhancing sequential activation and insulating signals from cross-talk. By organizing kinases into signaling complexes, scaffolds can significantly increase reaction rates compared to solution-phase catalysis. Additionally, subcellular localization plays a critical role in activation; for example, nuclear translocation of kinases like JNK allows access to transcription factor substrates, triggered by phosphorylation-dependent binding to importins.47492-0/fulltext) Inhibition of kinases occurs through multiple strategies that revert or block the active state, maintaining signaling homeostasis. Competitive inhibitors target the ATP-binding site, mimicking nucleotide structure to occupy the catalytic cleft and prevent substrate phosphorylation, as seen in the binding of staurosporine analogs to the ATP-binding site through interactions with the hinge region. Allosteric inhibition, conversely, involves sites distant from the active center; pseudosubstrate inhibitors, such as the inhibitory domain of PKB/Akt, bind to the substrate site in an inactive kinase conformation, sterically blocking access. Dephosphorylation by protein phosphatases, like PP2A or PTPs, rapidly reverses activation loop modifications, with reaction rates tuned to match kinase kinetics for balanced signaling duration.00245-8) Feedback loops are integral to kinase regulation, often through autoinhibitory mechanisms where inactive conformations shield the active site. In the basal state, many kinases adopt a "DFG-out" conformation, burying the activation loop and requiring energy input for activation. Dimerization provides another activation cue, particularly in RTKs, where ligand-induced dimerization juxtaposes intracellular kinase domains, enabling trans-autophosphorylation and cooperative activation. These loops ensure self-limiting signaling, preventing pathological hyperactivity. Cross-talk between kinases and phosphatases maintains signaling fidelity, with phosphatase activity counterbalancing kinase phosphorylation to set steady-state levels of phospho-substrates. This balance is dynamically adjusted by scaffold-mediated localization of phosphatase-kinase pairs, ensuring localized dephosphorylation. Disruptions in this equilibrium, such as phosphatase sequestration, can amplify signaling, highlighting the phosphatase-kinase rheostat's role in cellular decision-making. Recent advances have introduced optogenetic tools for precise kinase control, enabling light-inducible activation or inhibition without chemical perturbations. For example, the LOV2 domain fused to kinase regulatory regions allows blue light-triggered conformational changes, mimicking phosphorylation effects with millisecond precision, as demonstrated in engineered ERK kinases. These techniques, developed since the 2010s, facilitate dissection of kinase dynamics in living cells, revealing temporal aspects of activation previously inaccessible.

Involvement in Signaling Pathways

Kinases serve as central hubs in cellular signaling pathways, orchestrating responses to extracellular cues by phosphorylating downstream targets to propagate signals and regulate cellular processes such as proliferation, survival, and stress adaptation.^[76] In the cell cycle, cyclin-dependent kinases (CDKs) drive key transitions, including G1/S and G2/M phases, through sequential phosphorylation events; for instance, CDK4/6 and CDK2 phosphorylate the retinoblastoma protein (Rb), releasing E2F transcription factors to promote expression of genes required for DNA synthesis and progression.^[47] This phosphorylation cascade ensures orderly cell division, with dysregulation leading to uncontrolled proliferation in diseases like cancer.^[77] Growth factor signaling exemplifies kinase integration in proliferation and survival pathways. Receptor tyrosine kinases (RTKs), upon ligand binding, autophosphorylate and activate the MAPK/ERK cascade, where Raf, MEK, and ERK kinases sequentially phosphorylate targets to drive gene expression for cell growth and division; this pathway is pivotal in epidermal growth factor (EGF)-induced mitogenesis.^[78] Paralleling this, the PI3K-Akt pathway, activated by RTKs or G-protein coupled receptors, promotes cell survival by phosphorylating substrates like FOXO transcription factors and Bad, inhibiting apoptosis and supporting metabolic adaptations for growth.^[79] These cascades often converge, amplifying proliferative signals in response to insulin-like growth factors.^[80] In stress responses, JNK and p38 MAPKs act as sensors for environmental insults, integrating signals from cytokines and UV radiation to modulate inflammation and apoptosis. JNK phosphorylates c-Jun to activate transcription of pro-inflammatory genes, while p38 regulates cytokine production and cytoskeletal changes, contributing to immune responses; both can trigger apoptosis via mitochondrial pathways when stress is prolonged.^[81] Dysregulation of these pathways underlies chronic inflammation in conditions like arthritis.^[82] Kinases also integrate diverse pathways, functioning as hubs in Wnt, Notch, and TGF-β signaling to coordinate development and homeostasis. In Wnt signaling, GSK3β kinase phosphorylates β-catenin for degradation, but pathway activation stabilizes it to drive transcription; Notch signaling involves γ-secretase-mediated release of the intracellular domain, which interacts with kinase-modulated RBPJ to influence cell fate, often cross-talking with Wnt via shared transcriptional targets.^[83] TGF-β receptors recruit SMAD kinases, phosphorylating SMAD2/3 for nuclear translocation and gene regulation, integrating with MAPK hubs to balance epithelial-mesenchymal transitions.00851-6) Aberrant kinase activity in these networks, such as hyperactive Wnt or TGF-β cascades, drives tumorigenesis through sustained proliferation and metastasis.^[84] Recent phosphoproteomics studies have unified these kinase networks, revealing dynamic, condition-specific interactions via large-scale mapping of phosphorylation sites. For example, 2025 analyses using mass spectrometry-based approaches have identified over 10,000 phosphosites across signaling cascades, enabling inference of kinase-substrate relationships and pathway crosstalk in real-time cellular contexts like cancer.^[76] These models highlight kinases as versatile integrators, where perturbations in one pathway ripple through others, informing disease mechanisms beyond isolated activations.^[85]

Therapeutic Applications

Kinase Inhibitors in Medicine

Kinase inhibitors represent a cornerstone of modern targeted cancer therapy, with the majority of approved agents focusing on oncology indications due to the frequent dysregulation of kinase signaling in tumorigenesis. These small-molecule drugs primarily target protein kinases, modulating aberrant pathways such as those involving receptor tyrosine kinases and cyclin-dependent kinases. As of November 2025, the U.S. Food and Drug Administration (FDA) has approved 100 small-molecule protein kinase inhibitors, underscoring their transformative impact on precision medicine.^[86] Kinase inhibitors are classified based on their binding mechanisms and conformational preferences. Type I inhibitors competitively bind to the ATP-binding site in the active (DFG-in) conformation of the kinase, exemplifying direct antagonism of catalytic activity. In contrast, Type II inhibitors engage both the ATP site and an adjacent allosteric pocket in the inactive (DFG-out) conformation, often enhancing selectivity by exploiting unique structural features. Covalent inhibitors, a growing class, form irreversible bonds with a cysteine residue near the active site via electrophilic warheads such as acrylamides, enabling prolonged target occupancy and overcoming certain resistance mechanisms.^[87]^[87]^[88] Pioneering examples illustrate the clinical success of these agents. Imatinib, a Type II inhibitor targeting BCR-ABL, was the first kinase inhibitor approved by the FDA in 2001 for chronic myeloid leukemia (CML), dramatically improving survival rates and establishing the paradigm for kinase-targeted therapies. Gefitinib, a Type I inhibitor of epidermal growth factor receptor (EGFR), received FDA approval in 2015 for metastatic non-small cell lung cancer (NSCLC) harboring EGFR mutations, offering response rates of around 70% in mutation-positive patients. Palbociclib, an ATP-competitive inhibitor of cyclin-dependent kinases 4 and 6 (CDK4/6), was approved in 2015 for hormone receptor-positive, HER2-negative advanced breast cancer, where it extends progression-free survival when combined with endocrine therapy. More recently, sotorasib, a covalent inhibitor of KRAS G12C approved in 2021 for NSCLC, marked the first direct targeting of this historically undruggable oncoprotein, with subsequent expansions including a 2025 approval for colorectal cancer in combination with panitumumab.^[33]^[89]^[90]^[91]^[92] Despite these advances, challenges persist in clinical application. Acquired resistance often arises through secondary mutations, such as the T790M substitution in EGFR, which sterically hinders Type I inhibitor binding and restores kinase activity. Off-target effects, stemming from polypharmacology across the kinome, can manifest as toxicities including cardiotoxicity, hypertension, and dermatological reactions, necessitating careful patient monitoring and combination strategies. Ongoing efforts focus on next-generation inhibitors to address these limitations while expanding therapeutic utility.^[93]^[94]

Emerging Targets in Drug Development

In recent years, the kinome has expanded to include previously undruggable targets such as pseudokinases, which lack catalytic activity but regulate signaling through scaffolding and allosteric mechanisms. These pseudokinases, comprising about 10% of the human kinome, are increasingly pursued in oncology. Similarly, the pseudokinase TYK2 has been successfully targeted with deucravacitinib, approved in 2022 for psoriasis, demonstrating that pseudokinases can be effectively modulated to achieve clinical benefits in inflammatory diseases.^[95]^[96]^[97] Lipid kinases, particularly the class I phosphoinositide 3-kinase δ isoform (PI3Kδ), represent another frontier for autoimmune disorders, where hyperactivation drives B-cell proliferation and survival. Selective PI3Kδ inhibitors like leniolisib, approved in 2023 for activated PI3Kδ syndrome (APDS), have exhibited efficacy in reducing immune dysregulation and autoantibody production, with ongoing trials exploring broader applications in rheumatoid arthritis and systemic lupus erythematosus. Dual PI3Kδ/γ inhibitors further enhance therapeutic windows by mitigating compensatory signaling, showing reduced chronic germinal center formation and autoantibody levels in preclinical autoimmune models.^[98]^[99]^[100] Innovative modalities are transforming kinase targeting, with proteolysis-targeting chimeras (PROTACs) enabling degradation of kinases resistant to inhibition. PROTACs incorporating motifs from FDA-approved kinase inhibitors, such as those for CDK9 and ALK, have achieved selective degradation in cancer cells, outperforming traditional inhibitors in overcoming resistance mutations. For the MAPK pathway, allosteric modulators like trametinib, which binds MEK1/2 outside the ATP site, continue to inspire next-generation designs that fine-tune pathway dynamics with reduced toxicity. These approaches allow for event-driven pharmacology, where kinase levels are depleted rather than merely inhibited.^[101]^[102]^[103] Beyond oncology, sphingosine kinase (SphK) inhibitors are gaining traction for fibrotic diseases, where SphK1-S1P signaling promotes fibroblast activation and extracellular matrix deposition. Preclinical studies in 2025 demonstrated that SphK1 inhibition post-injury attenuates pulmonary and liver fibrosis by downregulating TGF-β pathways and reducing fibrocyte infiltration, with candidates like PF-543 advancing toward clinical evaluation. In mitochondrial disorders, therapies for thymidine kinase 2 (TK2) deficiency, a cause of mtDNA depletion syndromes, involve nucleotide supplementation with deoxythymidine and deoxycytidine, which has shown potential to restore nucleotide pools and alleviate myopathy in patient-derived models and clinical trials.^[104]^[105]^[106] Artificial intelligence and machine learning are accelerating kinome-wide selectivity profiling, enabling prediction of off-target interactions from vast datasets of over 5 million kinase assays. Models like graph neural networks and deep learning frameworks have improved hit-to-lead optimization, identifying selective inhibitors for underexplored kinome subsets with up to 90% accuracy in virtual screening. In neurodegenerative applications, dual kinase inhibitors targeting combinations such as GSK3β/HDAC or p38α/BChE are under preclinical investigation for Alzheimer's disease, with potential to reduce tau hyperphosphorylation and neuroinflammation.^[107]^[108]^[109]

References

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Definition of kinase - NCI Dictionary of Cancer Terms
A type of enzyme (a protein that speeds up chemical reactions in the body) that adds chemicals called phosphates to other molecules, such as sugars or proteins.
[2]
Catalytic Mechanisms and Regulation of Protein Kinases - PMC
Mar 25, 2015 · Eukaryotic protein kinases are enzymes that catalyze phosphoryl transfer from MgATP to Ser/Thr and Tyr side chains in proteins.
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Regulation and Function of Protein Kinases and Phosphatases - PMC
Nov 3, 2011 · Protein kinases and phosphatases are enzymes catalysing the transfer of phosphate between their substrates.
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How many kinases are druggable? A review of our current ...
Amongst the nearly 20 000 proteins encoded by our genome [1], humans have around 500 protein kinases. How many of these kinases are druggable? Well of ...
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Protein kinases play a predominant regulatory role in nearly every aspect of cell biology and they can modify the function of a protein in almost every ...
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(PDF) A Kinome-Wide siRNA Screen Identifies Multiple Roles for ...
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Cryo-EM structures of CRAF/MEK1/14-3-3 complexes in ... - Nature
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Human members of the eukaryotic protein kinase family
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Sphingosine kinases, sphingosine 1-phosphate, apoptosis and ...
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Multi-Omic analyses characterize the ceramide/sphingomyelin ...
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Regulation of mammalian nucleotide metabolism and biosynthesis
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Regulation of Adenine Nucleotide Metabolism by Adenylate Kinase ...
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Carbohydrate Metabolism
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(PDF) Going for broke: Targeting the human cancer pseudokinome
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Structural and evolutionary insights into understudied bacterial ...
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SPHK1-S1p Signaling Drives Fibrocyte-Mediated Pulmonary Fibrosis
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Docking-Informed Machine Learning for Kinome-wide Affinity ...
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