Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030027

Authors: Nicolas Gomez-Sequeda Marlene Jimenez-Del-Rio Carlos Velez-Pardo

Familial Alzheimer’s disease (FAD) is an accelerated form of dementia affecting cholinergic neurons. Despite several efforts, no single drug or treatment has demonstrated complete efficacy. Therefore, finding effective therapeutic agents is imperative. Previous studies have shown that the PSEN1 I416T variant induces FAD-like neuropathology in cholinergic-like neurons (ChLNs), characterized by the intracellular accumulation of the Aβ (iAβ) peptide, the oxidation of the stress sensor protein DJ-1, the abnormal phosphorylation of the tau protein at serine 202/threonine 205 (pS202/T205), the loss of mitochondrial membrane potential (ΔΨm), and activation of the pro-apoptotic proteins tumor protein 53 (TP53), Jun proto-oncogene, AP-1 transcription factor subunit (c-JUN), p53 upregulated modulator of apoptosis (PUMA), and cleaved caspase-3 (CC3). We report for the first time that PSEN1 I416T induces abnormal phosphorylation of Leucine-rich repeat kinase 2 (LRRK2) kinase at residue serine 935 (S935), concomitant with phosphorylated alpha-synuclein (αSYN) at residue serine 129 (S129) and abnormal accumulation of autophagosomes and atypical increase in vesicular lysosomal pH, thereby provoking a profound alteration in autophagy in ChLNs. Here, we also demonstrate for the first time that the potent LRRK2 inhibitor PF-06447475 (hereafter referred to as PF475) almost completely attenuated PSEN1 I416T-induced proteinopathy, oxidative stress (OS), and apoptosis and improve autophagy to an activity comparable to untreated wild-type (WT) ChLNs. Overall, PF475 restored the survival of mutant ChLNs. Taken together, these findings suggest that PF475 is an excellent pharmacological tool with which to investigate the regulation of LRRK2-associated pathological signaling in the PSEN1 I416T familial Alzheimer’s disease (FAD) model.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030026

Authors: Luca Cesaro Mauro Salvi

Acidophilic kinases are serine/threonine protein kinases that preferentially phosphorylate substrates bearing negatively charged determinants near the phosphoacceptor site. These determinants may be encoded by aspartate or glutamate, or introduced by prior phosphorylation of serine, threonine, or tyrosine residues. CK2 is the most representative of this historically small group of kinases because of its high basal activity, broad localization, and extensive substrate repertoire. Kinome-wide specificity profiling covering more than 84% of the active human S/T kinome has now provided a near-comprehensive view of acidophilic kinases across several families. Here, we compare these enzymes through three interconnected features: subcellular localization, substratome size, and consensus-motif specificity. We broadly categorize them as D/E-directed kinases or phosphate-directed/primed kinases, while recognizing that these preferences are not mutually exclusive. We then compare intrinsic preferences measured with peptide libraries with those observed in bona fide substrates. Despite their shared preference for negative charge, acidophilic kinases display markedly different positional requirements for acidic or phosphorylated determinants. For kinases that rely strongly on consensus-sequence recognition, these preferences can generate distinctive kinase-specific fingerprints that can support the attribution of experimentally validated phosphosites, particularly when combined with subcellular localization.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030025

Authors: Daphne E. Cruz-Villarreal Karla D. Hernandez-Gonzalez J. Alberto Olivares-Reyes

One mechanism contributing to insulin resistance is the serine/threonine phosphorylation of critical proteins involved in insulin signaling, particularly the insulin receptor, its downstream substrates, and the activation of protein tyrosine phosphatases. These modifications are associated with decreased insulin signaling, leading to insulin resistance. Protein kinase C (PKC), a family of serine/threonine kinases activated by lipids and/or Ca2+, is essential for regulating metabolism and maintaining cellular homeostasis. These kinases regulate glucose uptake and lipid storage, thereby influencing energy balance through tissue-specific mechanisms. However, dysregulation of PKC activity is closely associated with the development of metabolic syndrome (MetS), a cluster of interconnected physiological and biochemical alterations, including insulin resistance, lipid dysregulation, chronic inflammation, hypertension, and obesity, all of which increase the risk of cardiovascular disease (CVD) and type 2 diabetes (T2D). Notably, alterations in PKC signaling can impair insulin’s ability to facilitate glucose uptake and storage and disrupt lipid storage mechanisms, thereby exacerbating insulin resistance. These dysfunctions significantly contribute to the pathophysiology of MetS. This review aims to examine PKC activation under normal physiological conditions, with particular emphasis on its role in insulin signaling, and to explore how PKC dysregulation participates in the pathophysiology of insulin resistance and MetS.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030024

Authors: Joel Karikari Nyarkoh Matthew Wolan David M. Feliciano

The phosphotransferase activity of the protein kinase known as the mechanistic Target of Rapamycin (mTOR) is arguably one of the most studied biochemical events in biomedical sciences because of its importance to human health and evolution. Despite progress being made in understanding the structure, biochemical characteristics, and function of the enzyme, tremendous knowledge gaps remain unfilled. Altered mTOR activity occurs in numerous neurological disorders, including those that present with seizures and neoplasms. Advances in cancer biology have identified that neuron activity is a critical driver of neoplastic growth. Here, we discuss mTOR, examples of neoplasms with altered neuron activity, and the potential utility of using mTOR inhibitors to modulate tumor-associated neurons.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030023

Authors: Lucinda Fitzgibbons Yuanqin Zhang Xiangwei Fang Maddox Gerger Lynn Dinh Jiuhui Wang Krishna Rao Daotai Nie

Breast cancer remains one of the most common cancers in women, in which the majority of cases exhibit a hormone receptor-positive subtype. Although several treatment options are available for patients with this subtype, first-line therapies mainly rely on the patient’s sensitivity to endocrine therapy. Therapy resistance, which frequently develops over the treatment course, remains a key obstacle for clinical intervention. Efforts are currently underway to elucidate additional therapeutic targets to restore endocrine therapy sensitivity and treat hormone receptor-positive breast cancer. Here, we summarize work surrounding the sigma-2 receptor (σ2R) and its potential role in endocrine therapy resistance pathways, including PI3K-mTOR signaling and cholesterol metabolism. Although σ2R was pharmacologically characterized decades ago, its molecular identity remained elusive until 2017, when transmembrane protein 97 (TMEM97) was established as the sigma-2 receptor. TMEM97/σ2R is highly expressed in hormone receptor-positive breast cancer and its RNA expression levels are associated with endocrine resistance. High expression of TMEM97/σ2R elevates estrogen receptor activities and confers breast cancer cells with increased resistance to endocrine therapy via enhanced mTOR signaling. Given the role of TMEM97 in cholesterol homeostasis, understanding the connections between TMEM97/σ2R, breast cancer, and cholesterol regulation may reveal new pathways to aid in the development of targeted therapies. Evidence remains preclinical, and further investigation is needed to confirm hypothesized pathways involving TMEM97/σ2R in breast cancer endocrine resistance.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030022

Authors: Juan Diego Guarimata Leandro Martínez Heredia Estefanía Montiel Patricia Araceli Quispe Martin Jose Lavecchia

Protein kinases are the most intensively targeted protein family for small-molecule drugs, and the large volume of inhibitory-assay data reported for them makes the family particularly well suited to data-driven and machine-learning approaches to drug discovery. This data, however, is scattered across heterogeneous assays, reports and publications, and its reuse for modeling requires substantial curation. Here, we present Kinoteca, a curated database of kinase inhibitory-activity data derived from ChEMBL and accessible through a web interface for browsing, filtering, visualization and download. Kinoteca reconciles the multiple raw independent measurements reported for each combination of compound, kinase and activity type into a single fused activity value, together with a dispersion score based on the mean unsigned error (MUE) that quantifies how consistent the underlying measurements were. The database currently organizes curated data for 585 kinases and arranges them along biologically meaningful groupings such as kinome family, pathway and source organism. Curated activities can be filtered by the physicochemical properties of the assayed molecules or by measurement quality, explored through summary statistics, activity distributions and structural clustering, and exported either as curated or semi-raw data tables or as molecular structure files. These data formats are suitable for the direct training of machine learning models, such as activity prediction models. By delivering reconciled, analysis-ready data with its provenance preserved, Kinoteca aims to lower the barrier to reproducible, data-driven kinase drug discovery.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030021

Authors: Sofia F. Forti Fabio L. Forti

Protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) constitute two major superfamilies of signaling enzymes in mammals, displaying comparable genomic representation (~100 genes each) and numbers of catalytically active proteins (~80 enzymes each). Both families include receptor and non-receptor forms; however, their distributions differ substantially. PTKs comprise 58 receptor tyrosine kinases (RTKs), whereas PTPs include only 21 receptor protein tyrosine phosphatases (RPTPs). Despite these differences, RTKs and RPTPs share a common structural organization consisting of (i) an extracellular domain responsible for ligand recognition; (ii) a single-pass transmembrane domain anchoring the receptor to the plasma membrane; and (iii) an intracellular catalytic domain containing either kinase or phosphatase activity. Signal transduction mediated by RTKs and RPTPs generally depends on ligand binding and receptor dimerization. Remarkably, although these receptor families regulate signaling through fundamentally opposite molecular mechanisms, both are essential for controlling cell proliferation, adhesion, migration, differentiation, development, and survival. RTKs have been more extensively characterized than RPTPs; nevertheless, both receptor classes function as critical regulators of intercellular and intracellular communication pathways. Moreover, their membrane-associated localization makes them attractive targets for therapy in multiple human diseases, particularly cancer and neurological disorders.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030020

Authors: Daylen Aguilar-Noriega Ying Yi Jamilet Miranda Yanelda García Dania M. Vázquez Yaqin Lan Ricardo Bringas Wen Li Yasser Perera Silvio E. Perea

HMGB-1 is an alarmin representative of DAMP playing a central role in immunogenic cell death (ICD), a necessary condition in the dialog established between dying tumor cells and the immune system during some anticancer therapies. Therefore, early screening for ICD inducers represents a major priority in drug development today. In this work, we investigated the effect elicited by the clinical-grade CIGB-300 peptide, which impairs Protein Kinase CK2-mediated phosphorylation and other CK2 signaling connected kinases. Here, HMGB-1 extracellular release was investigated in an 18-cell line panel from blood malignancies, uterine-cervical cancer and NSCLC treated with CIGB-300 at equipotent doses (IC50) over 24 h. Interestingly, CIGB-300 treatment upregulated the HMGB-1 protein levels at the culture supernatant in most of the cell lines (p = 0.01) and fold-change increases ≥ 2 were associated with intrinsic cell line sensitivity towards CIGB-300’s cytotoxic effect. However, the HMGB-1 release by CIGB-300 was context-specific with clear induction on blood and uterine-cervical cancer cells and a diffused response pattern in NSCLC. Importantly, CIGB-300 treatment of blood cancer patients enrolled in a Phase I study induced plasma HMGB-1 alarmin in 4 out of 7 subject who received the entire treatment plan. Altogether, our data reveal for the first time that CIGB-300 treatment is able to induce extracellular HMGB-1 release in vitro and in vivo which could be indicative of ICD induction in some kinds of tumors; furthermore, the induction of extracellular HMGB-1 alarmin as a putative CIGB-300 response biomarker merits further investigation.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030019

Authors: Cody Reid Dotson Lilly Underwood Priscila Y. Sato

Sustained neurohormonal stress, adverse myocardial remodeling, and inflammation are major components of heart failure (HF) progression. Alterations in circulating neurohormonal signaling are directly sensed by the β-adrenergic receptor (βAR), a system mainly responsible for chronotropic and inotropic cardiac responses. βARs are regulated by G-protein-coupled receptor (GPCR) kinase 2 (GRK2). Within this context, decades of study have unraveled mechanistic details on how GRK2 canonically imposes a “brake” on βARs and other GPCR-mediated signaling. Notably, an expanding body of evidence demonstrates that GRK2 functions in a highly compartment- and cell-dependent manner, with roles extending far beyond GPCR regulation. These noncanonical activities span metabolic control, maintenance of organelle integrity, and regulation of inter-cellular signaling networks, particularly those governing immune–vascular interactions. In this review, we will discuss recent advances in our understanding of the cell-specific functions of GRK2, its emerging biological roles in cardiac diseases, and the opportunities these findings present for advancing mechanistic insights in cardio-oncology. We propose that the therapeutic value of GRK2 is directly dependent on a deeper understanding of its noncanonical functions in a compartment- and cell-specific manner within a disease-specific context.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4030018

Authors: Rebeca Acín-Pérez Marta Pérez-Hernández Pablo Hernansanz-Agustín José Antonio Enríquez

Mitochondria coordinate cellular energy production, metabolism, and signalling through the organization of the electron transport chain (ETC) and formation of respiratory supercomplexes. These structures facilitate efficient electron transfer and enable coenzyme Q (CoQ) channelling, allowing differential regulation of NADH- and succinate-driven respiration while modulating reactive oxygen species (ROS) production. Beyond their damaging potential, ROS act as key signalling molecules that regulate mitochondrial function through redox-sensitive modifications. Mitochondrial protein kinases add an additional layer of control, with Src-family kinases playing a central role. In particular, the mitochondrial tyrosine-kinase Fgr is activated by H2O2 and promotes phosphorylation of succinate dehydrogenase, boosting complex II activity, delivering more electrons to CoQ and inducing reverse electron transfer (RET) through CI, in a ROS-induced ROS generation amplification cycle. This induces a metabolic rewiring aimed at supporting stress adaptation, immune cell activation, and macrophage polarization. Overall, the interplay between supercomplex organization, ROS signalling, and kinase activity is critical for metabolic flexibility and represents a promising target for therapeutic intervention.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020017

Authors: Mozart Silvio Pereira Heveline Oliveira Morais Arruda Diego Magno Martins Philipe Oliveira Fernandes Adriano Paula Sabino Adolfo Henrique Moraes

Janus kinase 2 (JAK2) occupies a central position in cytokine signaling and plays essential roles in hematopoiesis, immune regulation, and cancer. Although recent advances in structural biology, cryo-EM, receptor modeling, and biophysical analysis have substantially expanded current views of JAK2 function, key mechanistic questions remain regarding how receptor geometry, JH2-mediated autoinhibition, and disease-associated mutations are structurally integrated. In this review, we discuss the multidomain organization of JAK2 and examine how the FERM–SH2 module, the pseudokinase domain (JH2), and the catalytic kinase domain (JH1) cooperate to govern receptor specificity, allosteric control, and cytokine-induced activation. We further analyze how pathogenic mutations rewire this regulatory system by weakening autoinhibitory contacts, altering linker-mediated communication, or stabilizing active dimeric conformations. Finally, we assess current and emerging therapeutic strategies, from ATP-competitive inhibitors to macrocyclic and JH2-selective allosteric modulators, with emphasis on how structural insight can guide next-generation drug design. These advances support a more integrated view of JAK2 regulation and define new opportunities for selective therapeutic intervention.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020016

Authors: Venu Pandit Luke Fracek Md Tamzid Hossain Tanim Aarushi Patel Daniel Halloran Anja Nohe

Osteoarthritis (OA) remains a challenging disease due to the increased rate of incidence in the older population and the lack of a disease-modifying drug. BMP signaling plays a crucial role in chondrogenic differentiation and in the stability of articular cartilage. However, because BMP-2 also induces chondrocyte hypertrophy, it is not a viable drug for OA treatment. In contrast, the Bmpr1a biomimetic peptide can repair articular cartilage without inducing chondrocyte hypertrophy in the OA mouse model and in chondrocytes derived from patients diagnosed with OA. Despite this benefit, the mechanism by which the peptide drives chondrogenesis remains elusive. To explore this, we use a phosphoproteomics approach to identify pathways differentially activated by CK2.1. Specifically, we identified differentially phosphorylated phosphosites by CK2.1. Based on these phosphosites that we identified, we propose a molecular mechanism by which CK2.1 activates chondrogenesis. Notably, we predict that the mitogen-activated protein kinase (MAPK) pathway is regulated by CK2.1 to induce proteoglycan synthesis in C3H10T1/2 cells.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020015

Authors: Nathan A. Mullins Patrick A. Roberto Amya T. Sallee Amy N. Abell

During development, stem cells rapidly proliferate and differentiate to form the embryo and the placenta, requiring intensive increases in cellular protein synthesis and changes to the cell architecture. Chaperone proteins, including the small heat shock proteins (HSPs), are critical assistants to protein folding, preventing protein aggregation, and promoting autophagy. Mitogen-activated protein kinase kinase kinase 4 (MAP3K4) is a stress-activated kinase that promotes fetal and placental growth. MAP3K4 directly activates p38 and JNK in trophoblast stem (TS) cells by phosphorylating MAP2K3 and MAP2K4/7, respectively. In addition, MAP3K4 promotes activation of the Akt signaling pathway by controlling Igf1r expression. TS cells differentiate to placental trophoblasts comprising the junctional zone (JZ) and labyrinth (LAB) placental layers. In this study, we demonstrate that JZ differentiation transiently increases JNK activity, whereas LAB differentiation induces sustained p38, JNK, and Akt activation. Each of these pathways is inhibited in MAP3K4 kinase-inactive (KI) LABKI trophoblasts. JZ and LAB differentiation also induces HSP22 and HSP27 expression and HSP27 phosphorylation; these are also reduced in TSKI and LABKI cells. JZ and LAB differentiation induces GABARAP-positive autophagosomes that are deficient in KI cells. Altogether, our findings demonstrate that MAP3K4 is critical for responses during differentiation in placental trophoblasts.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020014

Authors: Andrzej Günther Barbara Bednarczyk-Cwynar

Oleanolic acid (OA) is a pentacyclic triterpenoid with broad biological activity, but its primary molecular points of engagement remain incompletely resolved. Most available studies describe OA through selected pathway markers, particularly within PI3K/AKT/mTOR, AMPK/mTOR, MAPK, NF-κB, and Nrf2 signaling, without clearly distinguishing direct target engagement from downstream adaptive responses. This limits mechanistic interpretation and weakens translational prioritization. This review focuses specifically on phosphoproteomics-centered and multi-omics-assisted target deconvolution of OA rather than providing a comprehensive catalog of all reported biological effects of OA. We examine why phosphoproteomics is particularly informative for capturing early signaling events, how it can be integrated with total proteomics, transcriptomics, metabolomics, and chemoproteomic approaches, and why orthogonal target-engagement methods remain essential for stronger causal inference. We also organize the current signaling evidence for OA and its derivatives, distinguishing pathway association, kinase/phosphatase activity inference, target prioritization, and direct target validation. The strongest mechanistic support for the parent compound currently concerns AMPK/mTOR-linked regulation of autophagy and apoptosis, whereas evidence for several other pathways remains more heterogeneous, derivative-dependent, or marker-based. Finally, we propose a stepwise workflow for OA target deconvolution based on time-resolved phosphoproteomics, informative phosphosite subsets, multi-omics integration, kinase/phosphatase activity inference, and experimental target validation. This framework may help move OA research from descriptive pathway pharmacology toward mechanism-based target prioritization and more rational derivative development.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020013

Authors: Yuka Kamada Tsukasa Okiyoneda

Cystic fibrosis (CF) is a monogenic disease caused by mutations in the CF transmembrane conductance regulator (CFTR), whose folding, trafficking, and stability are tightly controlled by ubiquitination-dependent protein quality control (PQC) pathways. Although CFTR modulators have transformed CF therapy, their efficacy remains limited by persistent ubiquitination and degradation of rescued CFTR. This limitation is particularly evident in class I mutations, where premature termination codons (PTCs) reduce full-length CFTR protein production and no approved mutation-specific therapies are broadly available for canonical PTC variants. Recent advances highlight ubiquitination as a critical and druggable determinant of CFTR stability. The E3 ligase RFFL regulates peripheral CFTR PQC, restricting the stability of rescued CFTR at the plasma membrane (PM). Inhibition of RFFL, including via antisense oligonucleotides (ASO) and small molecules, enhances CFTR rescue and improves outcomes in combination with modulators and translational readthrough therapies. In parallel, deubiquitinase (DUB)-targeting chimeras (DUBTACs) have emerged as a novel modality to stabilize proteins by reversing ubiquitination. Here, we review current advances in targeting CFTR ubiquitination, with a focus on RFFL inhibition and DUBTAC-based strategies, and discuss their opportunities and translational limitations as components of next-generation CF therapies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020012

Authors: Gustavo Adolfo Barraza Joselina Magali Mondaca Juan Manuel Fernandez Muñoz Bruno Mariano Vinante Marina Inés Flamini Angel Matias Sanchez

The tumor suppressor protein phosphatase 2A (PP2A) plays a crucial role in regulating oncogenic signaling. Its inactivation, specifically through inhibitory phosphorylation at Tyr307 mediated by SET and CIP2A, contributes to breast cancer (BC) progression. Modulation of these interactions represents a promising pharmacological strategy to restore PP2A function. We integrated computational approaches with experimental validation to analyse SET/CIP2A mechanisms and explore how PP2A reactivation suppresses tumor progression. Molecular docking and dynamics simulations showed that the SET inhibitor/FTY-720 forms stable hydrogen bond networks with SET, disrupting its interaction with PP2A. In contrast, CIP2A suppressor/erlotinib interacts with CIP2A through weaker hydrophobic and π-interactions. Protein–protein interaction analyses indicate reduced SET/CIP2A binding to PP2A upon treatment, supporting a structural basis for PP2A reactivation. Gene expression analyses revealed upregulation of PP2A, SET, CIP2A, and cytoskeletal markers in tumor and metastatic tissues. Studies on Triple Negative Breast Cancer (TNBC) cells showed that FTY-720 and erlotinib significantly reduce PP2A-Tyr307 phosphorylation, restoring its activity. Additionally, both compounds decreased c-Myc levels and inhibited Src/FAK/paxillin/PAK1 and ERK signaling, attenuating migratory and proliferative pathways. Our findings identify the SET/CIP2A–PP2A axis as a pharmacological target for the design of next-generation PP2A activators, highlighting the potential of inhibition as a therapeutic strategy to counteract TNBC progression.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020011

Authors: Gilberto Muñoz-Pérez Fátima Álvarez-Camarena Julio Vega-Arreguin

Plant–pathogen interactions are shaped by dynamic regulatory processes that control immune signaling. Among these, post-translational modifications (PTMs) play central roles in modulating protein activity, stability, and interaction networks. Increasing evidence indicates that Phytophthora effectors target PTM-dependent regulatory systems to suppress host immunity and promote infection. Here, we synthesize current knowledge on how Phytophthora virulence factors manipulate post-translational regulation through two mechanistically distinct strategies: (i) canonical mechanisms, involving direct enzymatic modification of host proteins or the recruitment of host PTM-modifying enzymes, and (ii) non-canonical mechanisms, in which effectors alter the activity, organization, or localization of PTM-associated regulatory systems without directly inducing covalent modification. These processes frequently involve protein–protein interactions and oligomerization-dependent regulation that reshape signaling complexes and enzymatic accessibility. By distinguishing effector-mediated PTM induction from regulatory interference, we provide a mechanistic framework for interpreting how diverse virulence strategies converge on the control of immune signaling pathways, including those governing reactive oxygen species production, transcriptional regulation, hormone signaling, and cell death. We further highlight current limitations in mechanistic understanding and emphasize the need for integrative approaches combining structural biology and proteomics to resolve how effectors reprogram host signaling systems.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020010

Authors: Osama AlOudat Omar S. Al-Odat

Pediatric gastrointestinal (GI) cancers are rare malignancies that differ fundamentally from their adult counterparts in molecular drivers, histology, and clinical behavior. While adult GI cancers are frequently driven by recurrent oncogenic mutations, pediatric tumors often exhibit pathway-level dysregulation involving developmental signaling networks. Among these, the RAS/MAPK pathway emerges as a central convergent axis integrating growth factor signaling, developmental programs, inflammatory cues, and post-translational regulatory mechanisms. Increasing evidence suggests that aberrant phosphorylation dynamics result from imbalanced kinase activation and phosphatase-mediated signal attenuation, which contribute to sustained MAPK signaling in pediatric GI malignancies, even in the absence of canonical RAS or RAF mutations. This review synthesizes current knowledge on RAS/MAPK signaling in pediatric GI cancers, emphasizing the role of kinase–phosphatase imbalance, signal duration, and regulatory failure in shaping oncogenic outcomes. We highlight how altered phosphorylation control may influence tumor differentiation, therapeutic responsiveness, and resistance mechanisms, and discuss emerging opportunities for targeting signaling dynamics rather than single genetic lesions. This signaling-centric framework provides a biologically grounded rationale for functional biomarker-driven precision therapy in pediatric GI malignancies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020009

Authors: Fábio Morato de Oliveira Fermino Sanches Lizarte Neto Eduardo Vignoto Fernandes Mayara Bocchi Bruno Machado Rezende Ferreira

Chronic lymphocytic leukemia (CLL) exhibits marked clinical heterogeneity that is closely associated with genomic instability. Although cytogenetic abnormalities are widely used for risk stratification, they do not fully capture the biological complexity of the disease. Telomere dysfunction and alterations in DNA damage response pathways have been implicated in disease progression, but their relationship with cytogenetic risk in CLL remains incompletely characterized. In this study, peripheral blood mononuclear cells (PBMCs) from 48 CLL patients were analyzed. The analyzed PBMC fractions were enriched in leukemic B cells, with an estimated median tumor content above 85–90%. Cytogenetic profiles were obtained by conventional karyotyping following in vitro immunostimulation with DSP30 and interleukin-2 and classified according to ERIC and Döhner criteria. Telomere length was assessed by quantitative PCR, and CHEK1 and CHEK2 expression levels were quantified by RT–qPCR. Molecular parameters were compared across cytogenetic risk groups. Distinct molecular profiles were observed across cytogenetic categories. Favorable-risk CLL cases showed preserved telomere length, low CHEK1 expression, and maintained CHEK2 levels. Intermediate-risk cases, predominantly characterized by trisomy 12, exhibited moderate telomere shortening accompanied by increased CHEK1 expression and partial reduction of CHEK2. High-risk CLL cases, defined by del(11q), del(17p), or complex karyotypes, displayed pronounced telomere shortening, marked CHEK1 upregulation, and strong suppression of CHEK2. Telomere length was inversely correlated with cytogenetic risk (Spearman’s ρ = −0.68, p < 0.0001), and the CHEK1/CHEK2 expression ratio increased progressively with genomic complexity. These findings indicate that telomere length and CHEK1/CHEK2 expression patterns are closely associated with cytogenetic risk in CLL and may provide complementary biological information for risk stratification.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4020008

Authors: Adil Ahiri Aziz Aboulmouhajir

Protein kinase inhibition can be achieved through various mechanisms, including blocking phosphorylation activity or disrupting regulatory interactions. While small molecule inhibitors have shown promise, their selectivity remains challenging due to the structural similarities among kinase catalytic sites. To design selective kinase inhibitors based on peptide terminal tail interactions with the activation segment, focusing on five kinases with different conformational states: GSK3, PAK4, TTN (OUT conformation) and PKB, FLT3 (IN conformation). Three-dimensional structures from RCSB PDB were optimized using MODELLER version 9.0. Peptide sequences were designed with PeptiDerive (Rosetta) and RosettaDesign version 3.5, followed by pharmacophore modeling based on key interaction residues. Virtual screening was then conducted with PyRx 0.8 and molecular docking with AutoDock Vina 1.1.2. Molecular dynamics simulations were performed using Desmond v6.6 (Schrödinger Suite 2016, Multisim v3.8.5.19) (100 ns, NPT ensemble, 300 K). Analysis of the five kinases revealed distinct interaction profiles with designed peptidomimetic compounds. Kinases displaying the IN conformation of the activation segment (PKB and FLT3) consistently showed superior stability and stronger interaction profiles compared to those in the OUT conformation. The designed compounds formed key hydrogen bonds and hydrophobic interactions with critical residues in the activation segment binding pocket. The most promising inhibitors demonstrated stability throughout the molecular dynamics simulations, with IN conformation kinases maintaining more consistent conformational profiles than their OUT conformation counterparts. Kinases with IN conformation of the activation segment demonstrated superior stability and interaction profiles compared to OUT conformations. These findings contribute to our understanding of selective kinase inhibition and provide a framework for developing novel inhibitors, particularly for PKB and FLT3. The implications of this study extend to rational drug design approaches that leverage natural regulatory mechanisms for therapeutic intervention, though further optimization is needed for GSK-3β, PAK4, and TTN to improve stability and binding affinity.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4010007

Authors: Abigail E. Conklin Colin L. Welsh Lalima K. Madan

Receptor protein tyrosine phosphatases (RPTPs) are transmembrane enzymes that counterbalance protein tyrosine kinase activity by catalyzing the removal of phosphate groups from tyrosine residues on target proteins. Despite their critical roles in regulating cellular proliferation, adhesion, differentiation, and survival, RPTPs remain significantly understudied compared to their kinase counterparts. Contrary to early assumptions that PTPs function as constitutive housekeeping enzymes, emerging evidence demonstrates that RPTPs exhibit highly context-dependent roles in cancer, functioning as tumor suppressors or tumor promoters, or displaying dual activities depending on tissue type, cellular environment, and the specific signaling networks involved. This review provides a comprehensive analysis of RPTP structure, catalytic mechanisms, regulatory processes, and interactions with signaling effectors in cancer. Through a systematic examination of RPTP expression patterns across ten cancer types using Clinical Proteomic Tumor Analysis Consortium (CPTAC) and International Cancer Proteogenome Consortium (ICPC) datasets, we identify subfamily-specific and cancer-type-specific expression alterations that correlate with established functional classifications. PTPσ and PTPμ emerge as uniformly downregulated tumor suppressors across diverse malignancies, whereas PTPα and PTPε display oncogenic potential by activating Src family kinases. Context-dependent RPTPs, such as LAR and DEP-1, exhibit variable expression patterns that reflect their complex, multifaceted signaling roles. These findings establish RPTPs as critical regulators of cancer signaling with significant therapeutic potential while underscoring the need to understand tissue-specific signaling architectures when developing RPTP-targeted interventions.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4010006

Authors: Jennie C. Holmberg Victoria A. Riley Aidan M. Sokolov Luke J. Fisher David M. Feliciano

Tuberous Sclerosis Complex (TSC) is a genetic disorder caused by mutations that inactivate TSC1 or TSC2 genes. TSC1 or TSC2 mutations activate the mammalian target of rapamycin complex 1 (mTORC1) protein kinase pathway. Although many patients inherit a single copy of a mutant TSC gene, somatic mutations that cause loss of heterozygosity in inhibitory neuroprogenitor cells are hypothesized to be one cause of abnormal development. This may lead to cortical malformations or benign growths along the ventricular-subventricular zone (V-SVZ), cortex, olfactory tract, and olfactory bulbs (OB). This idea is supported by focal single-cell knockout experiments that induce CRE-mediated recombination following neonatal electroporation of conditional Tsc2 or Tsc1 mice. Loss of Tsc2 causes mTORC1 pathway activation and the formation of striatal hamartomas composed of ectopic clusters of abnormal cells and cytomegalic neurons, including within the OB. Neural phenotypes in this model can be partially rescued with Rapalink-1, a bisteric mTOR inhibitor, demonstrating the importance of mTOR in pathogenesis. We previously demonstrated that global V-SVZ neural stem cell (NSC) Tsc2 mutation induced by nestin-CRE-ERT2 causes mTORC1 pathway activation, which is accompanied by transcriptional and translational errors. While we previously described cultured NSCs and OB granule cells from these mice, we did not thoroughly describe changes outside this region. Here, we provide evidence that removal of Tsc2 from neonatal V-SVZ NSCs causes subtle and rare brain malformations. This is exemplified by ectopic clusters of cytomegalic neurons and mTORC1 activation. This data supports that loss of Tsc2 in NSCs during neonatal development leads to heterotopic clusters in the adult brain. This model may be useful to study TSC, but the rarity and stochastic nature of lesions make the use challenging for identifying mechanisms and testing therapies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4010005

Authors: Claudia Tredup Susanne Müller

Kinases are signaling molecules that are central to all aspects of life. Consequently, their dysregulation is implicated in numerous diseases, making kinases one of the most successful family of drug targets. However, due to the conserved catalytic domain of kinases, these drugs are frequently not selective for a specific target, and selective inhibitors—‘chemical probes’—are therefore necessary to understand the role of specific proteins or isoforms. Through the SGC chemical probe program, selective kinase inhibitors have been made available, focusing on understudied kinases. Here, we discuss recent examples of this effort and showcase how selectivity for these probes has been achieved using different approaches.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4010004

Authors: Patrick A. H. Ehm

Oncogenic kinase pathways, including PI3K/AKT, RAS/ERK/MAPK and JAK/STAT, are central drivers of cancer cell proliferation, survival and metastatic potential. However, excessive activation of these pathways imposes intrinsic cellular stresses, such as oncogene-induced senescence, DNA damage responses and apoptosis. Recent evidence reveals that cancer cells mimic immunoregulatory programs to mitigate these stresses by ectopically expressing inhibitory receptors traditionally found on hematopoietic cells. These receptors recruit phosphatases such as DUSPs, SHP1, SHIP1 and PP2A, which directly counteract hyperactivated kinases. Acting as dynamic homeostatic buffers, these phosphatases attenuate oncogenic signaling intensity, maintaining a balance that permits continued proliferation while preventing the activation of fail-safe tumor-suppressive mechanisms. This mechanism appears particularly relevant in metastasizing cancer populations, where elevated co-expression of inhibitory receptors and phosphatases correlates with survival advantage and adaptation under selective pressures. Understanding the dual roles of phosphatases, not only as classical tumor suppressors but also as modulators of signaling homeostasis, provides insight into cancer cell adaptation to oncogenic stress. Targeting the phosphatase–inhibitory receptor axis may selectively destabilize this balance, exposing vulnerabilities in aggressive, resistant or metastatic cancer cells. This review highlights emerging evidence for the phosphatase-mediated buffering of oncogenic kinase signaling, the molecular mechanisms underlying inhibitory receptor engagement and the clinical implications for tumor progression and therapy resistance.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4010003

Authors: Michael Olaolu Arowolo Marian Emmanuel Okon Davis Austria Muhammad Azam Sulaiman Olaniyi Abdulsalam

Reversible protein phosphorylation is an important regulatory mechanism in cellular signalling and disease, regulated by the opposing actions of kinases and phosphatases. Modern computer methods predict kinase–substrate or phosphatase–substrate interactions in isolation and lack specificity for biological conditions, neglecting triadic regulation. We present SPINET-KSP, a multi-modal LLM–Graph foundation model engineered for the prediction of kinase–substrate–phosphatase (KSP) triads with contextual awareness. SPINET-KSP integrates high-confidence interactomes (SIGNOR, BioGRID, STRING), structural contacts obtained from AlphaFold3, ESM-3 sequence embeddings, and a 512-dimensional cell-state manifold with 1612 quantitative phosphoproteomic conditions. A heterogeneous KSP graph is examined utilising a cross-attention Graphormer with Reversible Triad Attention to mimic kinase–phosphatase antagonism. SPINET-KSP, pre-trained on 3.41 million validated phospho-sites utilising masked phosphorylation modelling and contrastive cell-state learning, achieves an AUROC of 0.852 for kinase-family classification (sensitivity 0.821, specificity 0.834, MCC 0.655) and a Pearson correlation coefficient of 0.712 for phospho-occupancy prediction. In distinct 2025 mass spectrometry datasets, it identifies 72% of acknowledged cancer-resistance triads within the top 10 rankings and uncovers 247 supplementary triads validated using orthogonal proteomics. SPINET-KSP is the first foundational model for simulating context-dependent reversible phosphorylation, enabling the targeting of dysregulated kinase-phosphatase pathways in diseases.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4010002

Authors: Chantal Reigada Melisa Sayé Fabio Augusto Digirolamo Mariana Reneé Miranda

Trypanosoma cruzi is the protozoan parasite responsible for Chagas disease, a neglected tropical disease caused by trypanosomatids. Its success as pathogen relies on remarkable metabolic adaptability, stress tolerance, and complex interactions with mammalian hosts. Among the proteins contributing to these processes, nucleoside diphosphate kinases (NDPKs) and arginine kinase (AK) have emerged as central enzymes for parasite metabolism. NDPKs, beyond their canonical role in nucleotide homeostasis, are implicated in DNA repair and oxidative stress responses and are also secreted enzymes. AK, on the other hand, serves as a unique energy-buffering system absent in mammals, supporting parasite growth and adaptation to oxidative and metabolic stresses, including modulation of host immunity. Both enzymes display distinct subcellular localizations all along the parasite and through the life cycle, linking them to multiple roles important for parasite biology and survival. Recent studies have highlighted the impact of interfering these enzymes with several compounds on the viability of the organisms, suggesting new avenues to explore them as drug targets. This review provides a general overview of NDPKs and AK in T. cruzi, aiming to underline their relevance to a broader context of trypanosomatids. Their study not only broadens our understanding of parasite biology but also opens perspectives for applied research, including therapeutic alternatives for Chagas and related diseases.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases4010001

Authors: Christian Werner Tatjana Barthel Hugo Harasimowicz Christelle Marminon Manfred S. Weiss Marc Le Borgne Karsten Niefind

CK2α and CK2α’, two paralogous members of the human kinome, are catalytic subunits of protein kinase CK2. Together with the regulatory subunit CK2β, they form heterotetrameric holoenzymes. CK2 is the subject of efforts to develop effective and selective inhibitors. For this, secondary binding sites remote from the canonical ATP/GTP cavity are critical. A crystallographic fragment screening with CK2α’ crystals and an established molecular fragment collection was performed to identify new ligands at known or novel sites. It resulted in fourteen CK2α’/fragment structures. Five fragments were found at the CK2β interface of CK2α’ and three fragments at the established αD pocket, which exhibits subtle differences between CK2α and CK2α’; comparative co-crystallisations with CK2α showed that one of them binds to the αD pocket of CK2α’ exclusively. No fragments bound at the substrate-binding region of CK2α’, but a CK2α’ structure with dp10, a decameric section of the substrate-competitive inhibitor heparin, and the indenoindole-type ATP-competitive inhibitor 4w was determined. A comparison with a published CK2α/dp10 structure revealed features consistent with reports about substrate specificity differences between the isoenzymes: dp10 binds to CK2α’ and CK2α with opposite strand orientations, and the local conformations of the isoenzymes in the helix αD region are significantly different.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040027

Authors: Patricia A. Quispe Daniel Lietha Ignacio E. León Martin J. Lavecchia

Focal Adhesion Kinase (FAK) is a key regulator of tumor cell migration and survival, and its persistent overexpression in aggressive cancers has motivated ongoing efforts to identify novel small-molecule inhibitors. Despite this interest, progress in discovering new potent scaffolds has been limited. In this work, we applied a multistep computational workflow followed by experimental testing to refine hit selection and reduce the false positives typically associated with docking. DrugBank and several commercial libraries were screened using Exponential Consensus Ranking (ECR) docking, and molecular dynamics simulations were used to assess pose stability and interaction persistence. A subset of predicted binders was then tested in MG-63 (bone cancer) and MDA-MB-231 (breast cancer) cells using cell viability and wound-healing assays, followed by direct autophosphorylation assays with recombinant FAK. Several repurposed compounds, including clofazimine and tafamidis, produced clear dose-dependent effects on cell migration, although their inhibitory activity in biochemical assays remained weak (IC50 values above 100 μM), far from the potency of the reference inhibitor TAE226. Retrospective analysis of the computational workflow showed that standard MM-GBSA calculations did not correlate with these experimental outcomes. However, incorporating explicit water molecules through the NWAT-MMGBSA approach improved agreement with the biochemical data and helped to rationalize the limited affinity observed experimentally. Taken together, the results underline the relevance of explicit solvation in modeling the FAK active site and suggest that refined solvent-aware protocols may provide more reliable guidance for future screening efforts.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040026

Authors: Arpana Yadav Phulwanti Kumari Sharma Mayuree Hazarika Pragya Gehlot Saloni Bage Mahesh Saini Kritika Gaur Acham Parambath Aswathi Malti Thakur Devesh Madhukar Sawant Agam Prasad Singh Daniela Brünnert Pankaj Goyal

Malaria remains one of the devastating illnesses, and drug-resistant malaria has incurred enormous societal costs. A few host kinases are vital for the liver stage malaria and might be promising drug targets against drug-resistant malaria. STK35L1 is one of the host kinases that is highly upregulated during the liver stage of malaria, and the knockdown of STK35L1 significantly suppresses Plasmodium sporozoite infection. In this study, we retrieved the promoter region of STK35L1 based on 5′ complete transcripts, transcription start sites, and cap analysis of gene expression tags. Furthermore, we identify transcriptionally active regions by analyzing CpG islands, histone acetylation (H3K27ac), and histone methylation (H3K4me3). It suggests that the identified promoter region is active and has cis-regulatory elements and enhancer regions. We identified various putative transcription factors (TFs) from the various high-throughput ChIP data that might bind to the promoter region of STK35L1. These TFs were differentially regulated during the infection of Plasmodium sporozoites in HepG2 cells. Our molecular modeling study suggests that, except for SMAD3, the identified TFs may be directly bound to the promoter. Together, the data suggest that these TFs may play a role in sporozoite infection and in regulating STK35L1 expression during the liver stage of malaria.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040025

Authors: Anna Karolyna da Costa Machado Beatriz Maria Dias Nogueira Deivide de Sousa Oliveira Caio Bezerra Machado Flávia Melo Cunha de Pinho Pessoa Leidivan Sousa Cunha Igor Valentim Barreto Isabelle Magalhães Farias Rodrigo Monteiro Ribeiro Ana Paula Lopes Moreira Kaira Mara Cordeiro de Albuquerque Mateus de Paula Gomes Fabiana Aguiar Carneiro Silva Lívia Andrade Gurgel Gésio Eduardo Antas Rodrigues Ricardo Parente Garcia Vieira André Salim Khayat Ana Virgínia Soares Van Den Berg Manoel Odorico de Moraes Filho Maria Elisabete Amaral de Moraes Caroline Aquino Moreira-Nunes

Acute myeloid leukemia (AML) is one of the most aggressive types of leukemia, represented by the clonal proliferation of hematopoietic precursors, which mainly promotes quantitative and differentiation alterations, as well as normal hematopoiesis suppression. Throughout leukemogenesis, modifications may occur in several elements that make up cellular signaling pathways; among these, AURKA, AURKB, and PLK1 are key related regulators of mitotic progression and cellular proliferation. This study investigated the hematological profile and the expression of the AURKA, AURKB, and PLK1 genes in a cohort of individuals with AML, in order to understand their roles in the pathophysiology of the disease. The analyses revealed a significant hypoexpression of AURKA in the bone marrow of AML individuals compared to the control group (p = 0.0254) and AURKB showed no significant difference in bone marrow and peripheral blood samples. It was also observed a hyperexpression of PLK1 in bone marrow (p < 0.0001) and in peripheral blood (p = 0.0144). Our results also point to PLK1 as a potential biomarker for AML, since its hyperexpression did not differ with respect to gender, risk stratification, or age of the individuals. Finally, survival analyses indicate that AURKA expression in the bone marrow is associated with a protective factor and increased survival, and that those with higher expression of the three target genes had a lower mortality rate (p = 0.043).

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040024

Authors: Exequiel E. Barrera Marina Uhart Diego M. Bustos

Eukaryotic phosphorylation of serine and threonine residues is a central regulatory mechanism in cell signalling, carried out by more than 500 kinases and a diverse array of phosphatases. Traditionally understood as a two-component system driven by writers (kinases) and erasers (phosphatases), this regulatory network is now appreciated to involve additional proteins that modulate or interpret phosphorylation-dependent changes. Among them, the 14-3-3 protein family has emerged as a prominent example due to its ability to bind phosphorylated serine/threonine motifs—typically located within intrinsically disordered regions—and influence the activity, stability, or localization of its partners. In this review, we discuss the importance, evolution, structure, and dynamics of 14-3-3 proteins, as well as their interactions with small molecules—both natural and designed—that bind to them. We highlight several underexplored aspects of their molecular behaviour, integrate recent discoveries, and emphasize how these insights contribute to a broader understanding of phosphorylation-dependent regulation across eukaryotes.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040023

Authors: Dina Bárbara Aguado-Herrera Yudith Cañizares-Carmenate Edeildo Ferreira da Silva-Júnior

Polo-like kinase 1 (PLK1) is a serine/threonine kinase that orchestrates multiple critical events during mitosis, including centrosome maturation, spindle assembly, kinetochore–microtubule attachment, and cytokinesis. Dysregulation and overexpression of PLK1 are frequently observed in various cancers, correlating with increased proliferation, metastatic potential, and poor prognosis, which highlights its potential as a therapeutic target. Traditional small-molecule inhibitors have predominantly focused on the ATP-binding site of the N-terminal kinase domain, effectively inducing mitotic arrest and apoptosis in tumor cells; however, these compounds often suffer from limited selectivity and off-target toxicity. The C-terminal Polo-box domain (PBD), responsible for substrate recognition and subcellular localization, has emerged as an alternative and highly selective target for inhibitor design, enabling the disruption of protein–protein interactions critical for PLK1 function. Here, we present a comprehensive review demonstrating the potential inhibition of several compounds against PLK1. This work establishes a foundation for future preclinical development of small molecule-based therapeutics against PLK1-dependent malignancies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040022

Authors: Nicholas G. Wilson Jesse S. Basra Isabel Dominguez

Protein kinase CK2 is an important regulator of cell, embryo, and organism function whose transcript levels are often dysregulated in disease. Previous studies have primarily focused on the regulation of CK2 gene expression via the proximal promoter. Here, we analyzed the core promoter of the CK2 genes and pseudogene to assess the structure and potential regulatory elements. Our analysis showed that CSNK2A1 contained 14 exons, rather than 13 exons as previously reported. Using FANTOM5 and DBTTS data, we found that transcription start sites were broadly distributed across a 100-nucleotide region in the CK2 gene core promoters, consistent with “broad” class promoter architecture. Using these databases, we found a dissimilar transcription start site usage between adult and cancer tissues compared to fetal tissues for each of the CK2 gene promoters. A further analysis of the CK2 gene core promoter subregions showed instances of core promoter subregion switching. All CK2 gene core promoters contained canonical and non-canonical initiator motifs, suggesting their potential as dual-initiator core promoters, while CSNK2A3 only had canonical initiator motifs. Additionally, all CK2 gene core promoters contain DCE motifs and pause buttons. In contrast, Wnt/β-catenin target genes c-MYC and CCND1 had DPEs, which can be regulated by protein kinase CK2. Collectively, our data provides new insights into the transcriptional regulation of CK2 genes and opens new avenues for research.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040021

Authors: Azizah Alamro Thanih Balbaied

Metal–organic frameworks (MOFs) have been increasingly recognized as promising platforms for enzyme modulation, owing to their tunable porosity, high surface area, and versatile chemical functionality. In this review, the potential of MOFs for the inhibition and modulation of protein kinases and phosphatases—key regulators of cellular signaling and disease progression—is examined. The structural fundamentals of MOFs are outlined, followed by a discussion of common synthesis strategies, including solvothermal, microwave-assisted, sonochemical, and mechanochemical methods. Emphasis is placed on how synthesis conditions influence critical features such as particle size, crystallinity, surface chemistry, and functional group accessibility, all of which impact biological performance. Four primary mechanisms of MOF–enzyme interaction are discussed: surface adsorption, active site coordination, catalytic mimicry, and allosteric modulation. Each mechanism is linked to distinct physicochemical parameters, including pore size, surface charge, and metal node identity. Special focus is given to biologically relevant metal centers such as Zr4+, Ce4+, Cu2+, Fe3+, and Ti4+, which have been shown to contribute to both MOF stability and enzymatic inhibition through Lewis acid or redox-mediated mechanisms. Recent in vitro studies are reviewed, in which MOFs demonstrated selective inhibition of disease-relevant enzymes with minimal cytotoxicity. Despite these advancements, several limitations have been identified, including scalability challenges, limited physiological stability, and potential off-target effects. Strategies such as post-synthetic modification, green synthesis, and biomimetic surface functionalization are being explored to overcome these barriers. Through an integration of materials science, coordination chemistry, and molecular biology, this review aims to provide a comprehensive perspective on the rational design of MOFs for targeted enzyme inhibition in therapeutic contexts.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3040020

Authors: Mark Bouska Eduardo Callegari Daniela Paez Xuejun Wang

SH3 Domain Binding Kinase Family Member 2 (SBK2) is a critical kinase in atrial cardiomyocyte differentiation. However, its phospho-targets, its role in ventricle function, and its role in cardiac disease progression are unknown. Notably, SBK2 has been shown to be downregulated in the ventricular myocardium of several mouse models that recapitulate human desmin-related cardiomyopathies. To restore SBK2 expression, adenoviruses were constructed to promote cardiomyocyte-restricted SBK2 expression and injected at postnatal day 0. This significantly increased ejection fraction at 1 month of age relative to control hearts. However, in 3-month nontransgenic (NTG) and desmin-related cardiomyopathy hearts, the overexpression of SBK2 opposed increases in ejection fraction and left ventricular posterior wall thickness. These findings provide the first in vivo evidence that SBK2 plays a vital role in left ventricular function. To elucidate the molecular mechanism behind the physiological effects of SBK2 on the heart, we performed mass spectrometry combined with phospho-enrichment on ventricular tissue with and without SBK2 overexpression. We identified multiple phosphorylation sites on SBK2 and used AlphaFold3 to model how this phosphorylation likely affects SBK2’s role in phosphorylating the splicing factor SRSF7. We propose a novel mechanism by which SBK2 regulates splicing to promote cardiomyocyte development.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3030019

Authors: Alexander Wlodawer Pawel Rubach Zbigniew Dauter Wojciech Dec Wladek Minor Dariusz Brzezinski Mariusz Jaskolski

We have evaluated the quality of all 325 deposits in the PDB (as of December 2024) that correspond to (or contain) the catalytic domain of cAMP-dependent protein kinases (PKA). Detailed analysis was possible for 289 deposits of crystal structures that included not only the atomic coordinates but also structure factors. These structures represent 35 years of studies, and it is not surprising that the more recent structures are generally of better quality than the older ones. We did not encounter deposits with very severe problems, although some minor problems were found. To assess whether a uniform method of structure re-refinement, as implemented in the pipeline and website PDB-REDO, leads to significant improvement of structural models, we compared structure quality indicators for the originally refined structures and their counterparts resulting from PDB-REDO refinement. The re-refinement procedure significantly improved only some older structures, while its success was generally limited. We paid particular attention to the quality of small-molecule ligands, finding that most of them fit the electron density very well. This type of analysis helps identify the highest quality structures among many deposits for certain protein families and, thus, could be extended to other groups of proteins as well.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3030018

Authors: Sara Sadat Aghamiri Rada Amin

Digital twin is a mathematical model that virtually represents a physical object or process and predicts its behavior at future time points. These simulation models enable a deeper understanding of tumorigenic processes and improve biomarker discovery in cancer research. Tumor microenvironment is marked by dysregulated signaling pathways, where kinases and phosphatases serve as critical regulators and promising sources for biomarker discovery. These enzymes operate within multiscale and context-dependent processes where spatial and temporal coordination determine cellular outcomes. Digital Twin technology provides a platform for multimodal and multiscale modeling of kinase and phosphatase processes at the patient-specific level. These models have the potential to transform biomarker validation processes, enhance the prediction of therapeutic responses, and support precision decision-making. In this review, we present the major alterations affecting kinases and phosphatase functions within the tumor microenvironment and their clinical relevance as biomarkers, and we address how digital twins in oncology can augment and refine each stage of the biomarker discovery pipeline. Introducing this emerging technology for cancer biomarker discovery will assist in accelerating its adoption and translation into precision diagnostics and targeted therapies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3030017

Authors: Mauro Salvi Maria Ruzzene

The first described instance of protein kinase activity dates back more than half a century [...]

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3030016

Authors: Ayan Saha Emily Wood Luna Omeragic Maya Minkara Kethain Marma Shipan Das Gupta Jannatul Ferdoush

Non-alcoholic fatty liver disease (NAFLD) is a common metabolic condition characterized by hepatic lipid deposits, insulin resistance, and inflammation which may progress to non-alcoholic steatohepatitis (NASH) and fibrosis. Protein kinases play an important role in NAFLD development by regulating metabolic and inflammatory pathways. Mitogen-activated protein kinases (MAPKs), protein kinase C (PKC), AMP-activated protein kinase (AMPK), phosphoinositide 3-kinase (PI3K)/AKT, and mechanistic target of rapamycin (mTOR) are all involved in NAFLD and NASH progression. Emerging evidence indicates that Farnesoid X Receptor (FXR) agonists have therapeutic potential by modulating bile acid metabolism, lipid balance, and inflammatory responses. This review examines the mechanistic interplay between FXR agonists and important protein kinases in NAFLD and NASH. FXR agonists activate AMPK, which promotes fatty acid oxidation and reduces hepatic steatosis. They also regulate MAPK signaling, which reduces c-Jun NH2-terminal kinase (JNK)- and p38 MAPK-mediated inflammation. Furthermore, FXR agonists activate the PI3K/AKT pathway, enhancing insulin sensitivity and modulating mTOR signaling to reduce hepatic fibrosis. Clinical studies in NAFLD/NASH indicate that FXR agonists confer metabolic and anti-inflammatory benefits, although optimizing efficacy and minimizing adverse effects remain challenging. Future studies should focus on combination therapies targeting FXR alongside specific kinases to improve therapeutic outcomes. This review highlights the potential of FXR agonists to modulate protein kinase signaling, opening new avenues for targeted NAFLD/NASH therapy.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3030015

Authors: Gregory A. Imbrie Nicholas G. Wilson David C. Seldin Isabel Dominguez

CK2α is a kinase important for essential cellular and biological processes. CK2α is ubiquitously expressed, albeit at different tissue levels, and its transcript levels are dysregulated in disease. However, there is limited knowledge on the regulation of CK2α gene expression. The best one studied, the human CSNK2A1 (CK2α) gene promoter, contains uncharacterized binding motifs for NF-κB. Our goal was to investigate the role of NF-κB in Csnk2a1 promoter regulation. We cloned the mouse Csnk2a1 promoter which had significant sequence homology with the human CSNK2A1 promoter. Using promoter deletions, we identified a minimal promoter region containing transcription factor motifs (NF-κB, Ets-1, Sp1) consistent with those published for the CSNK2A1 promoter. Electrophoretic mobility shift assays demonstrated specific NF-κB subunit binding to the minimal promoter. NF-κB subunit transfection and extracellular NF-κB stimulation in non-tumor cell lines led to increased transactivation of the mouse minimal promoter. These data, together with data on the regulation of NF-κB by CK2 kinase activity, suggest a positive-feedback loop between CK2α and NF-κB. Non-tumor cell line re-plating and increased percent confluence upregulated Csnk2a1 transcript levels which differed from tumor cell line published data. In summary, Csnk2a1 promoter is regulated by NF-κB signaling and during cellular proliferation.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3030014

Authors: Yong Everett Zhang

Protein kinases and phosphatases are essential for post-translational regulation, enabling bacteria to adapt to environmental stresses and modulate virulence. While prior reviews have broadly covered their roles in stress response, antibiotic resistance, and virulence, this article updates specifically on the roles of histidine kinases (HKs) and serine/threonine kinases (STKs) in mediating phage-bacteria interactions. A key aspect is phage-encoded kinases, which hijack bacterial signalling by phosphorylating and disrupting host processes to promote infection. Despite their importance, significant gaps remain in understanding these regulatory networks. This microreview highlights both the unresolved mechanisms and the therapeutic potential of targeting kinase pathways—for instance, by disrupting phage evasion strategies or enhancing phage-based antimicrobial therapies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3030013

Authors: Tomoya Nakamura Tomohiko Nakao Yuri Kominami Miho Ito Teruki Aizawa Yusuke Akahori Hideki Ushio

Obesity causes lifestyle-related diseases such as hypertension and type 2 diabetes and has become a global health concern. L-fucose (Fuc), a monosaccharide that can be derived from brown algae, has been shown to strongly suppress lipid droplet accumulation in 3T3-L1 murine adipocytes at high concentrations via the activation of AMP-activated kinase (AMPK). Although low concentrations of Fuc also exhibited similar effects, the underlying mechanisms remain unclear. In this study, we investigated the effects of low-level Fuc on lipid metabolism, focusing on the role of fucosylation. Low-level Fuc did not induce AMPK phosphorylation but suppressed lipid droplet accumulation. This suppressive effect was abolished by co-treatment with the fucosylation inhibitor 2F-Peracetyl-Fucose (2F-PAF), suggesting that fucosylation plays a key role in the observed metabolic regulation. Furthermore, proteomic analysis combined with click chemistry pulldown suggested that proteins involved in the regulation of lipid metabolism, such as acetoacetyl-CoA synthetase enzymes and catalytic subunit alpha of cAMP-dependent protein kinase, are fucosylated or interact with fucose. These findings provide novel insights into the anti-obesity mechanisms of Fuc and highlight the physiological significance of protein fucosylation in adipocyte lipid metabolism.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3020012

Authors: Arpana Yadav Kritika Gaur Phulwanti Kumari Sharma Pragya Gehlot Saloni Bage Mahesh Saini Daniela Brünnert Pankaj Goyal

Dysregulation of protein kinases is associated with developmental defects and various human diseases. The human kinome comprises 518 kinases, including several orphan kinases whose functions remain to be fully characterized. The NKF4 family, which includes STK35L1 and PDIK1L, is one such uncharacterized kinase family. STK35L1, also known as Clik1, was initially identified as a nuclear kinase associated with actin fibers. Subsequent studies have demonstrated that STK35L1 plays critical roles in cellular processes such as cell cycle regulation, migration, angiogenesis, the DNA damage response, and related processes such as spermatogenesis. STK35L1 has also been implicated in various developmental processes and its knockout mice exhibited defects in the testis, ovary, and eye. STK35L1 acts as a central regulator of the fundamental cellular functions, and its dysregulation leads to various diseases. Research has established that STK35L1 regulates tumor growth and proliferation in cancers such as osteosarcoma, colorectal cancer, and acute myeloid leukemia. Notably, it also affects chemosensitivity in colorectal cancer and metabolism in acute myeloid leukemia. Additionally, STK35L1 is crucial for the infection of hepatocytes by Plasmodium sporozoites during the liver stage of Malaria. This review discusses the current understanding of STK35L1, highlighting its role in various diseases.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3020011

Authors: Anastasia Tzereme Michalis Koureas Athanasios Manouras Eleni Malissiova Georgia Soultani Konstantina Poulianiti Eleni Gogou

The European Food Safety Authority (EFSA) has raised concerns regarding the use of alkaline phosphatase (ALP) as a pasteurization marker in non-cow milk due to compositional differences. This study investigates the thermal inactivation kinetics of ALP in six milk species (cow, sheep, goat, donkey, buffalo and camel) to assess its reliability as an indicator. The thermal inactivation of ALP in different milk types was evaluated by heating samples at 63–75 °C at various times, then measuring residual enzyme activity using a spectrophotometric method. The results revealed a sharp increase in ALP inactivation with rising temperatures, consistent with previous findings on the enzyme’s thermal sensitivity. Notably, donkey milk exhibited the highest ALP inactivation at 72 °C, probably due to lower fat content compared to the rest of milk types studied, while camel milk showed the lowest inactivation rate constant (kT) at 75 °C, highlighting its higher heat resistance compared to bovine milk. These findings highlight potential limitations of using the ALP test to verify pasteurization in non-bovine milk, which is directly linked to microbial safety, as well as the preservation of nutritional and sensory characteristics. This study reinforces the importance of considering milk composition, particularly fat and protein structures, in optimizing pasteurization conditions for diverse milk varieties.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3020010

Authors: Zahraa Qusairy Miran Rada

Bruton’s tyrosine kinase (BTK) is a key signaling molecule involved in both hematological malignancies and solid tumors. In B-cell malignancies such as chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphoma (NHL), BTK mediates B-cell receptor signaling, promoting tumor survival and proliferation, leading to the development of BTK inhibitors like ibrutinib that improve patient outcomes. In solid tumors, BTK isoforms, particularly p65BTK, contribute to tumor growth and therapy resistance, with inhibition showing promise in cancers like colorectal, ovarian, and non-small cell lung cancer. BTK also influences the tumor microenvironment by modulating immune cells such as myeloid-derived suppressor cells and tumor-associated macrophages, aiding immune evasion. BTK inhibition can enhance anti-tumor immunity and reduce inflammation-driven tumor progression. Additionally, BTK contributes to tumor angiogenesis, with inhibitors like ibrutinib showing anti-angiogenic effects. Beyond cancer, BTK is linked to aging, where its modulation may reduce senescent cell accumulation and preserve cognitive function. This review explores BTK’s dual role, focusing on its oncogenic effects and potential impact on aging processes. We also discuss the use of BTK inhibitors in cancer treatment and their potential to address age-related concerns, providing a deeper understanding of BTK as a therapeutic target and mediator in the complex relationship between cancer and aging.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3020009

Authors: Yana Gvozdeva

Kinase inhibitors are small molecules that block kinase activity and have significant applications in both therapy and diagnostics. Recent studies suggest that these inhibitors hold great potential as targets for treating a range of diseases, including autoimmune disorders, cardiovascular conditions, cancer, and inflammatory diseases like ulcerative colitis. Ongoing research focuses on developing effective carriers for tyrosine kinase inhibitors (TKIs) to enhance treatment outcomes while reducing side effects. The nano-scale drug carriers have demonstrated the ability to encapsulate a wide range of imaging and therapeutic agents, enhancing tumor diagnosis and treatment. Notably, the incorporation of drugs with poor pharmacokinetics into nanocarriers enhances their solubility and stability, offering a renewed opportunity to assess their full therapeutic potential. The entrapped agents can be released in a controlled manner to maintain a specific drug concentration within a treatment framework or triggered by specific stimuli such as time or pH to target particular tissues or cells. The multifunctionality of nanosystems offers a promising avenue for developing innovative tyrosine kinase inhibitor (TKI) delivery strategies that serve as alternative treatment options for cancer and other inflammatory diseases. This review aims to provide a comprehensive overview of innovative nano-scale delivery systems for TKIs, both as standalone treatments and in combination with other therapeutic agents or drug delivery approaches. We discuss their comparative advantages and limitations for future small-molecule TKIs research.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3020008

Authors: Bhuvanesh Sukhlal Kalal

Melanoma, known for its aggressive nature and propensity for developing drug resistance, remains a significant clinical challenge. The emergence of resistance to both targeted therapies (like BRAF/MEK inhibitors) and immunotherapies is a major obstacle to achieving durable responses and improving patient survival. HDACs, a class of epigenetic enzymes, modulate gene expression and chromatin structure by removing acetyl groups from histone and non-histone proteins. In melanoma, aberrant HDAC activity contributes to resistance through multiple mechanisms. HDACs influence key oncogenic signaling pathways frequently dysregulated in melanoma, such as the MAPK, PI3K/AKT, and WNT/β-catenin cascades. By altering the activity of these pathways, HDACs promote the survival and proliferation of melanoma cells even in the presence of therapy. Beyond their direct effects on tumor cells, HDACs also play a crucial role in shaping the tumor microenvironment. They can suppress anti-tumor immune responses by reducing immune cell infiltration, modulating cytokine production, and fostering an immunosuppressive milieu. This further contributes to resistance to immunotherapies. Given the central role of HDACs in these resistance mechanisms, HDAC inhibitors (HDACis) have emerged as potential therapeutic agents to restore drug sensitivity. HDACis can induce cell death, inhibit proliferation, and enhance immune responses in melanoma cells. Preclinical and clinical studies have explored the combination of HDACis with existing therapies to overcome resistance. While promising, the clinical application of HDACis is accompanied by challenges, including toxicity, the need for biomarkers to predict response, and the optimization of combination strategies. Ongoing research is dedicated to developing more selective and potent HDACis and to better understand how to effectively incorporate them into melanoma treatment regimens. This review provides a comprehensive overview of the multifaceted ways in which HDACs contribute to melanoma drug resistance and discusses the potential of HDAC-targeted therapies to improve patient outcomes.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3020007

Authors: Claudina A. Pérez-Novo Amber Driesen Maaike Van Trimpont Claudia Theys Emilie Logie Pieter Van Vlierberghe Wim Vanden Berghe

T-cell acute lymphoblastic leukaemia (T-ALL) is an aggressive neoplastic malignancy characterised by the accumulation of multiple oncogenic and epigenetic alterations in haematopoietic T-cell precursors leading to their uncontrolled proliferation and accumulation in the bone marrow. For many years it has been established that the occurrence of activating mutations, alterations in transcription factors expression, impairment in cell cycle regulators, and hyperactivation of NOTCH1 signalling play prominent roles in the pathogenesis of this disease. Recently, the introduction of high-resolution screening and next-generation sequencing platforms revealed that T-cell progenitors accumulate additional mutations, affecting protein kinase signalling, protein translation, and epigenetic control mechanisms, providing novel attractive targets for therapy. While the contributions of direct genomic events are well understood as causative agents of hyperactive kinase signalling pathways, the epigenetic rewiring of kinase signalling cascades via DNA methylation, histone post-translational modifications, and non-coding miRNAs remains less well explored. In this review, we provide novel perspectives on epigenetic regulatory aspects of kinase signalling heterogeneity in T-ALL pathogenesis and therapeutic outcomes.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3010006

Authors: Alison D. Axtman

Human protein kinases are ubiquitously expressed throughout the human body and embedded in signaling pathways that mediate diverse biology [...]

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3010005

Authors: Juan I. Cortelezzi Martina Zubillaga Victoria R. Scardino María N. Muñiz García Daniela A. Capiati

Protein phosphatase 2A (PP2A) is a highly conserved heterotrimeric enzyme complex present in all eukaryotic cells, consisting of a scaffolding A subunit, a catalytic C subunit, and a regulatory B subunit. The A and C subunits form the core enzyme, which interacts with the B subunit to determine the substrate specificity, subcellular localization, and enzymatic activity of the holoenzyme. The Arabidopsis thaliana genome encodes five C subunits, three A subunits, and 17 B subunits, enabling the formation of diverse holoenzymes with extensive functional versatility. Genetic evidence highlights the essential role of PP2A in regulating various physiological processes in plants, including responses to abiotic and biotic stresses and developmental programs. Notably, PP2A can act as both a positive and negative regulator within the same pathway, while individual subunits often participate in multiple processes. This functional diversity arises from the structural flexibility of PP2A. This review examines the structural diversity of plant PP2A and its regulatory roles across diverse physiological contexts.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3010004

Authors: Luca P. Otvos Giulia I. M. Garrito Gabriel E. Jara Paulo S. Lopes-de-Oliveira Luciana E. S. F. Machado

Coronavirus disease 2019 is a multi-systemic syndrome that caused a pandemic. Proteomic studies have shown changes in protein expression and interaction involved in signaling pathways related to SARS-CoV-2 infections. Protein phosphatases play a crucial role in regulating cell signaling. In this study, we assessed the potential involvement of protein phosphatases and their associated signaling pathways during SARS-CoV-2 infection by conducting a meta-analysis of proteome databases from COVID-19 patients. We identified both direct and indirect interactions between human protein phosphatases and viral proteins, as well as the expression levels and phosphorylation status of intermediate proteins. Our analyses revealed that PPP2CA and PTEN are key phosphatases involved in cell cycle and apoptosis regulation during SARS-CoV-2 infection. We also highlighted the direct involvement of PPP2CA in the cell division throughout its interaction with CDC20 protein (cell division cycle protein 20 homolog). This evidence strongly suggests that both proteins play critical roles during SARS-CoV-2 infection and represent potential targets for COVID-19 treatment.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3010003

Authors: Tadashi Nakagawa Makiko Nakagawa

Phosphodegrons are critical motifs that play a pivotal role in the regulation of protein stability and function via phosphorylation-dependent signaling pathways. These motifs serve as recognition elements for ubiquitin ligases, facilitating the targeted degradation of proteins. By modulating key cellular processes such as cell cycle progression, DNA repair, and apoptosis, phosphodegrons are essential for maintaining cellular homeostasis. Dysregulation of phosphodegrons has been implicated in a wide range of diseases, including cancer and neurodegenerative disorders, highlighting their potential as therapeutic targets. This review provides an overview of phosphodegron functions along with their biological significance in health and disease. Additionally, we discuss current methodologies for studying phosphodegrons and explore emerging trends in their identification and therapeutic targeting. By synthesizing recent advances in the field, this article aims to offer insights into the future directions and challenges in phosphodegron research, ultimately underscoring their importance in cellular regulation and disease pathology.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3010002

Authors: Djamilatou Adom Jiuhui Wang Man-Tzu Wang Daotai Nie

Tribbles Pseudokinase 3 (TRIB3) is a negative regulator of cellular signaling, particularly the PI3K-Akt and NF-κB pathways. Aberrant TRIB3 expressions have been reported in a number of cancers, but its role in tumor growth and progression remains controversial since both oncogenic and tumor suppressive activities have been reported. The goal of this study is to understand the roles of TRIB3 in prostate cancers through bioinformatic queries of public databases and experimental evaluations through gain-of-function and loss-of-function approaches. Here we report that there was increased TRIB3 gene expression with a Z-score over 2, relative to normal samples, in 26% of prostate cancers. Increased TRIB3 expression was associated with increased mutation counts and aneuploidy scores of prostate cancers. Increased TRIB3 expression was also associated with reduced progression-free or disease-free survival of prostate cancer patients. However, our experiments found that increased TRIB3 expression actually had an antiproliferative effect and increased cell cycle arrest at the G2/M phase. Depletion of the endogenous TRIB3 expression enhanced cell proliferation and reduced the level of Cdc25C phosphatase. Our results suggest that although TRIB3 expression was increased in prostate cancers in association with increased genomic instabilities, TRIB3 actually promoted cell cycle arrest and reduced tumor cell proliferation.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases3010001

Authors: Olawale O. Taiwo Kenneth B. Storey

Freeze tolerance is a remarkable adaptive trait exhibited by wood frogs (Rana sylvatica) during their hibernation period. To show the epigenetic mechanisms that contribute to kidney protection during freezing stress, this present study provides the first investigation of the role and dynamics of histone arginine methylation and the expression of protein arginine methyltransferases (PRMTs) in a freeze-tolerant vertebrate. Kidney samples from three groups were assessed: (a) control frogs acclimated at 5 °C, (b) 24 h frozen frogs, and (c) 8 h thawed frogs. Our findings revealed significant downregulation of PRMT1, PRMT3, and PRMT5 in kidneys from frozen wood frogs compared to the control group. This downregulation indicates a potential role for PRMT enzymes in the regulation of arginine methylation under freezing stress. In addition, we observed distinct changes in histone marks. H3R17me2a showed significant upregulation after 24 h of freezing, potentially indicating its involvement in the activation of genes related to freezing survival. By contrast, H3R26me2a was downregulated after both 24 h freezing and 8 h thawing, whereas H3R8me2a showed sustained levels after freezing but was downregulated after thawing. These findings highlight the dynamic nature of histone arginine methylation and PRMT expression in wood frog kidneys during freezing–thawing. Our results indicate that epigenetic modifications play a crucial role in shaping the adaptive responses of wood frog kidneys to freezing stress and contribute new information on the underlying biochemical modifications that support vertebrate freeze tolerance.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2040025

Authors: Sara Sadat Aghamiri Rada Amin

Glioblastoma stem cells (GSCs) are key drivers of relapse, metastasis, and therapy resistance in glioblastoma due to their adaptability and diversity, which make them challenging to target effectively. This study explores the O-glycosylation in differentiating two key GSC subtypes, CD133 and CD44. We utilized the TCGA dataset of GBM and presented the reproducible bioinformatics analysis for our results. Our profiling showed enriched O-glycosylation signatures in CD44-expressing GBM cells over CD133, with Cosmc, the chaperone for core mucin-type O-glycosylation, significantly upregulated in the CD44-positive group. Moreover, Cosmc was associated with shorter progression-free intervals, suggesting its potential as an indicator of aggressive disease. High Cosmc expression also enriched immune-related pathways, including inflammatory response and antigen presentation, and was associated with presence of myeloid cells, T cells, and NK cells. Additionally, elevated Cosmc correlated with extracellular matrix (ECM) pathways and stromal cell populations, such as perivascular fibroblasts. These findings position O-glycosylation, specially, Cosmc as a promising biomarker for distinguishing GSC subclones, with relevance to immune modulation, and ECM dynamics, identifying it as a potential target for novel GBM therapies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2040024

Authors: Luiz Fernando Carvalho-Kelly Anita Leocadio Freitas-Mesquita Thaís Souza Silveira Majerowicz José Roberto Meyer-Fernandes

Phytomonas is the only kinetoplastid that can parasitize plants, causing economically relevant issues. Phytomonas serpens share similarities with pathogenic trypanosomatids, including surface enzymes that are involved in adhesion to the salivary gland of their experimental host, the insect Oncopeltus fasciatus. Ectophosphatases are cell surface enzymes involved in host–parasite interactions that are widely distributed among microorganisms. This work aimed to perform the biochemical characterization of P. serpens ectophosphatase activity, investigating and discussing its possible physiological role. This activity presented an acidic profile, and its kinetic parameters Km and Vmax were calculated as 1.57 ± 0.08 mM p-NPP and 10.11 ± 0.14 nmol p-NP/(h × 108 flagellates), respectively. It was stimulated by cobalt, inhibited by zinc, and insensitive to EDTA, a divalent metal chelator. The inhibitor sodium orthovanadate was able to decrease P. serpens ectophosphatase activity and growth, suggesting its involvement in cell proliferation. Given that P. serpens can uptake inorganic phosphate (Pi) from the extracellular medium, it is likely that its ectophosphatase activity acts together with the transport systems in the Pi acquisition process. The elucidation of the molecular mechanisms involved in this process emerges as a relevant perspective, providing new strategies for controlling Phytomonas infection.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2040023

Authors: Lorena Martínez-Alcantar Laura Hernández-Padilla Alma Laura Díaz-Pérez Lizbeth Guadalupe Villalón-Magallán Mayra Xóchitl Durán-Maldonado César Díaz-Pérez Marlene E. Campos-Morales Citlali Figueroa-Guzmán Jesús Campos-García

Protein kinases (PKs) are an important and very popular family of enzymes that play a vital role in regulating cellular processes via the phosphorylation of targets. Nevertheless, modifications in the expression due to mutations or their dysregulation can lead to diseases, including autoimmune disorders, cardiovascular problems, diabetes, neurological diseases, and cancers. Cyclic ultra-short peptides are amazing structures with unique properties. The cyclicity of cyclic peptides (CPs) can mimic the interactions between PKs and natural substrates, influencing the enzyme activity essential in health and disease physiology. Our review summarized that interference in the signal transduction mechanism of the PKs by CPs implies the inhibition of substrate phosphorylation at the level of the active site, similar to anti-neoplastic drugs. The remarkable capacity of CPs to interact with targets positions them as promising candidates for developing protein kinase inhibitors in treating diseases. This review offers new insights for CPs in molecular mechanisms, cytotoxicity, target selectivity, and the possibility of designing more effective and safe therapeutic agents.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2040022

Authors: Swati Jaiswal Sanjay Kumar

Non-tuberculous mycobacteria (NTM) represent a diverse group of mycobacterial species known for causing opportunistic infections, especially in individuals with underlying health conditions. Unlike Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, NTM species exhibit different pathogenic characteristics and drug resistance mechanisms, making them increasingly relevant in clinical settings. PtkA is a crucial protein tyrosine kinase that regulates bacterial growth, stress response, and virulence by phosphorylating various substrates in Mtb. Understanding whether PtkA homologs exist in NTM could provide insights into their virulence and resistance mechanisms. In silico approaches, which utilize computational tools for sequence alignment, structure prediction, and functional annotation, offer a powerful means to identify homologous proteins across different species. In this article, we have employed tools like BLAST (Basic Local Alignment Search Tool), protein structure databases, and the NTM database to identify PtkA homologs in NTM genomes, providing a foundation for further studies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2040021

Authors: Tarikul I. Milon Krishna Rauniyar Sara Furman Khairum H. Orthi Yingchun Wang Vijay Raghavan Wu Xu

Protein kinases and phosphatases are key signaling proteins and are important drug targets. An explosion in the number of publicly available 3D structures of proteins has been seen in recent years. Three-dimensional structures of kinase and phosphatase have not been systematically investigated. This is due to the difficulty of designing structure-based descriptors that are capable of quantifying conformational changes. We have developed a triangular spatial relationship (TSR)-based algorithm that enables a unique representation of a protein’s 3D structure using a vector of integers (keys). The main objective of this study is to provide structural insight into conformational changes. We also aim to link TSR-based structural descriptors to their functions. The 3D structures of 2527 kinases and 505 phosphatases are studied. This study results in several major findings as follows: (i) The clustering method yields functionally coherent clusters of kinase and phosphatase families and their superfamilies. (ii) Specific TSR keys are identified as structural signatures for different types of kinases and phosphatases. (iii) TSR keys can identify different conformations of the well-known DFG motif of kinases. (iv) A significant number of phosphatases have their own distinct DFG motifs. The TSR keys from kinases and phosphatases agree with each other. TSR keys are successfully used to represent and quantify conformational changes of CDK2 upon the binding of cyclin or phosphorylation. TSR keys are effective when used as features for unsupervised machine learning and for key searches. If discriminative TSR keys are identified, they can be mapped back to atomic details within the amino acids involved. In conclusion, this study presents an advanced computational methodology with significant advantages in not only representing and quantifying conformational changes of protein structures but also having the capability of directly linking protein structures to their functions.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2040020

Authors: Douglas B. Craig

Chemical studies usually consist of measurements made on large ensembles of molecules with data representing average values for the population. It has been shown that individual molecules of a given enzyme have different properties. Large-scale averaging has in the past masked these differences. Alkaline phosphatase has been used as a model to study this enzyme heterogeneity. The catalytic rates of the individual molecules have been found to differ by over 10-fold, and the activation energy of catalysis by more than two-fold. Differences in properties indicate that differences in structure must exist between the molecules. For alkaline phosphatase, the structural differences have been suggested to be differences in glycosylation, differences due to partial proteolysis, and due to some molecules containing mixtures of active and inactive subunits. The determination of the distribution of activities of populations of this enzyme within a sample has also been shown to be a useful tool in diagnostics. This review discusses the advent of single-molecule enzymology and summarizes its use in the study of alkaline phosphatase using capillary electrophoresis, microscopic well assays, and single-molecule tracking.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2030019

Authors: Ankita B. Jaykumar Sakina Plumber Derk Binns Chonlarat Wichaidit Katherine Luby-Phelps Melanie H. Cobb

Angiogenesis is essential for remodeling and repairing existing vessels, and this process requires signaling pathways including those controlled by transforming growth factor beta (TGF-β). We have previously reported crosstalk between TGF-β and the protein kinase With No lysine (K) 1 (WNK1). Homozygous disruption of the gene encoding WNK1 results in lethality in mice near embryonic day E12 due to impaired angiogenesis, and this defect can be rescued by the endothelial-specific expression of an activated form of the WNK1 substrate kinase Oxidative Stress-Responsive 1 (OSR1). However, molecular processes regulated via a collaboration between TGF-β and WNK1/OSR1 are not well understood. Here, we show that WNK1 interacts with the E3 ubiquitin ligases SMURF1/2. In addition, we discovered that WNK1 regulates SMURF1/2 protein stability and vice versa. We also demonstrate that WNK1 activity regulates TGF-β receptor levels, in turn, controlling TGF-β signaling.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2030018

Authors: Jacob J. Lemon Comfort Ogbu Manisha Gupte

Obesity has become a global epidemic, contributing to various metabolic diseases. Despite existing therapies, the need to investigate new molecular targets to combat obesity-associated pathologies persists. Glycogen Synthase Kinase-3 (GSK-3), a serine/threonine kinase with two paralogs (GSK-3α and GSK-3β), has emerged as a critical player in obesity-associated metabolic pathologies such as type 2 diabetes (T2D), and cardiovascular diseases (CVDs). However, its ubiquitous dynamic expression and complex context-dependent signaling pathways present challenges in understanding its precise role in metabolic perturbations. In the present review, we will highlight the specific role and the proposed mechanisms via which the two GSK-3 paralogs impact obesity-associated pathologies such as T2D, diabetic cardiomyopathy (DCM), and cognitive impairment, a hallmark of Alzheimer’s disease (AD). We will also highlight studies delineating the role of GSK-3s using either GSK-3 inhibitors or non-pharmacological compounds to inhibit/taper GSK-3 activity in metabolic diseases. Thus, the primary goal of this review is to highlight recent findings delineating the regulation/dysregulation of GSK-3α/β in tissues such as heart, liver, skeletal muscle, pancreas, brain, and adipose tissue that undergo morphological and metabolic changes with diet-induced obesity which predisposes obese individuals to numerous devastating chronic conditions by GSK-3 overactivity.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2030017

Authors: Yüksel Aydar Sanara S. Rambukkanage Lauryn Brown Juan Wang Ji Sung Seo Keming Li Yong Cheng Laura Biddlestone-Thorpe Caila Boyd Amrita Sule Kristoffer Valerie

ATM kinase is becoming an important therapeutic target for tumor radiosensitization. Radiation is known to cause neuro-inflammation and neurodegeneration; however, the effects of small molecule ATM inhibitors (ATMi’s) and radiation on normal tissue, including healthy brain, are largely unexplored. Therefore, we examined the mouse CNS after ATMi radiosensitization with a focus on the fate of neurons. We used several approaches to assess the effects on the DNA damage response (DDR) and apoptosis of neurons using immunostaining. In vivo, a significant decrease in viable neurons and increase in degenerating neurons and apoptosis was observed in mice treated with radiation alone. On the other hand, an ATMi alone had little to no effect on neuron viability and did not induce apoptosis. Importantly, the ATMi’s did not further increase radiation toxicity. In fact, multiplex immunostaining showed that a clinical candidate ATMi (AZD1390) protected mouse neurons from apoptosis by 90% at 4 h after radiation. We speculate that the lack of toxicity to neurons is due to a normal ATM–p53 response that, if blocked transiently with an ATMi, is protective. Altogether, in line with previous work using ATM knockout mice, we provide evidence that ATM kinase inhibition using small molecules does not add to neuronal radiation toxicity, and might, in fact, protect them from radiation-induced apoptosis at least in the short term.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2030016

Authors: Sara Valero-Diaz Camilla Amato Berta Casar

Cutaneous T-cell lymphomas (CTCLs) are a heterogeneous group of T-cell lymphomas characterised by high relapse rates and no curative treatments unless the allogeneic stem cell transplantation. The main complication in the management of this kind of malignancy is the variability that characterises the genetic and clinical features among the CTCL subtypes. JAK/STAT, MAPK/ERK, PI3K/Akt, and NF-kB are those signalling pathways that are found altered in CTCL and that are responsible for promoting both T-cell malignancy and the pro-tumorigenic microenvironment. Thus, targeting key players of these pathways can be an advantageous therapeutic option for CTCL. In this review, we aim to summarise the different approaches that precisely inhibit the kinases of each cited signalling. JAK inhibitors seem to be the most promising kinase inhibitors for CTCL. However, adverse events have been reported especially in patients with immunosuppression or an underlying autoimmune disease. More studies are needed, especially clinical trials, to investigate the benefits of these drugs for the treatment of cutaneous T-cell lymphomas.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2030015

Authors: Rafael Hospodar Felippe Valverde Jennifer Lowe

Copper is an essential heavy metal for diverse biological functions but toxic in excess. Consequently, a tightly regulated protein system is required to ensure adequate intracellular levels. In recent decades, several studies have explored the role of Cu+-ATPases in copper transport and homeostasis, revealing that these proteins are subject to kinase-mediated phosphorylation that significantly impacts their function. Techniques such as phosphoproteomic screening, site-directed mutagenesis, and artificial neural network tools demonstrated the regulatory effect of phosphorylation on these ATPases. Different protein kinases regulate Cu+-ATPases, modulating the active copper transport by affecting specific steps of the catalytic cycle, long-range intramolecular crosstalks, protein trafficking, gene expression, and protein stability. Therefore, the regulatory phosphorylation of Cu+-ATPases by kinases ultimately influences the intracellular copper distribution. This study aims to present a review of the scientific literature on the regulation of Cu+-ATPases by kinase-mediated phosphorylation as a crucial mechanism for copper homeostasis. This regulation offers new perspectives for developing therapies for disorders related to copper metabolism, such as Wilson and Menkes diseases, as well as cancer, diabetes mellitus, Parkinson’s, and Alzheimer’s diseases. These findings emphasize the need to further comprehend the signaling pathways involving protein kinases in the context of copper regulation.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2030014

Authors: Emiko Kinoshita-Kikuta Kento Nishikawa Kento Hiraishi Kaku Shimoji Kenichi Nagase Eiji Kinoshita

The phosphorylation state of 20 types of intracellular proteins in the presence of the protein phosphatase 1 (PP1)- and PP2A-specific Ser/Thr phosphatase inhibitor calyculin A or the Tyr phosphatase inhibitor pervanadate was visualized by Phos-tag SDS-PAGE followed by immunoblotting. All blots showed a Phos-tag pattern indicating increased phosphorylation in the presence of one or both phosphatase inhibitors. The increase in phosphorylation stoichiometry per protein tends to be greater for Ser/Thr phosphatase inhibition than for Tyr phosphatase inhibition. This is consistent with the fact that the number of Ser/Thr kinase genes in the human genome is greater than that of Tyr kinases and with the fact that the phospho-Ser/phospho-Thr ratio in the actual human phosphoproteome is far greater than that of phospho-Tyr ratio. This suggests that cellular proteins are routinely and randomly phosphorylated by different kinases with no biological significance, simply depending on the frequency of substrate encounters. Phosphatase is responsible for routinely removing these unwanted phosphate groups systematically and maintaining the dynamic equilibrium of physiological protein phosphorylation. Phos-tag SDS-PAGE visualized that the kinase reaction involves many incidental phosphorylation and that phosphatases play broader roles besides being strict counterparts to kinases.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2020013

Authors: Taufiq Nawaz Shah Fahad Ruanbao Zhou

Protein phosphorylation serves as a fundamental regulatory mechanism to modulate cellular responses to environmental stimuli and plays a crucial role in orchestrating adaptation and metabolic homeostasis in various diverse organisms. In cyanobacteria, an ancient phylum of significant ecological and biotechnological relevance, protein phosphorylation emerges as a central regulatory axis mediating adaptive responses that are essential for survival and growth. This exhaustive review thoroughly explores the complex terrain of protein phosphorylation in cyanobacterial adaptation and metabolism, illustrating its diverse forms and functional implications. Commencing with an overview of cyanobacterial physiology and the historical trajectory of protein phosphorylation research in prokaryotes, this review navigates through the complex mechanisms of two-component sensory systems and their interplay with protein phosphorylation. Furthermore, it investigates the different feeding modes of cyanobacteria and highlights the complex interplay between photoautotrophy, environmental variables, and susceptibility to photo-inhibition. The significant elucidation of the regulatory role of protein phosphorylation in coordinating light harvesting with the acquisition of inorganic nutrients underscores its fundamental importance in the cyanobacterial physiology. This review highlights its novelty by synthesizing existing knowledge and proposing future research trajectories, thereby contributing to the deeper elucidation of cyanobacterial adaptation and metabolic regulation through protein phosphorylation.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2020012

Authors: Nourah Nayef Lakhan Ekal Ewald H. Hettema Kathryn R. Ayscough

Mitochondria are organelles involved in cellular energetics in all eukaryotes, and changes in their dynamics, fission, fusion, or localization can lead to cell defects and disease in humans. Budding yeast, Saccharomyces cerevisiae, has been shown to be an effective model organism in elucidating mechanisms underpinning these mitochondrial processes. In the work presented here, a genetic screen was performed to identify overexpressing kinases, phosphatases, and ubiquitin ligases, which resulted in mitochondrial defects. A total of 33 overexpressed genes showed mitochondrial phenotypes but without severe growth defects. These included a subset that affected the timing of mitochondrial inheritance and were the focus of further study. Using cell and biochemical approaches, the roles of the PAK-family kinase Cla4 and the E3-ubiquitin ligases Dma1 and Dma2 were investigated. Previous studies have indicated the roles of kinase Cla4 and ligases Dma1 and Dma2 in triggering the degradation of trafficking adaptors in the bud, which leads to disruption of the interaction with the transporting class V myosin, Myo2. Here, we map a key interface between Cla4 and the mitochondrial adaptor Mmr1 necessary for phosphorylation and identify a region of Mmr1 required for its degradation via Dma1 and Dma2. Together, our data provide insights into key regulatory regions of Mmr1 responsible for its function in mitochondrial inheritance.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2020011

Authors: Keli Lima João Agostinho Machado-Neto

Cancer, characterized by uncontrolled cell growth and metastasis, represents a significant challenge to public health. The IGF1/IGF1R axis plays a pivotal role in tumor proliferation and survival, presenting an attractive target for intervention. NT157, a small molecule tyrphostin, has emerged as a promising inhibitor of this axis, displaying potent antineoplastic effects across various cancer types. This review synthesizes the literature on NT157’s mechanism of action and its impact on cellular processes in experimental cancer models. Initially identified for inducing the serine phosphorylation of IRS1 and IRS2, leading to their degradation and inhibiting the IGF1R signaling cascade, subsequent studies revealed additional targets of NT157, including STAT3, STAT5, and AXL, suggesting a multifaceted mechanism. Experimental evidence demonstrates that NT157 effectively suppresses tumor growth, metastasis, and angiogenesis in diverse cancer models. Additionally, NT157 enhances chemotherapy efficacy in combination therapy. Moreover, NT157 impacts not only tumor cells but also the tumor microenvironment, modulating inflammation and immune responses by targeting cancer-associated fibroblasts, myeloid cells, and immune cells, creating a suppressive milieu hindering tumor progression and metastasis. In conclusion, NT157 exhibits remarkable versatility in targeting multiple oncogenic pathways and hallmarks of cancer, underscoring its potential as a promising therapeutic agent.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2020010

Authors: Moeka Nakashima Naoko Suga Satoru Matsuda

It has been proposed that procedures which upregulate mitochondrial biogenesis and autophagy by replacing damaged mitochondria with healthy ones may prevent the development of several heart diseases. A member of serine and threonine kinases, adenosine monophosphate-activated protein kinase (AMPK), could play essential roles in the autophagy and/or mitophagy. AMPK is widely distributed in various cells, which might play diverse regulatory roles in different tissues and/or organs. In fact, changes in the kinase function of AMPK due to alteration of activity have been linked with diverse pathologies including cardiac disorders. AMPK can regulate mitochondrial biogenesis via peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) signaling and also improve oxidative mitochondrial metabolism through inhibition of mechanistic/mammalian target of rapamycin (mTOR) pathway, which may also modulate the autophagy/mitophagy through autophagy activating kinase 1 (ULK1) and/or transforming growth factor beta (TGF-β) signaling. Therefore, the modulation of AMPK in autophagy/mitophagy pathway might probably be thought as a therapeutic tactic for several cardiac disorders. As kinases are amongst the most controllable proteins, in general, the design of small molecules targeting kinases might be an eye-catching avenue to modulate cardiac function. Some analyses of the molecular biology underlying mitophagy suggest that nutraceuticals and/or drugs including specific AMPK modulator as well as physical exercise and/or dietary restriction that could modulate AMPK may be useful against several heart diseases. These observations may virtually be limited to preclinical studies. Come to think of these, however, it is speculated that some nutraceutical regimens might have positive potential for managing some of cardiac disorders.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2020009

Authors: Sara Sadat Aghamiri Rada Amin

Cancer stem cells (CSCs), found within tumors, are powerful drivers of disease recurrence and metastasis. Their abilities to self-renew and maintain stem-like properties make treatment difficult, as their heterogeneity and metastatic properties can lead to resistance and limit the effectiveness of standard therapies. Given their significance, CSCs are typically isolated based on combinations of markers, which often indicate heterogeneous populations of CSCs. The lack of consensus in cell characterization poses challenges in defining and targeting these cells for effective therapeutic interventions. In this review, we suggest five promising molecules—ABCB5, CD26, CD66c, uPAR, and Trop-2—chosen specifically for their distinct distribution within cancer types and clinical relevance. These markers, expressed at the cell surface of CSCs, could significantly enhance the specificity of cancer stemness characterization. This review focuses on describing their pivotal roles as biomarker checkpoints for metastasis. Additionally, this review outlines existing literature on glycosylation modifications, which present intriguing epitopes aimed at modulating the stability and function of these markers. Finally, we summarize several promising in vivo and clinical trial approaches targeting the mentioned surface markers, offering potential solutions to overcome the therapeutic resistance of CSCs and addressing current gaps in treatment strategies.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2020008

Authors: Jiuhui Wang Yande Guo Xiangwei Fang Yuanqin Zhang Daotai Nie

Short-chain fatty acids (SCFAs), derived from fermentation of dietary fibers and resistant starch by the microbiota in the colon, exert multiple effects on colonic functions, including tumor suppressing activities. Our previous studies found that SCFAs induced autophagy in colon cancer cells via downregulating mTOR signaling, but the mechanism involved in mTOR suppression still needs to be defined. In this study, we identified rhabdomyosarcoma 2 associated transcript (RMST), a long non-coding RNA, as a key mediator for SCFAs to suppress mTOR activation in colon cancer cells. RMST could be significantly induced by SCFAs in a time- and dose-dependent manner. RMST, by itself, was sufficient to suppress mTOR signaling and augment autophagosome formation. Depletion of RMST, through siRNA or CRISPR knockdown, reduced the abilities of SCFAs to suppress mTOR activation or to induce autophagic responses. RMST increased the expression level of TSC2, a negative regulator of the mTOR signaling pathway. Our data delineate a novel RMST/TSC2 cellular pathway, enlisted by SCFAs, to modulate mTOR activities in colon cancer cells.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2020007

Authors: Sophie Day-Riley Rebekah M. West Paul D. Brear Marko Hyvönen David R. Spring

CK2 is a protein kinase that plays an important role in numerous cellular pathways involved in cell growth, differentiation, proliferation, and death. Consequently, upregulation of CK2 is implicated in many disease types, in particular cancer. As such, CK2 has gained significant attention as a potential therapeutic target in cancer, and over 40 chemical probes targeting CK2 have been developed in the past decade. In this review, we highlighted several chemical probes that target sites outside the conventional ATP-binding site. These chemical probes belong to different classes of molecules, from small molecules to peptides, and possess different mechanisms of action. Many of the chemical probes discussed in this review could serve as promising new candidates for drugs selectively targeting CK2.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2010006

Authors: Paulo F. Santos António Francisco Ambrósio Hélène Léger

Kinases play crucial roles in the pathophysiology of retinal degenerative diseases. These diseases, such as diabetic retinopathy, age-related macular degeneration, glaucoma, and retinitis pigmentosa, are characterized by progressive degeneration of retinal cells, including photoreceptors, ganglion cells, vascular cells, and retinal pigment epithelium, among others. The involvement of kinases in cell survival and apoptosis, immune responses and inflammation regulation, mitochondrial functions and mitophagy, autophagy, and proteostasis is crucial for maintaining cellular homeostasis and responding to various stressors. This review highlights the importance of studying kinases to better understand their functions and, regulation permitting, enable the identification of novel molecular players or potential drug targets and, consequently, the development of more effective and precise treatments to slow or halt the progression of retinal degenerative diseases.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2010005

Authors: Neera Yadav Sun-Yeou Kim

Tissue transglutaminase2 (TG2) has emerged as a key enigmatic protein in the development of various metabolic and age-related diseases. It catalyzes covalent cross-linking of countless proteins and provides strength to the extracellular matrix and resistance to proteolytic degradation via different pathways, including NF-kβ, TGF-β and PI3K/Akt as the major signaling pathways. The etiology of diabetes and associated diseases has been found to be linked to unbalanced TG2 activity that may not only result in impaired or delayed wound healing in diabetics but also worsen degenerative and metabolic disease conditions. TG2 is usually overexpressed in diabetes, fibrosis, cancer, and neurodegenerative disorders. These TG2-linked diseases are usually associated with prolonged activation of inflammatory pathways. Therefore, reducing the inflammatory mechanisms and improving tissue remodeling appear to be the main treatment strategies to exterminate TG2-linked diseases. The present review aims to deliver a detailed overview of the existing understanding of TG2 in diabetes and associated diseases’ progression, as well as treatment strategies to regulate TG2 tightly and its potential clinical applications. Our research endorses the notion that TG2 can serve as an effective early-stage diagnostic biomarker for metabolic diseases and a therapeutic target for the development of potential drug.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2010004

Authors: Venu Pandit Kailey DeGeorge Anja Nohe

Protein kinase CK2 (CK2) influences one-fifth of the cellular phosphoproteome. It regulates almost all cellular pathways and is thus a critical switch between biological processes within a cell. Inhibition of CK2 reverses oncogene addiction of tumor and alters tumor microenvironment. The success of this strategy and its clinical translation opens new opportunities. Targeting CK2 in musculoskeletal disorders is promising. Clinical manifestations of these disorders include dysfunctional inflammation, dysregulated cell differentiation, and senescence. Processes regulated by CK2 include all of these. Its emerging role in senescence also indicates its function’s centrality in cellular metabolism. This review summarizes considerations for targeting CK2 in musculoskeletal disorders. We have discussed the implications of CK2-regulated processes in musculoskeletal disorders.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2010003

Authors: Omamuyovwi M. Ijomone Ann-Kathrin Weishaupt Vivien Michaelis Olayemi K. Ijomone Julia Bornhorst

Nickel (Ni) and vanadium (V) are characteristic heavy metal constituents of many crude oil blends in Sub-Saharan Africa, and we have previously demonstrated their neurotoxic impact. However, molecular mechanisms driving Ni and V neurotoxicity are still being elucidated. The p38- and ERKs-MAPK pathways, which are mostly known for their involvement in human immune and inflammatory signalling, have been shown to influence an array of neurodevelopmental processes. In the present study, we attempt to elucidate the role of p38- and ERK-MAPK in neurotoxicity after early life exposures to Ni and V using the Caenorhabditis elegans model. Synchronized larvae stage-1 (L1) worms were treated with varying concentrations of Ni and V singly or in combination for 1 h. Our results show Ni induces lethality in C. elegans even at very low concentrations, while much higher V concentrations are required to induce lethality. Furthermore, we identified that loss-of-function of pmk-1 and pmk-3, which are both homologous to human p38-α (MAPK14), is differentially affected by Ni and V exposures. Also, all exposure scenarios triggered significant developmental delays in both wild-type and mutant strains. We also see increased mitochondrial-derived reactive oxygen species following Ni and V exposures in wild-type worms with differential responses in the mutant strains. Additionally, we observed alterations in dopamine and serotonin levels after metal exposures, particularly in the pmk-1 strain. In conclusion, both Ni and V induce lethality, developmental delays, and mitochondrial-derived ROS in worms, with V requiring a much higher concentration. Further, the results suggest the p38- and ERK-MAPK signalling pathways may modulate Ni and V neurodevelopmental toxicity, potentially affecting mitochondrial health, metal bioavailability, and neurotransmitter levels.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2010002

Authors: Abdalla M. Abdrabou

IκB kinases (IKKs), specifically IKKα and IKKβ, have long been recognized for their pivotal role in the NF-κB pathway, orchestrating immune and inflammatory responses. However, recent years have unveiled their dual role in cancer, where they can act as both promoters and suppressors of tumorigenesis. In addition, the interplay with pathways such as the MAPK and PI3K pathways underscores the complexity of IKK regulation and its multifaceted role in both inflammation and cancer. By exploring the molecular underpinnings of these processes, we can better comprehend the complex interplay between IKKs, tumor development, immune responses, and the development of more effective therapeutics. Ultimately, this review explores the dual role of IκB kinases in cancer, focusing on the impact of phosphorylation events and crosstalk with other signaling pathways, shedding light on their intricate regulation and multifaceted functions in both inflammation and cancer.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases2010001

Authors: Karla Villalobos-Nova María de los Ángeles Toro Pablo Pérez-Moreno Ignacio Niechi Julio C. Tapia

The endothelin-1 (ET1) peptide has a pathological role in the activation of proliferation, survival and invasiveness pathways in different cancers. ET1’s effects rely on its activation by the endothelin-converting enzyme-1 (ECE1), which is expressed as four isoforms, differing only in their cytoplasmic N-terminuses. We already demonstrated in colorectal cancer, glioblastoma, and preliminarily lung cancer, that the isoform ECE1c heightens aggressiveness by promoting cancer stem cell traits. This is achieved through a non-canonical ET1-independent mechanism of enhancement of ECE1c’s stability upon CK2-dependent phosphorylation at S18 and S20. Here, a K6 residue is presumably responsible for ECE1c ubiquitination as its mutation to R impairs proteasomal degradation. However, how phosphorylation enhances ECE1c’s stability and how this translates into aggressiveness are still open questions. In this brief report, by swapping residues to either phospho-mimetic or phospho-resistant amino acids, we propose that the N-terminus may also be phosphorylated at Y5 and/or T9 by an unknown kinase(s). In addition, N-terminus phosphorylation may lead to a blockage of K6 ubiquitination, increasing ECE1c’s stability and presumably activating the Wnt/β-catenin signaling pathway. Thus, a novel CK2/ECE1c partnership may be emerging to promote aggressiveness and thus become a biomarker of poor prognosis and a potential therapeutic target for several cancers.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1040018

Authors: Christian Werner Dirk Lindenblatt Kaido Viht Asko Uri Karsten Niefind

The structural knowledge about protein kinase CK2 is dominated by crystal structures of human CK2α, the catalytic subunit of human CK2, and the product of the CSNK2A1 gene. In contrast, far fewer structures of CK2α′, its paralogous isoform and the product of the CSNK2A2 gene, have been published. However, according to a PDB survey, CK2α′ is the superior alternative for crystallographic studies because of the inherent potential of the single mutant CK2α′Cys336Ser to provide crystal structures with atomic resolution. In particular, a triclinic crystal form of CK2α′Cys336Ser is a robust tool to determine high-quality enzyme-ligand complex structures via soaking. In this work, further high-resolution CK2α′Cys336Ser structures in complex with selected ligands emphasizing this trend are described. In one of these structures, the “N-terminal segment site”, a small-molecule binding region never found in any eukaryotic protein kinase and holding the potential for the development of highly selective substrate-competitive CK2 inhibitors, was discovered. In order to also address the binding site for the non-catalytic subunit CK2β, which is inaccessible in these triclinic CK2α′Cys336Ser crystals for small molecules, a reliable path to a promising monoclinic crystal form of CK2α′Cys336Ser is presented. In summary, the quality of CK2α′Cys336Ser as an exquisite crystallographic tool is solidified.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1040017

Authors: Han Wee Ong David H. Drewry Alison D. Axtman

Protein kinase casein kinase 2 (CK2/CSNK2) is a pleiotropic kinase involved in many cellular processes and, accordingly, has been identified as a potential target for therapeutic intervention for multiple indications. Significant research effort has been invested into identifying CK2 inhibitors as potential drug candidates and potent and selective CK2 chemical probes to interrogate CK2 function. Here, we review the small molecule inhibitors reported for CK2 and discuss various orthosteric, allosteric, and bivalent inhibitors of CK2. We focus on the pyrazolo[1,5-a]pyrimidines and naphthyridines, two chemotypes that have been extensively explored for chemical probe development. We highlight the uptake and demonstrated utility of the pyrazolo[1,5-a]pyrimidine chemical probe SGC-CK2-1 by the scientific community in cellular studies. Finally, we propose criteria for an ideal in vivo chemical probe for investigating CK2 function in a living organism. While no compound currently meets these metrics, we discuss ongoing and future directions in the development of in vivo chemical probes for CK2.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1040016

Authors: Colin L. Welsh Abigail E. Conklin Lalima K. Madan

Protein kinase A (PKA) signaling exemplifies phosphorylation-based signaling as we understand it today. Its catalytic-subunit structure and dynamics continue to advance our understanding of kinase mechanics as the first protein kinase catalytic domain to be identified, sequenced, cloned, and structurally detailed. The PKA holoenzyme elaborates on the role of its regulatory subunits and maintains our understanding of cAMP-dependent cellular signaling. The activation of PKA holoenzymes by cAMP is an example of specialized protein allostery, emphasizing the relevance of protein binding interfaces, unstructured regions, isoform diversity, and dynamics-based allostery. This review provides the most up-to-date overview of PKA structure and function, including a description of the catalytic and regulatory subunits’ structures. In addition, the structure, activation, and allostery of holoenzymes are covered.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1040015

Authors: Luca Cesaro Angelica Maria Zuliani Valentina Bosello Travain Mauro Salvi

Protein kinase CK2 (formerly known as casein kinase 2 or II), a ubiquitous and constitutively active enzyme, is widely recognized as one of the most pleiotropic serine/threonine kinases. It plays a critical role in numerous signaling pathways, with hundreds of bona fide substrates. However, despite considerable research efforts, our understanding of the entire CK2 substratome and its functional associations with the majority of these substrates is far from being completely deciphered. In this context, we aim to provide an overview of how CK2 recognizes its substrates. We will discuss the pros and cons of the existing methods to manipulate CK2 activity in cells, as well as exploring the dynamic response of substrate phosphorylation to CK2 modulation.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1040014

Authors: Julie Ledoux Marina Botnari Luba Tchertanov

Receptor tyrosine kinase (RTK) KIT is key regulator of cellular signalling, and its deregulation contributes to the development and progression of many serious diseases. Several mutations lead to the constitutive activation of the cytoplasmic domain of KIT, causing the aberrant intracellular signalling observed in malignant tumours. Elucidating the molecular basis of mutation-induced effects at the atomistic level is absolutely required. We report the first dynamic 3D model (DYNASOME) of the full-length cytoplasmic domain of the oncogenic mutant KITD816V generated through unbiased long-timescale MD simulations under conditions mimicking the natural environment of KIT. The comparison of the structural and dynamical properties of multidomain KITD816V with those of wild type KIT (KITWT) allowed us to evaluate the impact of the D816V mutation on each protein domain, including multifunctional well-ordered and intrinsically disordered (ID) regions. The two proteins were compared in terms of free energy landscape and intramolecular coupling. The increased intrinsic disorder and gain of coupling within each domain and between distant domains in KITD816V demonstrate its inherent self-regulated constitutive activation. The search for pockets revealed novel allosteric pockets (POCKETOME) in each protein, KITD816V and KITWT. These pockets open an avenue for the development of new highly selective allosteric modulators specific to KITD816V.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1030013

Authors: Thanih Balbaied Eric Moore

Alkaline phosphatase is a vital enzyme used in separation studies and as a biomarker for liver, bone, and certain cancer conditions. Its stability and specific properties enable insights into enzyme behavior, aiding in the development of detection methods with broader applications in various scientific fields. Alkaline phosphatase has four main isoenzymes: GCAP, IAP, PLAP, and TNAP, each with distinct roles. TNAP is found in the liver, kidney, and bones, playing a role in bone mineralization. The functions of the other isoenzymes are not fully known. Separation techniques like electrophoresis and chromatography are valuable for studying enzymes and proteins, revealing insights into their structure and function in pharmaceutical research and PTM studies. The main goal of this review paper is to thoroughly evaluate how capillary electrophoresis is applied to analyze alkaline phosphatase. It seeks to investigate the latest advancements in capillary electrophoresis and how they can improve the sensitivity, selectivity, and efficiency of alkaline phosphatase analysis.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1030012

Authors: Verónica Rey Isaac Tamargo-Gómez

Adenosine Monophosphate-Activated Protein Kinase (AMPK) is the major conserved regulator of cellular metabolism in eukaryotic cells, from yeast to mammals. Given its pivotal role, it is not surprising that alterations in its function may contribute to the pathogenesis of numerous human diseases. Indeed, AMPK has become a promising therapeutic target for several pathologies. In this context, significant efforts have been dedicated to discovering new pharmacological agents capable of activating AMPK based on next-generation sequencing (NGS) technology and personalized medicine. Thanks to computational methodologies and high-throughput screening, the identification of small molecules and compounds with the potential to directly activate AMPK or modulate its intricate signaling network has become viable. However, the most widely used drug to activate AMPK in human patients is still metformin, which has shown promising results in the treatment of various diseases, such as type II diabetes, atherosclerosis, Alzheimer’s disease, Huntington’s disease, and several types of cancer. In this review, we present a comprehensive analysis of the involvement of AMPK in human pathology, emphasizing its significant potential as a therapeutic target.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1030011

Authors: Samantha Y. Hayashi Barbara P. Craddock W. Todd Miller

Ack1 is a nonreceptor tyrosine kinase that is associated with cellular proliferation and survival. The receptor tyrosine kinase Mer, a member of the TAM family of receptors, has previously been reported to be an upstream activator of Ack1 kinase. The mechanism linking the two kinases, however, has not been investigated. We confirmed that Ack1 and Mer interact by co-immunoprecipitation experiments and found that Mer expression led to increased Ack1 activity. The effect on Ack1 was dependent on the kinase activity of Mer, whereas mutation of the Mer C-terminal tyrosines Y867 and Y924 did not significantly decrease the ability of Mer to activate Ack1. Ack1 possesses a Mig6 Homology Region (MHR) that contains adjacent regulatory tyrosines (Y859 and Y860). Using synthetic peptides, we showed that Mer preferentially binds and phosphorylates the MHR sequence containing phosphorylated pY860, as compared to the pY859 sequence. This suggested the possibility of sequential phosphorylation within the MHR of Ack1, as has been observed previously for other kinases. In cells co-expressing Mer and Ack1 MHR mutants, the Y859F mutant had higher activity than the Y860F mutant, consistent with this model. The interaction between Mer and Ack1 could play a role in immune cell signaling in normal physiology and could also contribute to the hyperactivation of Ack1 in prostate cancer and other tumors.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1030010

Authors: Andréa Hemmerlin

The recycling of metabolic products is a major way to reduce the energy cost of de novo biosynthesis. The salvage pathways involved not only regain a metabolic product but also generate additional molecules that might serve specific physiological, developmental and/or defensive functions. The isoprenoid pathway is a perfect example of a fine-regulated biosynthetic pathway, by virtue of the large number of molecules with different functions that must be synthesized simultaneously. Additionally, isoprenoid salvage pathways have been characterized. Thus, to produce isoprenoid precursors such as farnesyl diphosphate or phytyl diphosphate, short-chain isoprenols recovered from end-chain metabolites are phosphorylated. In the first instance, the so-called FPP-salvage machinery recycles farnesyl diphosphate from proteolyzed farnesylated proteins. In a second example, phytyl diphosphate is recycled from degraded chlorophyll, to be used for the biosynthesis of vitamin E. Both compounds are recovered as alcohols and require two phosphorylation events to be reactivated and reintegrated into the isoprenoid biosynthetic pathway. This review covers current knowledge of isoprenol biosynthesis, metabolism and function, as well as potential benefits of recycling pathways for plants, with a particular focus on stress responses.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1020009

Authors: Camila Paz Quezada Meza Maria Ruzzene

Protein kinase CK2 is a Ser/Thr protein kinase that phosphorylates hundreds of substrates mainly related to survival and proliferation pathways. It has long been considered an anti-cancer drug target. However, during the recent COVID-19 pandemic, CK2 inhibitors have been repurposed as anti-SARS-CoV-2 drugs. This was based on the initial finding of CK2 among the proteins of the host cell that interact with the viral proteins and modulate the infection. Since then, several studies have deepened our understanding of the CK2/COVID-19 connection, and we deem it is time to review all the findings. Interestingly, other coronaviruses cross-talk with CK2 as well, with similarities and differences compared to the SARS-CoV-2 case. Therefore, we believe that the analysis of the effects obtained by targeting CK2 in case of coronavirus infections, both at the molecular and phenomenological level, will help in extrapolating information that could be useful not only for COVID-19 (whose pandemic emergency is hopefully turning off) but also for other infections.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1020008

Authors: Soham Choudhuri Manas Yendluri Sudip Poddar Aimin Li Koushik Mallick Saurav Mallik Bhaswar Ghosh

The goal of drug discovery is to uncover new molecules with specific chemical properties that can be used to cure diseases. With the accessibility of machine learning techniques, the approach used in this search has become a significant component in computer science in recent years. To meet the Precision Medicine Initiative’s goals and the additional obstacles that they have created, it is vital to develop strong, consistent, and repeatable computational approaches. Predictive models based on machine learning are becoming increasingly crucial in preclinical investigations. In discovering novel pharmaceuticals, this step substantially reduces expenses and research times. The human kinome contains various kinase enzymes that play vital roles through catalyzing protein phosphorylation. Interestingly, the dysregulation of kinases causes various human diseases, viz., cancer, cardiovascular disease, and several neuro-degenerative disorders. Thus, inhibitors of specific kinases can treat those diseases through blocking their activity as well as restoring normal cellular signaling. This review article discusses recent advancements in computational drug design algorithms through machine learning and deep learning and the computational drug design of kinase enzymes. Analyzing the current state-of-the-art in this sector will offer us a sense of where cheminformatics may evolve in the near future and the limitations and beneficial outcomes it has produced. The approaches utilized to model molecular data, the biological problems addressed, and the machine learning algorithms employed for drug discovery in recent years will be the emphasis of this review.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1020007

Authors: Arathi Nair Bhaskar Saha

Ras, a GTP-GDP binary switch protein, transduces signals from diverse receptors to regulate various signaling networks. Three Ras genes encode for protein isoforms, namely, Harvey Ras (H-Ras), Kirsten Ras (K-Ras, with two splice variants, K-Ras4A and K-Ras4B), and Neuroblastoma Ras (N-Ras). The isoforms undergo a series of post-translational modifications that enable their membrane attachment and biological activity. The activation of Ras isoforms is tightly regulated, and any dysregulation affects cellular processes, such as cell division, apoptosis, differentiation, cell migration, etc. The Ras gene is highly prone to mutation, and ~30% of cancers carry somatic mutations in Ras, whereas germline mutations clinically manifest as various rasopathies. In addition to regulation by the Guanine nucleotide exchange factors and the GTPase activation proteins, Ras signaling, and localization are also regulated by phosphorylation-dephosphorylation, ubiquitination, nitrosylation, and acetylation. Herein, we review the regulation of Ras signaling and localization by various regulatory enzymes in depth and assess the current status of Ras drug discovery targeting these regulatory enzymes.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1010006

Authors: Tadeu L. Montagnoli Daniela R. de Oliveira Carlos A. Manssour Fraga

Cerebral cavernous malformations (CCM) are developmental venous dysplasias which present as abnormally dilated blood vessels occurring mainly in the brain. Alterations in vascular biology originate from somatic mutations in genes regulating angiogenesis and endothelial-to-mesenchymal transition. Vascular lesions may occur at any time and develop silently, remaining asymptomatic for years. However, symptomatic disease is often debilitating, and patients are prone to develop drug-resistant epilepsy and hemorrhages. There is no cure, and surgical treatment is recommended only for superficial lesions on cortical areas. The study of lesion biology led to the identification of different pathways related to disease onset and progression, of which RhoA/Rho-associated protein kinase (ROCK) shows activation in different subsets of patients. This work will explore the current knowledge about the involvement of ROCK in the many aspects of CCM disease, including isoform-specific actions, and delineate the recent development of ROCK inhibitors for CNS-targeted diseases.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1010005

Authors: Julie Ledoux Luba Tchertanov

The kinase insert domain (KID) of RTK KIT is a key recruitment region for downstream signalling proteins (DSPs). KID, as a multisite phosphorylation region, provides alternative recognition sites for DSPs and activates them by binding a phosphotyrosine (pY) to their SH2 domains. Significant steric, biochemical, and biophysical requirements must be fulfilled by each pair of interacting proteins as the adaptation of their configurations is mandatory for the selective activation of DSPs. The accurate 3D atomistic models obtained by modelling and molecular dynamics (MD) simulations of phosphorylated KID (p-KID) have been delivered to describe KID INTERACTOME. By taking phosphorylated KIDpY721 and the N-terminal SH2 domain of phosphatidylinositol 3-kinase (PI3K), a physiological partner of KID, we showed the two proteins are intrinsically disordered. Using 3D models of both proteins, we probe alternative orientations of KIDpY721 relative to the SH2 binding pocket using automatic docking (HADDOCK) and intuitive user-guided docking. This modelling yields to two possible models of the functionally related non-covalent complex KIDpY721/SH2, where one can be regarded as the first precursor to probe PI3K activation via KIT KID. We suggest that such generation of a KID/SH2 complex is best suited for future studies of the post-transduction effects of RTK KIT.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1010004

Authors: Pathum M. Weerawarna Timothy I. Richardson

LYN proto-oncogene, Src family tyrosine kinase (Lyn) is a tyrosine kinase that belongs to the Src family (SFK). It is expressed as two isoforms in humans, LynA and LynB. Like other SFKs, Lyn consists of five protein domains, an N-terminal SH4 domain followed by a unique domain, the SH3 and SH2 domains, and a catalytic SH1 domain. The autophosphorylation of Tyr397 activates the protein, while the phosphorylation of the C-terminal inhibitory Tyr508 by C-terminal Src kinase (Csk) or Csk homologous kinase (Chk) inhibits the catalytic activity. The interaction of the SH2 domain with the phosphorylated Tyr508 stabilizes a compact, self-inhibited state. The interaction of the SH3 domain with a linker between the SH2 and catalytic domains further stabilizes this inactive conformation. The two critical structural features of the catalytic domain are a conserved DFG moiety and the αC helix, which can adopt in or out conformations. In the active state, both the DFG moiety and αC helix adopt in conformations, while in the inactive state, they adopt out conformations. Lyn has well-established functions in various hematopoietic cell types and more recent studies have revealed its roles in non-hematopoietic cells. At the molecular level, these functions are mainly exerted by phosphorylating specific tyrosine residues in immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and immunoreceptor tyrosine-based activator motifs (ITAMs) associated with cell surface receptors. The phosphorylation of ITAMs by Lyn can initiate either activating or inhibitory (ITAMi) cell signaling depending on the receptor, targeting mode (crosslinking or monovalent targeting), and the cellular context. The phosphorylation of ITIMs by Lyn initiates inhibitory cell signaling via the recruitment of phosphatases to the ITIM-bearing receptor. The role of Lyn in cancer and autoimmune diseases has been extensively discussed in the literature. The involvement of Lyn in neurodegenerative diseases has been described more recently and, as such, it is now an emerging target for the treatment of neurodegenerative diseases.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1010003

Authors: Susumu Tanaka Yoshiko Honda Misa Sawachika Kensuke Futani Namika Yoshida Tohru Kodama

Serine/threonine-protein kinase 16 (STK16) is a novel member of the Numb-associated family of protein kinases with an atypical kinase domain. In this study, we aimed to investigate the involvement of STK16 in sleep–wake mechanisms. We confirmed the expression of Stk16 in the murine hypothalamus, the sleep–wake center, and found considerable changes in STK16 protein levels in the anterior hypothalamus during the light–dark cycle. We found that the coexistence of the potassium channel tetramerization domain containing 17 (KCTD17), an STK16 interactor, caused STK16 degradation. In contrast, the proteasome inhibitor MG132 inhibited the degradation of STK16. In addition, polyubiquitinated STK16 was observed, suggesting that KCTD17 acts as an adapter for E3 ligase to recognize STK16 as a substrate, leading to STK16 degradation via the ubiquitin–proteasome system. The vast changes in STK16 in the anterior hypothalamus, a mammalian sleep center, as well as the reported sleep abnormalities in the ubiquitin B knockout mice and the Drosophila with the inhibition of the KCTD17 homolog or its E3 ligase cullin-3, suggest that STK16 plays a major role in sleep–wake regulation.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1010002

Authors: Hajar Yaakoub Sara Mina Agnès Marot Nicolas Papon Alphonse Calenda Jean-Philippe Bouchara

Scedosporium species are opportunistic filamentous fungi found in human-impacted areas. Clinically relevant species, such as S. apiospermum, rank as the second most frequent colonizers of the airways of patients with cystic fibrosis (CF), which are characterized by persistent oxidative stress. This raises the question of how Scedosporium species abate conditions imposed in hostile environments. Since the High Osmolarity Glycerol (HOG) pathway plays a central role in fungal adaptation to stress, we aimed to pheno-profile the involvement of the pathway in response to stress in S. apiospermum using Western blot. We show for the first time that a wide range of stress distinctively activates the HOG pathway in S. apiospermum, including oxidants (H2O2, menadione, cumene hydroperoxide, diamide, paraquat, and honokiol), osmotic agents (sorbitol and KCl), cell-wall stress agents (caffeine, calcofluor white, and Congo Red), heavy metals (cadmium and arsenite), fungicides (fludioxonil and iprodione), antifungals (voriconazole and amphotericin B), and acid stress (pH 4). We suggest that the function of the HOG pathway as a general stress regulator is also conserved in S. apiospermum.

Kinases and Phosphatases doi: 10.3390/kinasesphosphatases1010001

Authors: Mauro Salvi

On behalf of all the Editorial Board members and the MDPI staff, I’m pleased to announce the publishing of the inaugural issue of the Kinases and Phosphatases journal [...]