Kinases and Phosphatases

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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 K_m and V_max 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 (P_i) from the extracellular medium, it is likely that its ectophosphatase activity acts together with the transport systems in the P_i acquisition process. The elucidation of the molecular mechanisms involved in this process emerges as a relevant perspective, providing new strategies for controlling Phytomonas infection. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article

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. Full article