The protein kinase complement of the human genome

Key events relating to homeostasis and regeneration of freshwater planarians (Dugesia Japonica) after exposure to various ZnO-forms

This study aims to investigate the toxicity and underlying mechanisms of ZnO nanoparticles (ZnO NPs), bulk ZnO (ZnO MPs), and zinc ions (Zn2 +) on Dugesia japonica planarians, with a focus on their bioaccumulation, transformation, and associated biological effects. Using advanced techniques such as synchrotron X-ray fluorescence (XRF), X-ray Absorption Near Edge Structure (XANES) and single particle ICP-MS (sp-ICP-MS), we measured the accumulation, distribution, and transformation of these materials in planarians. All treatments caused significant Zn accumulation: ZnO NPs increased Zn by 120-fold, ZnO MPs by 100-fold, and Zn2+ by 430-fold. XANES and sp-ICP-MS analysis confirmed that ZnO NPs remained largely in particulate form (40-60 %) following uptake by planarians. Toxicity tests revealed that all treatments impaired blastema growth, locomotion, stem cell proliferation, differentiation, and neural regeneration. ZnO MPs exhibited higher toxicity than ZnO NPs, while Zn2+ resulted in elevated oxidative stress. ZnO NPs induced severe energy damage and triggered cell apoptosis, whereas ZnO MPs caused more pronounced necrosis cell death. Transcriptomic and proteomic analyses showed that all treatments disrupted pathways related to oxidative stress response, energy metabolism and cell apoptosis. ZnO NPs primarily affected the membrane integrity pathway, ZnO MPs altered cell homeostasis and membrane potential, while Zn2+ exposure triggered metal ion-specific cellular reactions. These molecular and cellular changes collectively explain the observed phenotypic outcomes, which align with the Adverse Outcome Pathway framework. The findings provide insights into the environmental risks of different ZnO forms and highlight their distinct toxicity mechanisms.

Photocaging of N-pyridinyl amide scaffold-based PIM inhibitors for spatiotemporal controlled anticancer bioactivity

Photocaging is an ideal way to enable spatiotemporal control over the release of bioactive compounds for cancer treatments. In this work, a series of photocaged N-pyridinyl amide scaffold-based PIM inhibitors were developed by rendering the amino group unable to bind to the Asp128/Glu171 sites of PIM kinase with a photoremovable protecting group (PPG). Upon light irradiation, our studies revealed the structure-dependent photouncaging efficiency and screened out the photocaged PIM inhibitor FD1024-PPG. Its spatiotemporally controlled bioactivity was confirmed by cell-based in-vitro assays and revealed that it exerts the antiproliferation and induction of cell apoptosis through inhibition of PIM kinase upon light irradiation. Furthermore, the spatiotemporal control over the in-vivo anticancer activity was demonstrated using zebrafish xenograft model.

CD28 signaling domain boosts persistence and in vivo anti-tumor activity of stem cell-derived CD19-CAR-NK cells

Allogeneic natural killer (NK) cell-based therapies with an outstanding safety profile, are a compelling alternative to autologous T cell-based approaches for cancer immunotherapy, offering innate tumor-killing ability that can be further augmented via introduction of tumor antigen-specific chimeric antigen receptors (CARs). In this study, we genetically engineered primary human hematopoietic stem cells using an optimized lentiviral backbone carrying CD19 CAR cassettes with varied hinge, transmembrane, and signaling domains to evaluate their role in CAR-NK development and function. Our platform integrates early genetic modification with our unique expansion/differentiation system, enabling high CAR expression with low vector copy numbers. Notably, CARs incorporating CD28 transmembrane and signaling domains with CD3ζ, promoted enhanced tonic signaling, accelerated NK differentiation, enhanced antigen-specific kinome activation, and improved cytotoxicity and persistence both in vitro and in vivo. These findings offer a robust strategy for development of stem cell-based CAR-NK immunotherapies, combining potent innate, and antigen-specific antitumor responses.

The PI3K/Akt pathway: a target for curcumin's therapeutic effects

Purpose

The purpose of this review study is to investigate the effect of curcumin on the phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway in various diseases. Curcumin, the main compound found in turmeric, has attracted a lot of attention for its diverse pharmacological properties. These properties have increased the therapeutic potential of curcumin in chronic diseases such as cardiovascular disease, Type 2 diabetes, obesity, non-alcoholic fatty liver disease, kidney disease, and neurodegenerative diseases. One of the main mechanisms of the effect of curcumin on health is its ability to modulate the PI3K/Akt signaling pathway. This pathway plays an important role in regulating vital cellular processes such as growth, cell survival, metabolism, and apoptosis. Disruption of the PI3K/Akt signaling pathway is associated with the incidence of several diseases.

Methods

Electronic databases including PubMed, Google Scholar, and Scopus were searched with the keywords "phosphoinositide 3-kinase" AND "protein kinase B "AND "curcumin" in the title/abstract. Also, following keywords "non-alcoholic fatty liver disease" AND "diabetes" AND "obesity" AND "kidney disease" and "neurodegenerative diseases" was searched in the whole text.

Results

Research indicates that curcumin offers potential benefits for several health conditions. Studies have shown it can help regulate blood sugar, reduce inflammation, and protect the heart, kidneys, and brain.

Conclusion

This protective effect is partially achieved by regulating the PI3K-Akt survival pathway, which helps improve metabolic disorders and oxidative stress. By examining how curcumin affects this vital cell pathway, researchers can discover new treatment strategies for a range of diseases.

VRK2 kinase pathogenic pathways in cancer and neurological diseases

The VRK2 ser-thr kinase, belonging to the dark kinome, is implicated in the pathogenesis of cancer progression, neurological and psychiatric diseases. The VRK2 gene codes for two isoforms. The main isoform (VRK2A) is mainly located in the cytoplasm, and anchored to different types of membranes, such as the endoplasmic reticulum, mitochondria and nuclear envelope. The VRK2A isoform interacts with signaling modules assembled on scaffold proteins such as JIP1 or KSR1, forming stable complexes and blocking the activation of regulatory signaling pathways by altering their intracellular localization and the balance among them. VRK2 regulates apoptosis, nuclear membrane organization, immune responses, and Cajal bodies. Wild-type VRK2 is overexpressed in tumors and contributes to cancer development. In cells and tumors with low levels of nuclear VRK1, VRK2 generates by alternative splicing a shorter isoform (VRK2B) that lacks the C-terminal hydrophobic tail and permits its relocation to nuclei. Furthermore, rare VRK2 gene variants are associated with different neurological or psychiatric diseases such as schizophrenia, epilepsy, bipolar disorder, depression, autism, circadian clock alterations and insomnia, but their pathogenic mechanism is unknown. These diseases are a likely consequence of an altered balance among different signaling pathways that are regulated by VRK2.

Molecular evolution and functional characterization of PKC-α-like in Lamprey

Protein kinase C-α (PKC-α) is a serine/threonine protein kinase categorized within the lipid-regulated PKC family. Despite considerable research on PKC-α in various vertebrates, information about its presence and characteristics in lampreys-among the few extant jawed vertebrates and the most primitive-remains limited. In this study, we report the first identification of a PKC-α-like gene in lamprey by successfully cloning its coding region, composed of 1683 base pairs that encode 560 amino acids, from the constructed cDNA library of Lampetrajaponica. Sequence analysis demonstrated a high degree of homology between the PKC-α-like sequence in lamprey and those in other vertebrates. Phylogenetic analysis indicated that lamprey PKC-α-like occupies an intermediate position between vertebrates and invertebrates, supporting the principles of species evolution. Gene structure analysis revealed low conservation throughout evolution, possibly due to events like chromosomal rearrangements or homologous recombination which may have caused significant changes in gene arrangement patterns. Additionally, we generated polyclonal antibody against PKC-α-like and investigated its tissue distribution in Lampetrajaponica. Our results demonstrated widespread expression of PKC-α-like across all tissues with varying mRNA expression levels in response to different pathogenic stimuli. Specifically, PKC-α-like expression was consistently up-regulated in response to polyinosine-polycytidylic acid (Poly (I:C)) stimulation, especially in immune-related tissues. Furthermore, we confirmed that PKC-α-like is primarily localized in the cytoplasm of lamprey cells. Moreover, our findings indicate that PKC-α-like promotes cell proliferation, prompting us to undertake a preliminary investigation of the underlying molecular mechanisms. In summary, this study establishes a theoretical foundation for further exploration of the evolutionary process of PKC-α and its role in cell proliferation mechanisms.

Current understanding of PEAK family members in regulation of cellular signaling pathways and cancer therapy

Cancer evades therapy by multiple mechanisms, leading to uncontrolled cell growth and metastasis. Targeted therapies have shown promise in treating cancer by focusing on pathways within cancer cells. The PEAK family, comprising PEAK1 (SgK269), PEAK2 (SgK223/Pragmin), and the latest addition, PEAK3 (C19orf35), plays a crucial role in modulating cellular processes. Dysregulation and hyperactivity of these proteins, through overexpression or mutations, are associated with a wide range of cancers. This review delves into the different roles of the PEAK family members in regulating cell signaling pathways and highlights their potential in cancer therapy.

A review on quinolines: New green synthetic methods and bioactive potential

Quinolines have been an interest of study for a few decades due to the importance of this system in natural and pharmaceutical products. Since their discovery in the nineteenth century, many medicinal properties have been found for quinoline compounds. Firstly, as an anti-parasitic agent against malaria and then against many other diseases, such as, other parasitic infections, HIV, bacterial infections and cancer. Consequently, many synthetic methods have been developed to afford the quinoline ring. In this review we look back at traditional methods and look forward to the most recent and promising "green" methods for the synthesis of quinolines. Also, we review the newest advances in therapeutic compounds based on the quinoline skeleton for the treatment of parasitic and cancer diseases and the most recent applications of quinoline derivatives in drug delivery systems.

Molecular Targets in Alveolar Rhabdomyosarcoma: A Narrative Review of Progress and Pitfalls

Alveolar rhabdomyosarcoma (ARMS) is a highly aggressive pediatric soft-tissue sarcoma driven by PAX3/7-FOXO1 fusion proteins. Despite intensive multimodal therapy, outcomes remain poor for patients with fusion-positive ARMS. This review integrates recent advances in the molecular pathogenesis of ARMS, highlighting key diagnostic and therapeutic targets. We discuss the central role of fusion proteins in transcriptional reprogramming, impaired myogenic differentiation, and super-enhancer activation. Emerging biomarkers (YAP, TFAP2B, P-cadherin) and oncogenic kinases (Aurora A, CDK4, PLK1) are evaluated alongside receptor tyrosine kinases (FGFR, MET) and transcription factors involved in metabolic rewiring (FOXF1, ETS1). Additionally, we examine immunotherapeutic strategies, epigenetic modifiers, and noncoding RNAs as potential therapeutic avenues. Together, these insights provide a comprehensive framework for developing biomarker-guided, multi-targeted therapies to improve outcomes in ARMS.

Characterization of molecular mechanisms of CaMKKα/1 oligomerization

Calcium/calmodulin-dependent protein kinase kinase (CaMKK) is an activating kinase for calcium/calmodulin-dependent protein kinase type 1 (CaMKI), calcium/calmodulin-dependent protein kinase type IV (CaMKIV), RAC-alpha serine/threonine-protein kinase (PKB), and AMP-activated protein kinase (AMPK) that has been reported to form an active oligomer in cells. Glutathione S-transferase (GST) pulldown assay from the extracts of COS-7 cells expressing GST- and His6-CaMKKα/1 mutants showed that the C-terminal region containing the autoinhibitory and calmodulin (CaM)-binding sequence (residues 438-463) is required for CaMKKα/1 homo-oligomerization. This was confirmed by the fact that the GST-CaMKKα/1 C-terminal domain (residues 435-505) directly interacted with EGFP-CaMKKα/1 residues 435-505 as well as with wild-type CaMKKα/1. Notably, once oligomerized in cells, CaMKKα/1 is neither exchangeable between the oligomeric complexes nor dissociated by Ca2+/CaM binding. These results support stable oligomerization of CaMKK in the cells by intermolecular self-association of its C-terminal region containing a regulatory domain.

Cytotoxic lycorine alkaloids of the plant family Amaryllidaceae

The plant family Amaryllidaceae is embellished with a diverse array of antiproliferative alkaloid principles. Chief amongst these are the lycorine alkaloids, which have attracted considerable attention as potential anticancer drugs. This account tracks developments in the field with these substances encompassing the years 2015-2019. Twenty-nine compounds were screened against nearly eighty cancer cell lines representing seventeen different types of cancer. Submicromolar level activities were recorded against leukemia, myeloma and breast cancer cells. The response of lycorine (IC50 0.6 μM) to HL-60 myeloid leukemia cells was particularly striking. Promising activities were also documented from in vivo models of brain, lung, colon, prostate and breast cancer cells (in the 5-10 mg/kg/day dosage range). The screenings indicated these compounds to be efficacious without attendant detrimental effects towards control animals. Structure-activity relationship studies afforded useful insight to the elements of the anticancer pharmacophore, such as the necessity for the A-ring methylenedioxy and C-ring hydroxy functionalities. The mechanisms of action were intensively examined, with over twenty individual areas identified wherein such probes have been made. Of prominence here was the apoptosis-inducing abilities of lycorine against (amongst others) leukemia, pancreatic, bladder, liver and bone cancer cells, involving the modulation of key mediators such as caspase-3, p53, PARP, Bax and Bcl-2. Useful insights also emerged from docking studies undertaken with various cancer-related proteins, such as VEGF, HDAC, PI3Kα, c-Met kinase and EGFR. The lycorine alkaloids have proved to be highly versatile entities, readily embracing multiple facets of anticancer drug discovery.

Comprehensive evaluation of phosphoproteomic-based kinase activity inference

Kinases regulate cellular processes and are essential for understanding cellular function and disease. To investigate the regulatory state of a kinase, numerous methods have been developed to infer kinase activities from phosphoproteomics data using kinase-substrate libraries. However, few phosphorylation sites can be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. Moreover, inferred activities vary across methods, necessitating evaluation for accurate interpretation. Here, we present benchmarKIN, an R package enabling comprehensive evaluation of kinase activity inference methods. Alongside classical perturbation experiments, benchmarKIN introduces a tumor-based benchmarking approach utilizing multi-omics data to identify highly active or inactive kinases. We used benchmarKIN to evaluate kinase-substrate libraries, inference algorithms and the potential of adding predicted kinase-substrate interactions to overcome the coverage limitations. Our evaluation shows most computational methods perform similarly, but the choice of library impacts the inferred activities with a combination of manually curated libraries demonstrating superior performance in recapitulating kinase activities. Additionally, in the tumor-based evaluation, adding predicted targets from NetworKIN further boosts the performance. We then demonstrate how kinase activity inference aids characterize kinase inhibitor responses in cell lines. Overall, benchmarKIN helps researchers to select reliable methods for identifying deregulated kinases.

Identification and validation a novel kinase-related gene signature for predicting prognosis and responsiveness to immunotherapy in hepatocellular carcinoma

Liver cancer research highlights the kinome's critical role in disease initiation and progression. However, comprehensive data analysis on the kinome's impact on hepatocellular carcinoma (HCC) prognosis is limited. We used the TCGA-LIHC mRNA expression profiles, analyzing them with various R packages. Key methods included univariate Cox regression for prognostic gene identification, consensus clustering for subtype classification, Gene Set Enrichment Analysis (GSEA), and immune landscape evaluation. A prognostic model was developed using LASSO Cox regression, and chemotherapy drug sensitivity was assessed using the pRRophetic package. We identified 45 kinases-related differentially expressed genes (DEGs), with 27 linked to HCC prognosis. Cluster analysis divided these genes into two subtypes, with distinct prognoses. We discovered 157 DEGs between kinase-related subtypes, 120 of which were prognostically relevant. A kinase-related gene signature (KRS) was developed for prognostic prediction. The high-KRS group showed poorer survival in TCGA-LIHC and validation cohorts, with notable differences in immune cell infiltration and checkpoint gene expression. This group also showed varying sensitivity to common drugs and anti-PD-L1 treatment. In contrast, the low-KRS group might respond better to anti-PD-1 immunotherapy. Our study introduces a kinase-related gene signature as a novel tool for predicting HCC prognosis. This signature aids in tailoring personalized treatment strategies, potentially improving clinical outcomes in HCC patients.

Platinum(II) and ruthenium(II) coordination complexes equipped with an anchoring site for binding the protein kinase enzyme pockets: synthesis, molecular docking and biological assays

To mimic the structural aspects of staurosporine, a potent but unspecific kinase inhibitor, several coordination compounds based on two readily available diimine ligands containing hydrogen bonding donor/acceptor sites (NH-CO fragment) have been designed and synthesized. These complexes are constructed around Ru(II) and Pt(II) metal centers. A total of 9 compounds, named Ru(1)-(5) and Pt(1)-(4), were obtained through straightforward synthetic approaches. The cytotoxicity of the compounds was evaluated on AGS gastric cancer cells (GC) through standard MTT assays. All ruthenium and platinum complexes with low toxicity, i.e.Ru(3), Ru(5), Pt(3) and Pt(4), were docked in the ATP binding pocket of two protein kinases (S6K1 and MST2). The docking scores highlighted a preferred affinity of Ru(5) for the MST2 binding pocket, whereas the platinum compounds are predicted to bind stronger to the S6K1 binding site. Inhibitory activity of the metal complexes on the MST2 and S6K1 signaling pathways was evaluated by analyzing via western blot experiments the phosphorylation state of YAP, a downstream component of the Hippo pathway and the protein expression of S6 and its phosphorylated analogue p-S6. A clear difference of behavior between the Pt(II) and the Ru(II) complexes depending on the type of kinase was observed.

The fast-evolving FIKK kinase family of Plasmodium falciparum can be inhibited by a single compound

Of 250 Plasmodium species, 6 infect humans, with P. falciparum causing over 95% of 600,000 annual malaria-related deaths. Its pathology arises from host cell remodelling driven by over 400 exported parasite proteins, including the FIKK kinase family. About one million years ago, a bird-infecting Plasmodium species crossed into great apes and a single non-exported FIKK kinase gained an export element. This led to a rapid expansion into 15-21 atypical, exported Ser/Thr effector kinases. Here, using genomic and proteomic analyses, we demonstrate FIKK differentiation via changes in subcellular localization, expression timing and substrate motifs, which supports an individual important role in host-pathogen interactions. Structural data and AlphaFold2 predictions reveal fast-evolving loops in the kinase domain that probably enabled rapid functional diversification for substrate preferences. One FIKK evolved exclusive tyrosine phosphorylation, previously thought absent in Plasmodium. Despite divergence of substrate preferences, the atypical ATP binding pocket is conserved and we identified a single compound that inhibits all FIKKs. A pan-specific inhibitor could reduce resistance development and improve malaria control strategies.

Data-driven extraction of human kinase-substrate relationships from omics datasets

Phosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as cell division and differentiation. In human, >90% of identified phosphosites don't have annotations regarding the relevant upstream kinase. At the same time around 30% of kinases (as annotated in Uniprot) have no known target. This knowledge gap stresses the need to make large scale, data-driven computational predictions. In this study, we have created a machine learning-based model to derive a probabilistic kinase-substrate network from omics datasets. Our methodology displays improved performance compared to other state-of-the-art kinase-substrate prediction methods and provides predictions for more kinases. Importantly, it better captures new experimentally-identified kinase-substrate relationships. It can therefore allow the improved prioritisation of kinase-substrate pairs for illuminating the dark human cell signalling space. Our model is integrated into a web server, SELPHI2.0, to allow unbiased analysis of phosphoproteomics data, facilitating the design of downstream experiments to uncover mechanisms of signal transduction across conditions and cellular contexts.

Efficient Design of Affilin® Protein Binders for HER3

Engineered scaffold-based proteins that bind to concrete targets with high affinity offer significant advantages over traditional antibodies in theranostic applications. Their development often relies on display methods, where large libraries of variants are physically contacted with the desired target protein and pools of binding variants can be selected. Herein, we use a novel combined artificial intelligence/physics-based computational framework and phage display approach to obtain ubiquitin based Affilin® proteins targeting the human epidermal growth factor receptor 3 (HER3) extracellular domain, a relevant tumor target. As traditional antibodies against the receptor have failed so far, we sought to provide molecules in a smaller more versatile format to cover the medical need in HER3 related diseases. We demonstrate that the developed in silico pipeline can generate de novo Affilin® proteins binding the biochemical HER3 target using a small training set of <1000 sequences. The classical phage display yielded primary candidates with low nanomolar affinities to the biochemical target and HER3-expressing cells. The latter could be further optimized by phage display and computational maturation alike. These combined efforts resulted in four HER3 ligands with high affinity, cell binding, and serum stability with theranostic potential.

Data- and knowledge-derived functional landscape of human solute carriers

The human solute carrier (SLC) superfamily of ~460 membrane transporters remains the largest understudied protein family despite its therapeutic potential. To advance SLC research, we developed a comprehensive knowledgebase that integrates systematic multi-omics data sets with selected curated information from public sources. We annotated SLC substrates through literature curation, compiled SLC disease associations using data mining techniques, and determined the subcellular localization of SLCs by combining annotations from public databases with an immunofluorescence imaging approach. This SLC-centric knowledge is made accessible to the scientific community via a web portal featuring interactive dashboards and visualization tools. Utilizing this systematically collected and curated resource, we computationally derived an integrated functional landscape for the entire human SLC superfamily. We identified clusters with distinct properties and established functional distances between transporters. Based on all available data sets and their integration, we assigned biochemical/biological functions to each SLC, making this study one of the largest systematic annotations of human gene function and a potential blueprint for future research endeavors.

The solute carrier superfamily interactome

Solute carrier (SLC) transporters form a protein superfamily that enables transmembrane transport of diverse substrates including nutrients, ions and drugs. There are about 450 different SLCs, residing in a variety of subcellular membranes. Loss-of-function of an unusually high proportion of SLC transporters is genetically associated with a plethora of human diseases, making SLCs a rapidly emerging but challenging drug target class. Knowledge of their protein environment may elucidate the molecular basis for their functional integration with metabolic and cellular pathways and help conceive pharmacological interventions based on modulating proteostatic regulation. We aimed at obtaining a global survey of the SLC-protein interaction landscape and mapped the protein-protein interactions of 396 SLCs by interaction proteomics. We employed a functional assessment based on RNA interference of interactors in combination with measurement of protein stability and localization. As an example, we detail the role of a SLC16A6 phospho-degron and the contributions of PDZ-domain proteins LIN7C and MPP1 to the trafficking of SLC43A2. Overall, our work offers a resource for SLC-protein interactions for the scientific community.

Protein kinases in neurodegenerative diseases: current understandings and implications for drug discovery

Neurodegenerative diseases (e.g., Alzheimer's, Parkinson's, Huntington's disease, and Amyotrophic Lateral Sclerosis) are major health threats for the aging population and their prevalences continue to rise with the increasing of life expectancy. Although progress has been made, there is still a lack of effective cures to date, and an in-depth understanding of the molecular and cellular mechanisms of these neurodegenerative diseases is imperative for drug development. Protein phosphorylation, regulated by protein kinases and protein phosphatases, participates in most cellular events, whereas aberrant phosphorylation manifests as a main cause of diseases. As evidenced by pharmacological and pathological studies, protein kinases are proven to be promising therapeutic targets for various diseases, such as cancers, central nervous system disorders, and cardiovascular diseases. The mechanisms of protein phosphatases in pathophysiology have been extensively reviewed, but a systematic summary of the role of protein kinases in the nervous system is lacking. Here, we focus on the involvement of protein kinases in neurodegenerative diseases, by summarizing the current knowledge on the major kinases and related regulatory signal transduction pathways implicated in diseases. We further discuss the role and complexity of kinase-kinase networks in the pathogenesis of neurodegenerative diseases, illustrate the advances of clinical applications of protein kinase inhibitors or novel kinase-targeted therapeutic strategies (such as antisense oligonucleotides and gene therapy) for effective prevention and early intervention.

An atlas of bacterial serine-threonine kinases reveals functional diversity and key distinctions from eukaryotic kinases

Bacterial serine-threonine kinases (STKs) regulate diverse cellular processes associated with cell growth, virulence, and pathogenicity and are evolutionarily related to the druggable eukaryotic STKs. A deeper understanding of how bacterial STKs differ from their eukaryotic counterparts and how they have evolved to regulate diverse bacterial signaling functions is crucial for advancing the discovery and development of new antibiotic therapies. Here, we classified more than 300,000 bacterial STK sequences from the NCBI RefSeq nonredundant and UniProt protein databases into 35 canonical and seven pseudokinase families on the basis of the patterns of evolutionary constraints in the conserved catalytic domain and flanking regulatory domains. Through statistical comparisons, we identified features distinguishing bacterial STKs from eukaryotic STKs, including an arginine residue in a regulatory helix (C helix) that dynamically couples the ATP- and substrate-binding lobes of the kinase domain. Biochemical and peptide library screens demonstrated that evolutionarily constrained residues contributed to substrate specificity and kinase activation in the Mycobacterium tuberculosis kinase PknB. Together, these findings open previously unidentified avenues for investigating bacterial STK functions in cellular signaling and for developing selective bacterial STK inhibitors.

Precise modulation of protein refolding by rationally designed covalent organic frameworks

Precisely regulating protein conformation (folding) for biomanufacturing and biomedicine is of great significance but remains challenging. In this work, we innovate a covalent organic framework (COF)-directed protein refolding strategy to modulate protein conformation by rationally designed covalent organic frameworks with adapted pore structures and customizable microenvironments. The conformation of denatured protein can be efficiently recovered through a simple one-step approach using covalent organic framework treatment in aqueous or buffer solutions. This strategy demonstrates high generality that can be applied to various proteins (for example, lysozyme, glucose oxidase, trypsin, nattokinase, and papain) and diverse covalent organic frameworks. An in-depth investigation of the refolding mechanism reveals that pore size and microenvironments such as hydrophobicity, π-π conjugation, and hydrogen bonding are critical to regulating protein conformation. Furthermore, we use this covalent organic framework platform to build up solid-phase columns for continuous protein recovery and achieved a ~ 100% refolding yield and excellent recycling performance (30 cycles), enabling an integrated process for the extracting and refolding denatured proteins (such as the harvest of protein in inclusion bodies). This study creates a highly efficient and customizable covalent organic framework platform for precisely regulating proteins refolding and enhancing their performance, opening up a new avenue for advanced protein manufacturing.

Chemically Synthesized Fluorescence-Based Kinase Sensing Systems for Signaling in Cancer

Kinases are an essential class of enzymes that regulate cellular processes through phosphorylation, influencing signal transduction, cell cycle progression, and apoptosis. Dysregulation of kinase activity is a hallmark of cancer, contributing to tumorigenesis, metastasis, and therapeutic resistance. Therefore, precise detection and monitoring of kinase activity are essential for understanding cancer biology and advancing diagnostics and therapeutics. Among various detection methods, fluorescence-based kinase sensing systems have emerged as highly sensitive, real-time tools for investigating kinase function. These systems leverage fluorescent moieties, either genetically encoded or chemically synthesized, to provide spatial and temporal insights into kinase activity in complex biological environments. This review focuses on chemically synthesized fluorescence-based kinase sensing systems, which offer unique advantages, including precise control over concentrations and compatibility with in vitro and in vivo applications. We have classified the chemically synthesized sensing systems into three categories: specific peptide substrate-based, adenosine triphosphate/adenosine diphosphate-recognition-based, and inhibitor-based sensing systems, each tailored to specific kinase activities. Compared to genetically encoded systems, chemically synthesized sensors demonstrate greater versatility and are better suited for quantitative high-throughput applications. This review explores the design, mechanisms, and applications of these systems in cancer biology, highlighting their potential for identifying kinase biomarkers, optimizing targeted therapies, and advancing personalized medicine.

PRKCQ Is Dispensable for Spermatogenesis in Mice

Protein kinase C (PKC) family is evolutionally conserved and involved in various signaling cascades in all cells. Of the family, PRKCQ is dominatingly expressed in testis, however, its molecular functionality in spermatogenesis and male fertility remains unclear. To evaluate the role of PRKCQ in spermatogenesis, Prkcq knockout mice were generated using CRISPR/Cas9 system. Histological and immunofluorescence assays by different markers were employed to assess the testicular cells variation. Sperm parameters were analyzed by computer-assisted sperm analyzer. qPCR assay was used to examine the expression levels of other PKC family genes. We found that PRKCQ was conserved throughout evolution and highly expressed in testis. Prkcq-/- mice were successfully generated and developed viably. Normal fertility was observed in Prkcq-/- males. Prkcq-/- mice exhibited no defects in spermatogenic cells and mature sperm were full in epididymis. Furthermore, there were no differences in sperm motility and progressive motility between Prkcq-/- males and controls. Our findings report a detailed phenotypic analysis of Prkcq-/- males and indicate that PRKCQ is not required for spermatogenesis in male mice, which can provide basic information for other researchers.

Identification of a Novel FLT4 c.3028A>C Variant Associated With Milroy Disease

VEGFR3 (FLT4) is crucial for embryonic lymphangiogenesis, and defects in this receptor can lead to congenital lymphedema type 1A (Milroy disease). This study analyses FLT4 gene sequence in 24 primary lymphedema patients, identifying genetic variants in five patients resembling typical Milroy disease. A novel likely pathogenic variant (c.3028A>C) was identified, and the pathogenicity of two previously described variants (c.3175G>C and c.3298T>C) was supported.

Dr. Kinase: predicting the drug-resistance hotspots of protein kinases

Protein kinases (PKs) regulate various cellular functions, and are targeted by small-molecule kinase inhibitors (KIs) in cancers and other diseases. However, drug resistance (DR) of KIs occurs through critical mutations in four types of representative hotspots, including gatekeeper, G-loop, αC-helix, and A-loop. KI DR has become a common clinical complication affecting multiple cancers, targeted kinases, and drugs. To tackle this challenge, we report an upgraded web server, namely Dr. Kinase, for predicting the loci of four DR hotspots and assessing effects of mutations on DR hotspots for PKs in our previous studies, by utilizing multimodal features and deep hybrid learning. The performance of Dr. Kinase has been rigorously evaluated using independent testing, demonstrating excellent accuracy with area under the curve values exceeding 0.89 in different types of DR hotspot predictions. We further conducted in silico analyses to evaluate and validate the epidermal growth factor receptor mutations on protein conformation and KIs' binding efficacy. Dr. Kinase is freely available at http://modinfor.com/drkinase, with comprehensive annotations and visualizations. We anticipate that Dr. Kinase will be a highly useful service for the basic, translational, and clinical community to unveil the molecular mechanisms of DR and the development of next-generation KIs for emerging cancer precision medicine.

Human ATP-binding proteins: Structural features, functional diversity, and pharmacotherapeutic potential in disease: A review

ATP-binding proteins (ABPs) form diverse and essential protein families across living organisms. Early life forms likely relied on simple chemical reactions for energy, but with the emergence of ABPs and their evolving functions, organisms became capable of more efficient energy storage and utilization, which drove the complexity of metabolic and life processes. By binding and hydrolyzing ATP through conserved structural motifs such as the Walker motifs, ABPs play critical roles in material transport, signal transduction, cellular structure maintenance, motility, and cell cycle regulation. Dysfunctions arising from mutations, deletions, or misregulation of ABPs are linked to a variety of human diseases, including cancer, neurodegenerative disorders, and cardiovascular diseases. The growing recognition of ABPs' significance in disease progression highlights their relevance not only in basic biology but also in clinical applications, particularly as biomarkers and therapeutic targets. This review provides a comprehensive overview of human ABPs, detailing their structural and functional roles, their involvement in disease mechanisms, and the latest advances in understanding their clinical relevance. Additionally, it identifies current research gaps and offers new perspectives for future investigations and therapeutic strategies.

A phylogenetic analysis of the CDKL protein family unravels its evolutionary history and supports the Drosophila model of CDKL5 deficiency disorder

The human CDK-like (CDKL) family of serine‒threonine kinases has five members (CDKL1-5), with a conserved N-terminal kinase domain and variable C-termini. Among these, CDKL5 is of particular interest because of its involvement in CDKL5 deficiency disorder (CDD), a rare epileptic encephalopathy with several comorbidities for which there are no specific treatments. Current CDD vertebrate models are seizure resistant, which could be explained by the genetic background, including leaky expression of other CDKLs. Thus, phylogenetic analysis of the protein family would be valuable for understanding current models and developing new ones. Our phylogenetic studies revealed that ancestral CDKLs were present in all major eukaryotic clades and had ciliary/flagellar functions, which may have diversified throughout evolution. The original CDKL, which was likely similar to human CDKL5, gave rise to the remaining family members through successive duplications. In addition, particular clades have undergone further gene duplication and loss, a pattern that suggests some functional redundancy among them. A separate study focusing on the C-terminal tail of CDKL5 suggested that this domain is only functionally relevant in jawed vertebrates. We have developed a model of CDD in Drosophila based on downregulation of the single Cdkl gene by RNAi, which results in phenotypes similar to those of CDD patients, that are rescued by re-expression of fly Cdkl and human CDKL5. CDKL proteins contain a conserved kinase domain, originally involved in ciliary maintenance; therefore, invertebrate model organisms can be used to investigate CDKL functions that involve the aforementioned domain.

Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome

The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with the outside world. Many disease-associated changes are hard-wired within the surfaceome, yet approved drugs target less than 50 cell surface proteins. In the past decade, the proteomics community has made significant strides in developing new technologies tailored for studying the surfaceome in all its complexity. In this review, we first dive into the unique characteristics and functions of the surfaceome, emphasizing the necessity for specialized labeling, enrichment, and proteomic approaches. An overview of surfaceomics methods is provided, detailing techniques to measure changes in protein expression and how this leads to novel target discovery. Next, we highlight advances in proximity labeling proteomics (PLP), showcasing how various enzymatic and photoaffinity proximity labeling techniques can map protein-protein interactions and membrane protein complexes on the cell surface. We then review the role of extracellular post-translational modifications, focusing on cell surface glycosylation, proteolytic remodeling, and the secretome. Finally, we discuss methods for identifying tumor-specific peptide MHC complexes and how they have shaped therapeutic development. This emerging field of neo-protein epitopes is constantly evolving, where targets are identified at the proteome level and encompass defined disease-associated PTMs, complexes, and dysregulated cellular and tissue locations. Given the functional importance of the surfaceome for biology and therapy, we view surfaceomics as a critical piece of this quest for neo-epitope target discovery.

DYRK1B phosphorylates FOXO1 to promote hepatic gluconeogenesis

Dual-specificity tyrosine phosphorylation-regulated kinase 1B (DYRK1B), a member of the CMGC group of kinases, is linked to metabolic syndrome, though the underlying molecular mechanisms remain unclear. In this study, we show that Dyrk1b expression is induced in the liver by fasting and in diabetic mice. Through both in vivo and in vitro experiments, we demonstrate that DYRK1B promotes hepatic gluconeogenesis and glucose intolerance. Liver-specific Dyrk1b conditional knockout mice were protected from diet-induced hyperglycemia. Mechanistically, DYRK1B interacts with and phosphorylates FOXO1, primarily at Thr467/Ser468, which is essential for its nuclear localization. Additionally, DYRK1B inhibits AKT-mediated FOXO1 phosphorylation at Thr24 and Ser256, enhancing its nuclear retention. DYRK1B-mediated phosphorylation increases the expression of gluconeogenic genes and promotes gluconeogenesis. Further, AZ191, a pharmacological inhibitor of DYRK1B, significantly reduced blood glucose levels in diabetic mice. Collectively, these findings provide new insights into the role of DYRK1B in glucose metabolism and identify it as a new therapeutic target for treating diabetes.

Regulatory mimicry of cyclin-dependent kinases by a conserved herpesvirus protein kinase

Herpesviruses encode conserved protein kinases (CHPKs) that target cellular cyclin-dependent kinase (CDK) phosphorylation sites; thus, they are termed viral CDK-like kinases. Tyrosine 15 in the GxGxxG motifs of CDK1 and CDK2, whose phosphorylation down-regulates their catalytic activities, is conserved in the corresponding motifs of CHPKs. We found that CHPK UL13, the corresponding Tyr-162 in herpes simplex virus 2 (HSV-2), was phosphorylated in HSV-2-infected cells. Mutational analyses of HSV-2 UL13 Tyr-162 suggested that phosphorylation of UL13 Tyr-162 reduced the phosphorylation of all UL13 substrates tested in HSV-2-infected cells. These findings suggested that HSV-2 UL13 mimicked the regulatory mechanism of CDKs and that this CHPK has regulatory and functional mimicry with CDKs. Furthermore, phosphorylation of HSV-2 UL13 Tyr-162 was suggested to be required for the downregulation of viral replication and pathogenicity, specifically in the brains of mice, and for efficient viral recurrence in guinea pigs. These findings highlight the dual impact of the regulatory mimicry of CDKs by CHPK on the fine-tuned regulation of lytic and latent HSV-2 infections in vivo.

Properties of FDA-approved small molecule protein kinase inhibitors: A 2025 update

Because of the deregulation of protein kinase action in many inflammatory diseases and cancer, the protein kinase family has become one of the most significant drug targets in the 21st century. There are 85 FDA-approved protein kinase antagonists that target about two dozen different enzymes and four of these drugs were approved in 2024 and a fifth was approved in 2025. Of these drugs, five target dual specificity protein kinases (MEK1/2), fourteen inhibit protein-serine/threonine protein kinases, twenty-one block nonreceptor protein-tyrosine kinases, and 45 target receptor protein-tyrosine kinases. The data indicate that 75 of these drugs are prescribed for the treatment of neoplasms. Seven drugs (abrocitinib, baricitinib, deucravacitinib, deuruxolitinib, ritlecitinib, tofacitinib, upadacitinib) are prescribed for the management of inflammatory diseases (atopic dermatitis, rheumatoid arthritis, psoriasis, alopecia areata, and ulcerative colitis). Of the 85 FDA-approved agents, about two dozen are used in the treatment of multiple diseases. The following four drugs received FDA approval in 2024 - deuruxolitinib (alopecia areata), ensartinib and lazertinib (non-small cell lung cancer), and tovorafenib (pediatric glioma) while mirdametinib was approved in 2025 for the treatment of type I neurofibromatosis (von Recklinghausen disease). Apart from netarsudil, temsirolimus, and trilaciclib, the approved protein kinase blockers are orally bioavailable. This article summarizes the physicochemical properties of all 85 FDA-approved small molecule protein kinase inhibitors including the molecular weight, number of hydrogen bond donors/acceptors, ligand efficiency, lipophilic efficiency, polar surface area, and solubility. A total of 39 of the 85 FDA-approved drugs have a least one Lipinski rule of 5 violation.

Kinase-Targeted Therapies for Glioblastoma

Protein phosphorylation and dephosphorylation are key mechanisms that regulate cellular activities. The addition or removal of phosphate groups by specific enzymes, known as kinases and phosphatases, activates or inhibits many enzymes and receptors involved in various cell signaling pathways. Dysregulated activity of these enzymes is associated with various diseases, predominantly cancers. Synthetic and natural single- and multiple-kinase inhibitors are currently being used as targeted therapies for different tumors, including glioblastoma. Glioblastoma IDH-wild-type is the most aggressive brain tumor in adults, with a median overall survival of 15 months. The great majority of glioblastoma patients present mutations in receptor tyrosine kinase (RTK) signaling pathways responsible for tumor initiation and/or progression. Despite this, the multi-kinase inhibitor regorafenib has only recently been approved for glioblastoma patients in some countries. In this review, we analyze the history of kinase inhibitor drugs in glioblastoma therapy.

Targeting kinases that regulate programmed cell death: a new therapeutic strategy for breast cancer

Breast cancer is one of the most prevalent malignant tumors among women and ranks as the second leading cause of cancer-related deaths in females, primarily due to delays in diagnosis and shortcomings in treatment strategies. Consequently, there is a pressing need to identify reliable therapeutic targets and strategies. In recent years, the identification of effective biomarkers-particularly novel molecular therapeutic targets-has become a focal point in breast cancer research, aimed at predicting disease aggressiveness and monitoring treatment responses. Simultaneously, advancements in understanding the molecular mechanisms underlying cellular programmed death have opened new avenues for targeting kinase-regulated programmed cell death as a viable therapeutic strategy. This review summarizes the latest research progress regarding kinase-regulated programmed death (including apoptosis, pyroptosis, autophagy, necroptosis, and ferroptosis) in breast cancer treatment. It covers the key kinases involved in this mechanism, their roles in the onset and progression of breast cancer, and strategies for modulating these kinases through pharmacological interventions.

Global analysis of actionable genomic alterations in thyroid cancer and precision-based pharmacogenomic strategies

Introduction

Thyroid cancer, a prevalent endocrine malignancy, has an age-standardized incidence rate of 9.1 per 100,000 people and a mortality rate of 0.44 per 100,000 as of 2024. Despite significant advances in precision oncology driven by large-scale international consortia, gaps persist in understanding the genomic landscape of thyroid cancer and its impact on therapeutic efficacy across diverse populations.

Methods

To address this gap, we performed comprehensive data mining and in silico analyses to identify pathogenic variants in thyroid cancer driver genes, calculate allele frequencies, and assess deleteriousness scores across global populations, including African, Amish, Ashkenazi Jewish, East and South Asian, Finnish and non-Finnish European, Latino, and Middle Eastern groups. Additionally, pharmacogenomic profiling, in silico drug prescription, and clinical trial data were analyzed to prioritize targeted therapeutic strategies.

Results

Our analysis examined 56,622 variants in 40 thyroid cancer-driver genes across 76,156 human genomes, identifying 5,001 known and predicted oncogenic variants. Enrichment analysis revealed critical pathways such as MAPK, PI3K-AKT-mTOR, and p53 signaling, underscoring their roles in thyroid cancer pathogenesis. High-throughput validation strategies confirmed actionable genomic alterations in RET, BRAF, NRAS, KRAS, and EPHA7. Ligandability assessments identified these proteins as promising therapeutic targets. Furthermore, our findings highlight the clinical potential of targeted drug inhibitors, including vandetanib, dabrafenib, and selumetinib, for improving treatment outcomes.

Discussion

This study underscores the significance of integrating genomic insights with pharmacogenomic strategies to address disparities in thyroid cancer treatment. The identification of population-specific oncogenic variants and actionable therapeutic targets provides a foundation for advancing precision oncology. Future efforts should focus on including underrepresented populations, developing population-specific prevention strategies, and fostering global collaboration to ensure equitable access to pharmacogenomic testing and innovative therapies. These initiatives have the potential to transform thyroid cancer care and align with the broader goals of personalized medicine.

Probing the Effect of Protein and Inhibitor Conformational Flexibility on the Reaction of Rocelitinib-Like Covalent Inhibitors of Epidermal Growth Factor Receptor. A Quantum Mechanics/Molecular Mechanics Study

Epidermal growth factor receptor (EGFR) is a tyrosine kinase and a validated target for non-small cell lung cancer (NSCLC). Drug discovery efforts on this target initially focused on traditional competitive, reversible ATP-binding site inhibitors; however, irreversible covalent binding EGFR inhibitors have become increasingly more popular. Covalent EGFR inhibitors have been developed using a range of different scaffolds, and unsurprisingly, the incorporation of an electrophilic acrylamide group can result in sizable orientation differences relative to the Cys797 nucleophile and the Asp800 general base. In this work, we report a QM/MM study aiming to better understand the aspects of covalent adduct formation, including the role of protein flexibility on chemical reactivity, the impact of electrophile location within the ATP binding site, and the impact of the acrylamide conformation (s-cis vs s-trans). We focus here on the diaminopyrimidine scaffold, as exemplified by Rocelitinib, where the electrophile is attached to its back pocket binding group. Our goal is to elucidate how electrophilic groups can be incorporated onto different inhibitor scaffolds targeting reactive active site residues. We find that irrespective of the EGFR MD conformation chosen, acrylamide, in both the s-cis or s-trans, can undergo reaction with rate-determining barriers of ∼20 kcal/mol. Interestingly, the nature of the rate-determining step for Rocelitinib-like inhibitors was found to be either direct nucleophilic attack or keto-enol tautomerization, depending on the precise protein and inhibitor conformation.

Positional distribution and conservation of major phosphorylated sites in the human kinome

The human protein kinome is a group of over 500 therapeutically relevant kinases. Exemplified by over 10,000 phosphorylated sites reported in global phosphoproteomes, kinases are also highly regulated by phosphorylation. Currently, 1008 phosphorylated sites in 273 kinases are associated with their regulation of activation/inhibition, and a few in 30 kinases are associated with altered activity. Phosphorylated sites in 196 kinases are related to other molecular functions such as localization and protein interactions. Over 8,000 phosphorylated sites, including all those in 517 kinases are unassigned to any functions. This imposes a significant bias and challenge for the effective analysis of global phosphoproteomics datasets. Hence, we derived a set of stably and frequently detected phosphorylated sites (representative phosphorylated sites) across diverse experimental conditions annotated in the PhosphoSitePlus database and presumed them to be relevant to the human kinase regulatory network. Analysis of these representative phosphorylated sites led to the classification of 449 kinases into four distinct categories (kinases with phosphorylated sites apportioned (PaKD) and enigmatic (PeKD), and those with predominantly within kinase domain (PiKD) and outside kinase domain (PoKD)). Knowledge-based functional analysis and sequence conservation across the family/subfamily identified phosphorylated sites unique to specific kinases that could contribute to their unique functions. This classification of representative kinase phosphorylated sites enhance our understanding of prioritized validation and provides a novel framework for targeted phosphorylated site enrichment approaches. Phosphorylated sites in kinases associated with dysregulation in diseases were frequently located outside the kinase domain, and suggesting their regulatory roles and opportunities for phosphorylated site-directed therapeutic approaches.

RNF144A-VRK2-G3BP1 axis regulates stress granule assembly

Under the cellular stress, stress granules (SGs) help survival and proliferation of the cell. Unfortunately, the same SGs help unwanted cancer cells under stressful environment, including anti-cancer chemotherapy treatment. While SGs elevate the cancer cell's resistance to chemotherapy, the mechanism behind the formation of SGs in cancer cell under chemotherapy treatment is still to be revealed. Here, we identified that the level of VRK2 and the phosphorylation of its novel substrate, G3BP1, are reduced when the cellular stress was increased by sodium arsenite (SA) or cisplatin treatment. We also demonstrated that the level of RNF144A is increased in response to the stress and further downregulates VRK2 through proteasomal degradation in various types of cancer cells. Furthermore, inhibition of SG formation by the overexpression of VRK2 sensitized the cells to the stress and chemotherapy. Together, our study establishes an RNF144A-VRK2-G3BP1 axis that regulates SG formation and suggest its potential usage in anti-cancer therapy.

MAST Kinases' Function and Regulation: Insights from Structural Modeling and Disease Mutations

Background/Objectives: The MAST kinases are ancient AGC kinases associated with many human diseases, such as cancer, diabetes, and neurodevelopmental disorders. We set out to describe the origins and diversification of MAST kinases from a structural and bioinformatic perspective to inform future research directions. Methods: We investigated MAST-lineage kinases using database and sequence analysis. We also estimate the functional consequences of disease point mutations on protein stability by integrating predictive algorithms and AlphaFold. Results: Higher-order organisms often have multiple MASTs and a single MASTL kinase. MAST proteins conserve an AGC kinase domain, a domain of unknown function 1908 (DUF), and a PDZ binding domain. D. discoideum contains MAST kinase-like proteins that exhibit a characteristic insertion within the T-loop but do not conserve DUF or PDZ domains. While the DUF domain is conserved in plants, the PDZ domain is not. The four mammalian MASTs demonstrate tissue expression heterogeneity by mRNA and protein. MAST1-4 are likely regulated by 14-3-3 proteins based on interactome data and in silico predictions. Comparative ΔΔG estimation identified that MAST1-L232P and G522E mutations are likely destabilizing. Conclusions: We conclude that MAST and MASTL kinases diverged from the primordial MAST, which likely operated in both biological niches. The number of MAST paralogs then expanded to the heterogeneous subfamily seen in mammals that are all likely regulated by 14-3-3 protein interaction. The reported pathogenic mutations in MASTs primarily represent alterations to post-translational modification topology in the DUF and kinase domains. Our report outlines a computational basis for future work in MAST kinase regulation and drug discovery.

Catalytically inactive subgroup VIII receptor-like cytoplasmic kinases regulate the immune-triggered oxidative burst in Arabidopsis thaliana

Protein kinases are key components of multiple cell signaling pathways. Several receptor-like cytoplasmic kinases (RLCKs) have demonstrated roles in immune and developmental signaling across various plant species, making them of interest in the study of phosphorylation-based signal relay. Here, we present our investigation of a subgroup of RLCKs in Arabidopsis thaliana. Specifically, we focus on subgroup VIII RLCKs: MAZ and its paralog CARK6, as well as CARK7 and its paralog CARK9. We found that both MAZ and CARK7 associate with the calcium-dependent protein kinase CPK28 in planta and, furthermore, that CPK28 phosphorylates both MAZ and CARK7 on multiple residues in areas that are known to be critical for protein kinase activation. Genetic analysis suggested redundant roles for MAZ and CARK6 as negative regulators of the immune-triggered oxidative burst. We provide evidence that supports homo- and heterodimerization between CARK7 and MAZ, which may be a general feature of this subgroup. Multiple biochemical experiments indicated that neither MAZ nor CARK7 demonstrate catalytic protein kinase activity in vitro. Interestingly, we found that a mutant variant of MAZ incapable of protein kinase activity can complement maz-1 mutants, suggesting non-catalytic roles of MAZ in planta. Overall, our study identifies subgroup VIII RLCKs as new players in Arabidopsis immune signaling and highlights the importance of non-catalytic functions of protein kinases.

NEK8, a NIMA-family protein kinase at the core of the ciliary INV complex

Here we describe the current knowledge about the ciliary kinase NEK8, highlighting what we know and what we don't know about its regulation, substrates and potential functions. We also review the literature about the pathological consequences of different NEK8 variants in patients of nephronophthisis, renal-hepatic-pancreatic dysplasia and autosomal dominant polycystic kidney disease, three different types of ciliopathies. NEK8 belongs to the NIMA family of serine/threonine protein kinases. Like its closest relative, NEK9, it contains a protein kinase and an RCC1 domain, but lacks the C-terminal region that is key for NEK9's regulation as a G2/M kinase. Importantly, NEK8 localizes to cilia as part of a multimeric protein complex that assembles in a fibrillar fashion at the proximal half of this signaling organelle, defining what is known as the INV compartment. NEK8 and its INV compartment partners inversin, ANKS6 and NPHP3 are necessary for left-right determination and the correct development of different organs such as the kidney, the heart and the liver. But the kinase substrates, regulatory mechanism and activating cues and thus the molecular basis of NEK8 important physiological roles remain elusive. We present the current findings regarding NEK8 and also highlight what we miss in order to progress towards the understanding of the kinase and the function of the INV complex at the cilia.

Advancing Src kinase inhibition: From structural design to therapeutic innovation - A comprehensive review

Src kinase, a non-receptor tyrosine kinase implicated in cellular signaling networks, plays a pivotal role in tumor progression and therapeutic resistance. Despite intensive research efforts spanning decades, no Src-selective kinase inhibitors have yet entered clinical use, highlighting the challenges in developing targeted therapeutics. Here we review recent advances in small-molecule Src inhibitor development, focusing on structural design strategies, binding mechanisms, and therapeutic applications. We analyze emerging approaches including fragment-based drug design, allosteric targeting, and substrate-competitive inhibition that have yielded promising new scaffold classes. Special attention is given to innovations in achieving isozyme selectivity, particularly through exploitation of non-ATP binding pockets and covalent inhibition strategies. Integration of artificial intelligence, living organoid platforms, and targeted protein degradation technologies is accelerating inhibitor optimization. We discuss key challenges in Src inhibitor development, including the need for enhanced selectivity, reduced off-target effects, and improved resistance profiles. Our analysis reveals promising directions for future therapeutic development, emphasizing the importance of rational design principles guided by structural insights and emerging technologies. These findings provide a framework for developing next-generation Src inhibitors with improved clinical potential.

Identifying key palmitoylation-associated genes in endometriosis through genomic data analysis

BACKGROUND

Palmitoylation, a post-translational lipid modification, has garnered increasing attention for its role in inflammatory processes and tumorigenesis. Emerging evidence suggests a potential association between palmitoylation and inflammatory responses in the pathogenesis of endometriosis. However, the precise mechanistic interplay remains elusive, necessitating further investigation.

METHODS

This study integrated transcriptomic analysis and Mendelian randomization (MR) to identify a causal gene set implicated in endometriosis. Differentially expressed genes (DEGs) were first identified in the training dataset using the limma package in R. Weighted gene co-expression network analysis (WGCNA) was subsequently performed, leveraging Single Sample Gene Set Enrichment Analysis (ssGSEA)-derived scores of palmitoylation-related genes (PRGs) as phenotypic traits to identify key modular genes. The intersection of these key modular genes with DEGs yielded a refined gene set. Machine learning algorithms were then applied to further optimize gene selection, followed by external validation, immune infiltration analysis, RNA network construction, and exploration of potential targeted drug candidates.

RESULTS

Through a rigorous screening process, VRK1, GALNT12, and RMI1 emerged as key genes associated with palmitoylation, exhibiting significant downregulation in endometriosis samples (P < 0.05), indicative of a potential protective role. Immune infiltration analysis further revealed strong correlations between these genes and M2 macrophages as well as resting Natural Killer (NK) cells. Additionally, investigations into the targeted RNA network and drug association profiling provided novel insights, laying the groundwork for future high-quality validation studies.

CONCLUSIONS

This study employed a comprehensive analytical framework to identify palmitoylation-associated key genes in endometriosis. The integration of immunoinfiltration analysis, RNA network construction, and drug association profiling offers valuable insights for advancing clinical diagnostics, disease monitoring, and therapeutic development in endometriosis.

CellEKT: a robust chemical proteomics workflow to profile cellular target engagement of kinase inhibitors

The human genome encodes 518 protein kinases that are pivotal for drug discovery in various therapeutic areas such as cancer and autoimmune disorders. The majority of kinase inhibitors target the conserved ATP-binding pocket, making it difficult to develop selective inhibitors. To characterize and prioritize kinase-inhibiting drug candidates, efficient methods are desired to determine target engagement across the cellular kinome. In this study, we present CellEKT (Cellular Endogenous Kinase Targeting), an optimized and robust chemical proteomics platform for investigating cellular target engagement of endogenously expressed kinases using the sulfonyl fluoride-based probe XO44 and two new probes ALX005 and ALX011. The optimized workflow enabled the determination of the kinome interaction landscape of covalent and non-covalent drugs across over 300 kinases, expressed as half maximum inhibitory concentration (IC50), which were validated using distinct platforms like phosphoproteomics and NanoBRET. With CellEKT, target engagement profiles were linked to their substrate space. CellEKT has the ability to decrypt drug actions and to guide the discovery and development of drugs.

A Probe-Based Target Engagement Assay for Kinases in Live Cells

The efficacy and safety of kinase inhibitor drugs are largely influenced by their selectivity. Available profiling technologies are primarily based on overexpressed or endogenously expressed kinases in cell extracts. We compared kinase capture with the cell penetrant covalent probe XO44 to three derivatives and found that replacing the alkyne handle with a trans-cyclooctene group allowed the development of a more robust kinase capture and enrichment protocol. An intracellular chemoproteomics target profiling and engagement assay was devised by optimizing probe concentration and incubation time and using an isobaric mass tag-based strategy for relative quantification. Comparing intracellular kinase profiles of the marketed drug dasatinib and the tool compound dinaciclib with the lysate-based kinobeads assay revealed excellent agreement in rank-order of binding. Dinaciclib showed a systematic shift to higher IC50s, suggesting that intracellular cosubstrate concentrations, cell penetration of the compound, as well as kinase localization and complexes in live cells influence target profiles. Further, we show that sepiapterin reductase SPR and multidrug resistance protein 1 ABCC1 are off-targets of kinase inhibitor scaffolds with potential implications on efficacy and safety.

Redox regulation and dynamic control of brain-selective kinases BRSK1/2 in the AMPK family through cysteine-based mechanisms

In eukaryotes, protein kinase signaling is regulated by a diverse array of post-translational modifications, including phosphorylation of Ser/Thr residues and oxidation of cysteine (Cys) residues. While regulation by activation segment phosphorylation of Ser/Thr residues is well understood, relatively little is known about how oxidation of cysteine residues modulate catalysis. In this study, we investigate redox regulation of the AMPK-related brain-selective kinases (BRSK) 1 and 2, and detail how broad catalytic activity is directly regulated through reversible oxidation and reduction of evolutionarily conserved Cys residues within the catalytic domain. We show that redox-dependent control of BRSKs is a dynamic and multilayered process involving oxidative modifications of several Cys residues, including the formation of intramolecular disulfide bonds involving a pair of Cys residues near the catalytic HRD motif and a highly conserved T-loop Cys with a BRSK-specific Cys within an unusual CPE motif at the end of the activation segment. Consistently, mutation of the CPE-Cys increases catalytic activity in vitro and drives phosphorylation of the BRSK substrate Tau in cells. Molecular modeling and molecular dynamics simulations indicate that oxidation of the CPE-Cys destabilizes a conserved salt bridge network critical for allosteric activation. The occurrence of spatially proximal Cys amino acids in diverse Ser/Thr protein kinase families suggests that disulfide-mediated control of catalytic activity may be a prevalent mechanism for regulation within the broader AMPK family.

Phosphoproteomic analysis of X-ray-irradiated planarians provides novel insights into the DNA damage response

Phosphorylation plays a crucial role in the cellular response to radiation and cancer therapies, yet phosphoproteomics studies in planarians remain underexplored despite the organism's remarkable regenerative capacities. This study utilized advanced ion mobility mass spectrometry for 4D-label-free quantitative proteomics to identify phosphorylation sites associated with irradiation in planarians. A total of 33,284 phosphorylation sites from 15,505 phosphorylated peptides and 4710 unique phosphoproteins were identified. In the sub-lethal dose irradiation group, 1695 phosphoproteins with 3483 phosphorylation sites exhibited significant changes, while exposure to lethal doses of radiation led to significant changes in 2308 phosphoproteins with 6112 phosphorylation sites, including many kinases, transcription factors, and cytoskeletal proteins. Functional enrichment analysis revealed that the altered phosphoproteins were primarily involved in transcription, RNA biosynthesis, mRNA processing regulation, and spliceosomal complex assembly. Functional validation of five differentially phosphorylated proteins revealed that their depletion impaired stem cell regeneration after irradiation by disrupting DNA repair, suggesting that these proteins are critical to planarian biology and their radiation response. By identifying the phosphorylation state and specific sites of planarian proteins, our study lays the foundation for further research on protein phosphorylation in the radiation-induced DNA damage response. In addition, our findings provide preliminary insights into the role of calnexin, a protein involved in interacting with newly synthesized N-linked glycoproteins, in planarians.

A stress-responsive p38 signaling axis in choanoflagellates

Animal kinases regulate cellular responses to environmental stimuli, including cell differentiation, migration, survival, and response to stress, but the ancestry of these functions is poorly understood. Choanoflagellates, the closest living relatives of animals, encode homologs of diverse animal kinases and have emerged as model organisms for reconstructing animal origins. However, efforts to identify key kinase regulators in choanoflagellates have been constrained by the limitations of currently available genetic tools. Here, we report on a framework that combines small molecule-driven kinase discovery with targeted genetics to reveal kinase function in choanoflagellates. To study the physiological roles of choanoflagellate kinases, we established two high-throughput platforms to screen the model choanoflagellate Salpingoeca rosetta with a curated library of human kinase inhibitors. We identified 95 diverse kinase inhibitors that disrupt S. rosetta cell proliferation. By focusing on one inhibitor, sorafenib, we identified a p38 kinase as a regulator of the heat shock response in S. rosetta. This finding reveals a conserved p38 function between choanoflagellates, animals, and fungi. Moreover, this study demonstrates that existing kinase inhibitors can serve as powerful tools to examine the ancestral roles of kinases that regulate modern animal development.

A Structural Insight Into Two Important ErbB Receptors (EGFR and HER2) and Their Relevance to Non-Small Cell Lung Cancer

The epidermal growth factor receptor (EGFR) family, comprising receptor tyrosine kinases (RTK) such as EGFR and HER2, plays a critical role in various signaling pathways related to cell proliferation, differentiation, and growth. EGFR overactivation due to aberrant signaling can lead to various cancers, including non-small cell lung cancer (NSCLC). To develop treatment for EGFR-related NSCLC, several tyrosine kinase inhibitors (TKIs) were designed: gefitinib, erlotinib, as first-generation; neratinib, dacomitinib as second-generation; osimertinib, lazertinib as third-generation, as examples. However, due to the acquired resistance by the mutations such as EGFRT790M and EGFRC797S together with the exon 20 insertion mutations, these drugs do not provide promising results for NSCLC patients. The development of fourth-generation inhibitors like EAI045 and further innovative drugs to overcome this resistance problem is a must to cure EGFR-related NSCLC. Among these, pyrazoline-thiazole scaffolds are found effective as EGFR-HER2 inhibitors against NSCLC, making them promising drug candidates. Although structures obtained so far for the EGFR family provide meaningful insights into the mechanisms, the quality and the quantity of the EGFR family structures are insufficient to elucidate the complete structures and functions to overcome NSCLC. This review evaluates the structures of EGFR-HER2 and investigates their relation to NSCLC.

From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies

In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.