The cAMP-dependent phosphorylation footprint in response to heat stress

KEY MESSAGE

cAMP modulates the phosphorylation status of highly conserved phosphosites in RNA-binding proteins crucial for mRNA metabolism and reprogramming in response to heat stress. In plants, 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) is a second messenger that modulates multiple cellular targets, thereby participating in plant developmental and adaptive processes. Although its role in ameliorating heat-related damage has been demonstrated, mechanisms that govern cAMP-dependent responses to heat have remained elusive. Here we analyze the role cAMP-dependent phosphorylation during prolonged heat stress (HS) with a view to gain insight into processes that govern plant responses to HS. To do so, we performed quantitative phosphoproteomic analyses in Nicotiana tabacum Bright Yellow-2 cells grown at 27 °C or 35 °C for 3 days overexpressing a molecular "sponge" that reduces free intracellular cAMP levels. Our phosphorylation data and analyses reveal that the presence of cAMP is an essential factor that governs specific protein phosphorylation events that occur during prolonged HS in BY-2 cells. Notably, cAMP modulates HS-dependent phosphorylation of proteins that functions in mRNA processing, transcriptional control, vesicular trafficking, and cell cycle regulation and this is indicative for a systemic role of the messenger. In particular, changes of cAMP levels affect the phosphorylation status of highly conserved phosphosites in 19 RNA-binding proteins that are crucial during the reprogramming of the mRNA metabolism in response to HS. Furthermore, phosphorylation site motifs and molecular docking suggest that some proteins, including kinases and phosphatases, are conceivably able to directly interact with cAMP thus further supporting a regulatory role of cAMP in plant HS responses.

Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast

The cell cycle is ordered by a controlled network of kinases and phosphatases. To generate gametes via meiosis, two distinct and sequential chromosome segregation events occur without an intervening S phase. How canonical cell cycle controls are modified for meiosis is not well understood. Here, using highly synchronous budding yeast populations, we reveal how the global proteome and phosphoproteome change during the meiotic divisions. While protein abundance changes are limited to key cell cycle regulators, dynamic phosphorylation changes are pervasive. Our data indicate that two waves of cyclin-dependent kinase (Cdc28Cdk1) and Polo (Cdc5Polo) kinase activity drive successive meiotic divisions. These two distinct phases of phosphorylation are ensured by the meiosis-specific Spo13 protein, which rewires the phosphoproteome. Spo13 binds to Cdc5Polo to promote phosphorylation in meiosis I, particularly of substrates containing a variant of the canonical Cdc5Polo motif. Overall, our findings reveal that a master regulator of meiosis directs the activity of a kinase to change the phosphorylation landscape and elicit a developmental cascade.

Protein Kinase A in neurological disorders

Cyclic adenosine 3', 5' monophosphate (cAMP)-dependent Protein Kinase A (PKA) is a multi-functional serine/threonine kinase that regulates a wide variety of physiological processes including gene transcription, metabolism, and synaptic plasticity. Genomic sequencing studies have identified both germline and somatic variants of the catalytic and regulatory subunits of PKA in patients with metabolic and neurodevelopmental disorders. In this review we discuss the classical cAMP/PKA signaling pathway and the disease phenotypes that result from PKA variants. This review highlights distinct isoform-specific cognitive deficits that occur in both PKA catalytic and regulatory subunits, and how tissue-specific distribution of these isoforms may contribute to neurodevelopmental disorders in comparison to more generalized endocrine dysfunction.

Innovative strategies for measuring kinase activity to accelerate the next wave of novel kinase inhibitors

The development of protein kinase inhibitors (PKIs) has gained significance owing to their therapeutic potential for diseases like cancer. In addition, there has been a rise in refining kinase activity assays, each possessing unique biological and analytical characteristics crucial for PKI development. However, the PKI development pipeline experiences high attrition rates and approved PKIs exhibit unexploited potential because of variable patient responses. Enhancing PKI development efficiency involves addressing challenges related to understanding the PKI mechanism of action and employing biomarkers for precision medicine. Selecting appropriate kinase activity assays for these challenges can overcome these attrition rate issues. This review delves into the current obstacles in kinase inhibitor development and elucidates kinase activity assays that can provide solutions.

AKAP2-anchored extracellular signal-regulated kinase 1 (ERK1) regulates cardiac myofibroblast migration

Cardiac fibrosis is a major cause of dysfunctions and arrhythmias in failing hearts. At the cellular level fibrosis is mediated by cardiac myofibroblasts, which display an increased migratory capacity and secrete large amounts of extracellular matrix. These properties allow myofibroblasts to invade, remodel and stiffen the myocardium and eventually alter cardiac function. While the enhanced ability of cardiac myofibroblasts to migrate has been proposed to contribute to the initiation of the fibrotic process, the molecular mechanisms controlling their motile function have been poorly defined. In this context, our current findings indicate that A-kinase anchoring protein 2 (AKAP2) associates with actin at the leading edge of migrating cardiac myofibroblasts. Proteomic analysis of the AKAP2 interactome revealed that this anchoring protein assembles a signaling complex composed of the extracellular regulated kinase 1 (ERK1) and its upstream activator Grb2 that mediates the activation of ERK in cardiac myofibroblasts. Silencing AKAP2 expression results in a significant reduction in the phosphorylation of ERK1 and its downstream effector WAVE2, a protein involved in actin polymerization, and impairs the ability of cardiac myofibroblasts to migrate. Importantly, disruption of the interaction between AKAP2 and F-actin using cell-permeant competitor peptides, inhibits the activation of the ERK-WAVE2 signaling axis, resulting in a reduction of the translocation of Arp2 to the leading-edge membrane and in inhibition of cardiac myofibroblast migration. Collectively, these findings suggest that AKAP2 functions as an F-actin bound molecular scaffold mediating the activation of an ERK1-dependent promigratory transduction pathway in cardiac myofibroblasts.

The interference between SARS-COV-2 and Alzheimer's disease: Potential immunological and neurobiological crosstalk from a kinase perspective reveals a delayed pandemic

Coronavirus disease 2019 (COVID-19) has infected over 700 million people, with up to 30% developing neurological manifestations, including dementias. However, there is a lack of understanding of common molecular brain markers causing Alzheimer's disease (AD). COVID-19 has etiological cofactors with AD, making patients with AD a vulnerable population at high risk of experiencing more severe symptoms and worse consequences. Both AD and COVID-19 have upregulated several shared kinases, leading to the repositioning of kinase inhibitors (KIs) for the treatment of both diseases. This review provides an overview of the interactions between the immune system and the nervous system in relation to receptor tyrosine kinases, including epidermal growth factor receptors, vascular growth factor receptors, and non-receptor tyrosine kinases such as Bruton tyrosine kinase, spleen tyrosine kinase, c-ABL, and JAK/STAT. We will discuss the promising results of kinase inhibitors in pre-clinical and clinical studies for both COVID-19 and Alzheimer's disease (AD), as well as the challenges in repositioning KIs for these diseases. Understanding the shared kinases between AD and COVID-19 could help in developing therapeutic approaches for both.

Recent drug design strategies and identification of key heterocyclic scaffolds for promising anticancer targets

Cancer, a noncommunicable disease, is the leading cause of mortality worldwide and is anticipated to rise by 75% in the next two decades, reaching approximately 25 million cases. Traditional cancer treatments, such as radiotherapy and surgery, have shown limited success in reducing cancer incidence. As a result, the focus of cancer chemotherapy has switched to the development of novel small molecule antitumor agents as an alternate strategy for combating and managing cancer rates. Heterocyclic compounds are such agents that bind to specific residues in target proteins, inhibiting their function and potentially providing cancer treatment. This review focuses on privileged heterocyclic pharmacophores with potent activity against carbonic anhydrases and kinases, which are important anticancer targets. Evaluation of ongoing pre-clinical and clinical research of heterocyclic compounds with potential therapeutic value against a variety of malignancies as well as the provision of a concise summary of the role of heterocyclic scaffolds in various chemotherapy protocols have also been discussed. The main objective of the article is to highlight key heterocyclic scaffolds involved in recent anticancer drug design that demands further attention from the drug development community to find more effective and safer targeted small-molecule anticancer agents.

Hsc70 phosphorylation patterns and calmodulin regulate AP2 Clathrin-Coated-Vesicle life span for cell adhesion protein transport

AP2 forms AP2 CCV with clathrin and over 60 additional coat proteins. Due to this complexity, we have a limited understanding of CCV life cycle regulation. Synapses contain canonical AP2 CCV, canCCV, and more stable, thereby longer lived, AP2 CCV. The more stable AP2 CCV can be distinguished from canCCV due to the stable binding of Hsc70 to clathrin. The AP1/σ1B complex knockout leads to impaired synaptic vesicle recycling and altered endosomal protein sorting. This causes as a secondary phenotype the twofold upregulation of endocytosis by canCCV and by more stable AP2 CCV. These stable CCV are more stabilized than their wt counterpart, hence stCCV. They have less of the uncoating proteins synaptojanin1 and Hsc70, and more of the coat stabilizing AAK1. Hsc70 clathrin dissociation activity is regulated by complex phosphorylation patterns. Two major groups of hyper- and of hypo-phosphorylated Hsc70 proteins are formed. The latter are enriched in wt stable CCV and stabilized stCCV. Hsc70 T265 phosphorylation regulates binding of CaM/Ca2+. CaM/Ca2+ binding to the T265 domain blocks Hsc70 homodimerization and its concentration in stCCV required for clathrin disassembly. Kinases DYRK1A and CaMK-IIδ can phosphorylate T265 preventing CaM/Ca2+ binding. Their and the levels of STK38L and STK39/Cab39, which are able to phosphorylate additional Hsc70 residues are reduced in stCCV. The stCCV pathway sorts specifically the cell adhesion proteins CHL1 and Neurocan, supporting our model of that the stCCV pathway fulfills specific functions in synaptic plasticity.

Phosphorylation of Tau Protein by CDK2/cyclin A and GSK3β Recombinant Kinases: Analysis of Phosphorylation Patterns by Nuclear Magnetic Resonance Spectroscopy

Posttranslational modifications (PTMs) of proteins can be investigated by Nuclear Magnetic Resonance (NMR) spectroscopy as a powerful analytical tool to define modification sites, their relative stoichiometry, and crosstalk between modifications. As a Structural Biology method, NMR provides important additional information on changes in protein conformation and dynamics upon modification as well as a mapping of binding sites upon biomolecular interactions. Indeed, PTMs not only mediate functional modulation in protein-protein interactions, but can also induce diverse structural responses with different biological outcomes. Here we present protocols that have been developed for the production and phosphorylation of the neuronal tau protein. Under its aggregated form, tau is a hallmark of Alzheimer's disease and other neurodegenerative diseases named tauopathies involving tau dysfunction and/or mutations. As a common feature shared by various tauopathies, tau aggregates are found into a form displaying an increased, abnormal phosphorylation, also referred to hyperphosphorylation. We have used NMR to investigate the phosphorylation patterns of tau induced by several kinases or cell extracts, how phosphorylation affects the local and overall conformation of tau, its interactions with partners (proteins, DNA, small-molecules, etc.) including tubulin and microtubules, and its capacity to form insoluble fibrillar aggregates. We present here detailed protocols for in vitro phosphorylation of tau by the recombinant kinases CDK2/cyclin A and GSK3β, the production of the recombinant kinases thereof, as well as the analytical characterization of phosphorylated tau by NMR spectroscopy.

Exploring Parkinson-associated kinases for CRISPR/Cas9-based gene editing: beyond alpha-synuclein

Parkinson's disease (PD) is a debilitating neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substania nigra (SN) and is associated with progressive motor impairment. PD is classified into familial and sporadic forms. The first genetic association studies in PD reported the involvement of Synuclein alpha (SNCA) mutations in the pathobiology of familial PD. Subsequent studies suggested mutations in PTEN-induced putative kinase 1 (PINK1), PARKIN, leucine repeat kinase-2 (LRRK2), and DJ-1 causing familial PD. In addition, kinase dysregulation has been embroiled in the pathogenesis of PD. The genome-editing mechanism CRISPR (clustered regularly interspaced short palindromic repeats) has recently influenced industry and scientific discoveries and is expected to expedite neurodegenerative disease research. This review will discuss the structure, function, and history of the CRISPR/Cas9 genome editing system. Moreover, it summarizes genes-encoding kinases involved in PD pathogenesis and targeted by CRISPR/Cas9 technology, including LRRK2, PINK1, Protein kinase C-delta (PKC-γ), and adenosine monophosphate-activated protein kinase (AMPK). We provide an overview of novel kinases to be targeted by the CRISPR/Cas9 system such as G-protein coupled receptor kinases (GRKs), cyclin-G-associated kinases (GAKs), cyclin-dependent kinase 5 (CDK5), Ataxia telangiectasia mutated (ATM), c-ABL, and rearranged during transfection (RET) receptors. Additionally, we will explain the off-target effects of CRISPR/Cas9 system and how to address them. Also, we will shed light on the associated challenges and future directions that are enabling the efficient use of CRISPR/Cas9 technology in kinases research in PD. In conclusion, gene editing, in addition to gene therapy, might be a possible promising strategy for PD therapy.

Potential Signature Therapeutic Biomarkers TOP2A, MAD2L1, and CDK1 in Colorectal Cancer: A Systems Biomedicine-Based Approach

Colorectal cancer is the third deadliest and fourth most diagnosed cancer. It is heterogeneously driven by varied mutations and mutagens, and thus, it is challenging for targeted therapy. The rapid advancement of high-throughput technology presents considerable opportunities for discovering new colon cancer biomarkers. In the present study, we have explored and identified the biomarkers based on molecular interactions. We curated cancer datasets that were not micro-dissected and performed gene expression analysis. The protein-protein interactions were curated, and a network was constructed for the up-regulated genes. The hub genes were analyzed using 12 different topological parameters. The correlation analysis selected TOP2A, CDK1, CCNB1, AURKA, and MAD2L1 as hub genes. Further, survival analysis was performed to determine the effectiveness of the hub gene on the patient's survival rate. Our findings explore various transcription factors such as E2F4, FOXM1, E2F6, MAX, and SIN3A, along with kinases CSNK2A1, MAPK14, CDK1, CDK4, and CDK2, as potential molecular signatures and aid researchers in understanding the pathophysiological mechanisms underlying CRC development and thus providing novel therapeutic and diagnostic recourse. Furthermore, investigating miRNAs, we focused on hsa-miR-215-5p, hsa-miR-192-5p, and hsa-miR-193b-3p due to their observed impact on a diverse set of colorectal cancer genes. Thereby, the current approach brings into light CRC- related genes at the RNA and protein levels that can potentially act as novel biomarkers opening doors to diagnostic and treatment purposes.

A pervasive phosphorylation cascade modulation of plant transcription factors in response to abiotic stress

MAIN CONCLUSION

Transcriptional regulation of stress-responsive genes is a crucial step in establishing the mechanisms behind plant abiotic stress tolerance. A sensitive method of regulating transcription factors activity, stability, protein interaction, and subcellular localization is through phosphorylation. This review highlights a widespread regulation mechanism that involves phosphorylation of plant TFs in response to abiotic stress. Abiotic stress is one of the main components limiting crop yield and sustainability on a global scale. It greatly reduces the land area that is planted and lowers crop production globally. In all living organisms, transcription factors (TFs) play a crucial role in regulating gene expression. They participate in cell signaling, cell cycle, development, and plant stress response. Plant resilience to diverse abiotic stressors is largely influenced by TFs. Transcription factors modulate gene expression by binding to their target gene's cis-elements, which are impacted by genomic characteristics, DNA structure, and TF interconnections. In this review, we focus on the six major TFs implicated in abiotic stress tolerance, namely, DREB, bZIP, WRKY, ABF, MYB, and NAC, and the cruciality of phosphorylation of these transcription factors in abiotic stress signaling, as protein phosphorylation has emerged as one of the key post-translational modifications, playing a critical role in cell signaling, DNA amplification, gene expression and differentiation, and modification of other biological configurations. These TFs have been discovered after extensive study as stress-responsive transcription factors which may be major targets for crop development and important contributors to stress tolerance and crop production.

Whole proteome copy number dataset in primary mouse cortical neurons

The functional diversity of neurons is specified through their proteome resulting in elaborate and tightly regulated protein interaction networks and signalling that regulates neuronal processes. Dysregulation of these dynamic networks in development or in adulthood lead to neurodevelopmental or neurological disorders respectively. Over the past few decades, mass spectrometry has become a powerful tool for quantifying and resolving any proteome, including complex tissues such as the brain proteome, with technological advances leading to higher levels of resolution and throughput than traditional biochemical techniques. In this article, we provide a proteomic reference dataset that has been generated to identify proteins and quantify their level of expression in primary mouse cortical neurons. It represents a summary analysis of previously published data in (Antico et al., 2021). Mouse cortical neurons were isolated from E16.5 C57Bl/6J mice and cultured for 21 days in vitro (DIV). We employed the mitochondrial uncouplers AntimycinA/Oligomycin (AO) to induce mitochondrial depolarisation that is a well-established paradigm to assess mitophagic signalling. Total lysates from mouse primary cortical neurons were subjected to label-free quantitative proteomic analysis using both data dependent acquisition (DDA) and data independent acquisition (DIA) modes. DDA proteomic analysis identified a total dataset of 9367 proteins in mouse cortical neurons and absolute abundance of proteins was calculated as copy numbers per cell. DDA dataset was also processed to generate a reference spectral library to fit in and quantify MS spectra generated in DIA mode. Quantitative DIA analysis identified more than 6000 protein groups and statistical comparison of the two analysed groups (untreated and AO-treated) revealed that the neuronal proteome was largely unchanged post mitochondrial depolarisation for 5 hours. To our knowledge, these files represent the most comprehensive DDA and DIA reference datasets of fully functional maturated mouse primary cortical neurons and serve as a valuable resource for further investigating the role of specific proteins involved in neurobiology and neurological disorders such as Alzheimer's disease (AD), Parkinson's disease (PD) and Autism Spectrum Disorders (ASD).

Sorafenib inhibits invasion of multicellular organoids that mimic Lymphangioleiomyomatosis nodules

Lymphangioleiomyomatosis (LAM) is a debilitating, progressive lung disease with few therapeutic options, largely due to a paucity of mechanistic knowledge of disease pathogenesis. Lymphatic endothelial cells (LECs) are known to envelope and invade clusters of LAM-cells, comprising of smooth muscle α-actin and/or HMB-45 positive "smooth muscle-like cells" however the role of LECs in LAM pathogenesis is still unknown. To address this critical knowledge gap, we investigated wether LECs interact with LAM-cells to augment their metastatic behaviour of LAM-cells. We performed in situ spatialomics and identified a core of transcriptomically related cells within the LAM nodules. Pathway analysis highlights wound and pulmonary healing, VEGF signaling, extracellular matrix/actin cytoskeletal regulating and the HOTAIR regulatory pathway enriched in the LAM Core cells. We developed an organoid co-culture model combining primary LAM-cells with LECs and applied this to evaluate invasion, migration, and the impact of Sorafenib, a multi-kinase inhibitor. LAM-LEC organoids had significantly higher extracellular matrix invasion, decreased solidity and a greater perimeter, reflecting increased invasion compared to non-LAM control smooth muscle cells. Sorafenib significantly inhibited this invasion in both LAM spheroids and LAM-LEC organoids compared to their respective controls. We identified TGFβ1ι1, a molecular adapter coordinating protein-protein interactions at the focal adhesion complex and known to regulate VEGF, TGFβ and Wnt signalling, as a Sorafenib-regulated kinase in LAM-cells. In conclusion we have developed a novel 3D co-culture LAM model and have demonstrated the effectiveness of Sorafenib to inhibit LAM-cell invasion, identifying new avenues for therapeutic intervention.

Structural elements that enable specificity for mutant EGFR kinase domains with next-generation small-molecule inhibitors

Specificity for a desired enzyme target is an essential property of small-molecule inhibitors. Molecules targeting oncogenic driver mutations in the epidermal growth factor receptor (EGFR) kinase domain have had a considerable clinical impact due to their selective binding to cancer-causing mutants compared to wild type. Despite the availability of clinically approved drugs for cancers driven by EGFR mutants, persistent challenges in drug resistance in the past decades have led to newer generations of drugs with divergent chemical structures. The current clinical challenges are mainly due to acquired resistance to third-generation inhibitors, including by the acquisition of the C797S mutation. Several diverse fourth-generation candidates and tool compounds that inhibit the C797S mutant have emerged, and their structural characterization has revealed molecular factors that allow for EGFR mutant selective binding. Here, we have reviewed all known structurally-characterized EGFR TKIs targeting clinically-relevant mutations to identify specific features that enable C797S inhibition. Newer generation EGFR inhibitors exhibit consistent and previously underutilized hydrogen bonding interactions with the conserved K745 and D855 residue side chains. We also consider binding modes and hydrogen bonding interactions of inhibitors targeting the classical ATP and the more unique allosteric sites.

Phosphoinositides in plant-pathogen interaction: trends and perspectives

Phosphoinositides are important regulatory membrane lipids, with a role in plant development and cellular function. Emerging evidence indicates that phosphoinositides play crucial roles in plant defence and are also utilized by pathogens for infection. In this review, we highlight the role of phosphoinositides in plant-pathogen interaction and the implication of this remarkable convergence in the battle against plant diseases.

Phosphorylated polysaccharides: Applications, natural abundance, and new-to-nature structures generated by chemical and enzymatic functionalization

Polysaccharides are foreseen as serious candidates for the future generation of polymers, as they are biosourced and biodegradable materials. Their functionalisation is an attractive way to modify their properties, thereby increasing their range of applications. Introduction of phosphate groups in polysaccharide chains for the stimulation of the immune system was first described in the nineteen seventies. Since then, the use of phosphorylated polysaccharides has been proposed in various domains, such as healthcare, water treatment, cosmetic, biomaterials, etc. These alternative usages capitalize on newly acquired physico-chemical or biological properties, leading to materials as diverse as flame-resistant agents or drug delivery systems. Phosphorylated polysaccharides are found in Nature and need to be extracted to assess their biological potential. However, they are not abundant, often present complex backbones hard to characterize, and most of them have a low phosphate content. These drawbacks have pushed forward the development of chemical phosphorylation employing a wide variety of phosphorylating agents to obtain polysaccharides with a large range of phosphate content. Chemical phosphorylation requires the use of harsh conditions and toxic, petroleum-based solvents, which hinders their exploitation in the food and health industry. Over the last 20 years, although enzymes are regiospecific catalysts that work in aqueous and mild conditions, enzymatic phosphorylation has been little investigated. To date, only three families of enzymes have been used for the in vitro phosphorylation of polysaccharides. Considering the number of unresolved metabolic pathways leading to phosphorylated polysaccharides, the huge diversity of kinase sequences, and the recent progress in protein engineering one can envision native and engineered kinases as promising tools for polysaccharide phosphorylation.

Genome-wide screening and identification of potential kinases involved in endoplasmic reticulum stress responses

AIM

This study aims to identify endoplasmic reticulum stress response elements (ERSE) in the human genome to explore potentially regulated genes, including kinases and transcription factors, involved in the endoplasmic reticulum (ER) stress and its related diseases.

MATERIALS AND METHODS

Python-based whole genome screening of ERSE was performed using the Amazon Web Services elastic computing system. The Kinome database was used to filter out the kinases from the extracted list of ERSE-related genes. Additionally, network analysis and genome enrichment were achieved using NDEx, the Network and Data Exchange software, and web-based computational tools. To validate the gene expression, quantitative RT-PCR was performed for selected kinases from the list by exposing the HeLa cells to tunicamycin and brefeldin, ER stress inducers, for various time points.

KEY FINDINGS

The overall number of ERSE-associated genes follows a similar pattern in humans, mice, and rats, demonstrating the ERSE's conservation in mammals. A total of 2705 ERSE sequences were discovered in the human genome (GRCh38.p14), from which we identified 36 kinases encoding genes. Gene expression analysis has shown a significant change in the expression of selected genes under ER stress conditions in HeLa cells, supporting our finding.

SIGNIFICANCE

In this study, we have introduced a rapid method using Amazon cloud-based services for genome-wide screening of ERSE sequences from both positive and negative strands, which covers the entire genome reference sequences. Approximately 10 % of human protein-protein interactomes were found to be associated with ERSE-related genes. Our study also provides a rich resource of human ER stress-response-based protein networks and transcription factor interactions and a reference point for future research aiming at targeted therapeutics.

Proteomic and phosphoproteomic analyses of Jurkat T-cell treated with 2'3' cGAMP reveals various signaling axes impacted by cyclic dinucleotides

Cyclic dinucleotides (CDNs), such as 2'3'-cGAMP, bind to STING to trigger the production of cytokines and interferons, mainly via activation of TBK1. STING activation by CDN also leads to the release and activation of Nuclear Factor Kappa-light-chain-enhancer of activated B cells (NF-κB) via the phosphorylation of Inhibitor of NF-κB (IκB)-alpha (IκBα) by IκB Kinase (IKK). Beyond the canonical TBK1 or IKK phosphorylations, little is known about how CDNs broadly affect the phosphoproteome and/or other signaling axes. To fill this gap, we performed an unbiased proteome and phosphoproteome analysis of Jurkat T-cell treated with 2'3'-cGAMP or vehicle control to identify proteins and phosphorylation sites that are differentially modulated by 2'3'-cGAMP. We uncovered different classes of kinase signatures associated with cell response to 2'3'-cGAMP. 2'3'-cGAMP upregulated Arginase 2 (Arg2) and the antiviral innate immune response receptor RIG-I as well as proteins involved in ISGylation, E3 ISG15-protein ligase HERC5 and ubiquitin-like protein ISG15, while downregulating ubiquitin-conjugating enzyme UBE2C. Kinases that play a role in DNA double strand break repair, apoptosis, and cell cycle regulation were differentially phosphorylated. Overall, this work demonstrates that 2'3'-cGAMP has a much broader effects on global phosphorylation events than currently appreciated, beyond the canonical TBK1/IKK signaling. SIGNIFICANCE: The host cyclic dinucleotide, 2'3'-cGAMP is known to bind to Stimulator of Interferon Genes (STING) to trigger the production of cytokines and interferons in immune cells via STING-TBK1-IRF3 pathway. Beyond the canonical phosphorelay via the STING-TBK1-IRF3 pathway, little is known about how this second messenger broadly affects the global proteome. Using an unbiased phosphoproteomics, this study identifies several kinases and phosphosites that are modulated by cGAMP. The study expands our knowledge about how cGAMP modulates global proteome and also global phosphorylations.

Mitotic kinase inhibitors as Therapeutic Interventions for Prostate Cancer: Evidence from In vitro Studies

Prostate cancer is one of the devastating diseases characterized by genetic changes leading to uncontrolled growth and metastasis of the cells of the prostate gland and affects men worldwide. Conventional hormonal and chemotherapeutic agents are effective in mitigating the disease if diagnosed at an early stage. All dividing eukaryotic cells require mitotic progression for the maintenance of genomic integrity in progeny populations. The protein kinases, upon activation and de-activation in an ordered fashion, lead to spatial and temporal regulation of the cell division process. The entry into mitosis along with the progression into sub-phases of mitosis is ensured due to the activity of mitotic kinases. These kinases include Polo-Like-Kinase 1 (PLK1), Aurora kinases, and Cyclin-Dependent-Kinase 1 (CDK1), among others. The mitotic kinases, among others, are usually overexpressed in many cancers and can be targeted using small molecule inhibitors to reduce the effects of these regulators on mechanisms, such as regulation of genomic integrity and mitotic fidelity. In this review, we attempted to discuss the appropriate functions of mitotic kinases revealed through cell culture studies and the impact of their respective inhibitors derived in pre-clinical studies. The review is designed to elucidate the growing field of small molecule inhibitors and their functional screening or mode of action at the cellular and molecular level in the context of Prostate Cancer. Therefore, studies performed specifically on cells of Prostatic-origin are narrated in this review, culminating in a comprehensive view of the specific field of mitotic kinases that can be targeted for therapy of Prostate cancer.

Regulation of autophagy of the heart in ischemia and reperfusion

Ischemia/reperfusion (I/R) of the heart leads to increased autophagic flux. Preconditioning stimulates autophagic flux by AMPK and PI3-kinase activation and mTOR inhibition. The cardioprotective effect of postconditioning is associated with activation of autophagy and increased activity of NO-synthase and AMPK. Oxidative stress stimulates autophagy in the heart during I/R. Superoxide radicals generated by NADPH-oxidase acts as a trigger for autophagy, possibly due to AMPK activation. There is reason to believe that AMPK, GSK-3β, PINK1, JNK, hexokinase II, MEK, PKCα, and ERK kinases stimulate autophagy, while mTOR, PKCδ, Akt, and PI3-kinase can inhibit autophagy in the heart during I/R. However, there is evidence that PI3-kinase could stimulate autophagy in ischemic preconditioning of the heart. It was found that transcription factors FoxO1, FoxO3, NF-κB, HIF-1α, TFEB, and Nrf-2 enhance autophagy in the heart in I/R. Transcriptional factors STAT1, STAT3, and p53 inhibit autophagy in I/R. MicroRNAs could stimulate and inhibit autophagy in the heart in I/R. Long noncoding RNAs regulate the viability and autophagy of cardiomyocytes in hypoxia/reoxygenation (H/R). Nitric oxide (NO) donors and endogenous NO could activate autophagy of cardiomyocytes. Activation of heme oxygenase-1 promotes cardiomyocyte tolerance to H/R and enhances autophagy. Hydrogen sulfide increases cardiac tolerance to I/R and inhibits apoptosis and autophagy via mTOR and PI3-kinase activation.

Regulation of inositol 1,2,4,5,6-pentakisphosphate and inositol hexakisphosphate levels in Gossypium hirsutum by IPK1

The IPK1 genes, which code for 2-kinases that can synthesize Ins(1,2,4,5,6)P₅ from Ins(1,4,5,6)P₄, are expressed throughout cotton plants, resulting in the highest Ins(1,2,4,5,6)P₅ concentrations in young leaves and flower buds. Cotton leaves contain large amounts of Ins(1,2,4,5,6)P₅ and InsP₆ compared to plants not in the Malvaceae family. The inositol polyphosphate pathway has been linked to stress tolerance in numerous plant species. Accordingly, we sought to determine why cotton and other Malvaceae have such high levels of these inositol phosphates. We have quantified the levels of InsP₅ and InsP₆ in different tissues of cotton plants and determined the expression of IPK1 (inositol 1,3,4,5,6-pentakisphosphate 2-kinase gene) in vegetative and reproductive tissues. Gossypium hirsutum was found to contain four IPK1 genes that were grouped into two pair (AB, CD) where each pair consists of very similar sequences that were measured together. More IPK1AB is expressed in leaves than in roots, whereas more IPK1CD is expressed in roots than in leaves. Leaves and flower buds have more InsP₅ and InsP₆ than stems and roots. Leaves and roots contain more InsP₅ than InsP₆, whereas flower buds and stems contain more InsP₆ than InsP₅. Dark-grown seedlings contain more InsP₅ and InsP₆ than those grown under lights, and the ratio of InsP₅ to InsP₆ is greater in the light-grown seedlings. During 35 days of the life cycle of the third true leaf, InsP₅ and InsP₆ gradually decreased by more than 50%. Silencing IPK1AB and IPK1CD with Cotton Leaf Crumple Virus-induced gene silencing (VIGS) resulted in plants with an intense viral phenotype, reduced IPK1AB expression and lowered amounts of InsP₅. The results are consistent with Ins(1,2,4,5,6)P₅ synthesis from Ins(1,4,5,6)P₄ by IPK1. This study detailed the central role of IPK1 in cotton inositol polyphosphate metabolism, which has potential to be harnessed to improve the resistance of plants to different kinds of stress.

A Review on Anticancer Profile of Flavonoids: Sources, Chemistry, Mechanisms, Structure-Activity Relationship and Anticancer Activity

BACKGROUND

Epidemiological studies have suggested that a regular intake of flavonoids is beneficial for cellular homeostasis and in the prevention of the transformation of normal cells into cancerous cells. Because of their multiple biological targets, flavonoids have been studied and investigated as phytoconstituents with potential anticancer properties. Flavonoids interfere in the development of cancerous cells by inhibition of topoisomerases, protein kinases, angiogenesis, induction of apoptosis, cell cycle arrest, modulation of multidrug resistance, and improvement in anti-oxidative activities.

OBJECTIVE

The current review summarizes the anticancer properties of flavonoids along with the key structural features and their mechanisms.

METHODS

The present study provides a detailed analysis of anticancer activities with previously published data on different flavonoids. The review highlighted the structural aspects and mechanism of action of flavonoids with their potential target sites.

RESULTS

Flavonoids induce anticancer activity by protein kinases inhibition, P-gp modulation, anti-angiogenesis, topoisomerases inhibition, etc. Open ring C, the double bond between C2-C3, the oxo group at C4, and the position of ring B are crucial determinants for their anticancer activity. Flavonoids act by multiple mechanisms but further studies on target selectivity and specificity of flavonoids are necessary to establish them as anticancer therapeutics.

CONCLUSION

The presence of a C2-C3 double bond and oxo group at C4 (also known as an enone moiety) or -OH in the neighbour of a double bond that can transform easily into an enone are common features present in flavonoids. Thus, it can be concluded that enone moiety or its precursor groups are mainly responsible for the anticancer activities of flavonoids via different mechanisms of action.

Phosphotyrosine Profiling Using SILAC

Tyrosine phosphorylation on proteins is an important posttranslational modification that regulates various processes in cells. Mass spectrometry-based phosphotyrosine profiling can reveal tyrosine kinase signaling activity in cells. Using quantitative proteomics strategies such as stable isotope labeling with amino acids in cell culture (SILAC) allows comparison of tyrosine kinase signaling activity across two to -three different conditions. In this book chapter, we discuss the reagents required and a step-by-step protocol to carry out phosphotyrosine profiling using SILAC.

Kinome-wide polypharmacology profiling of small molecules by multi-task graph isomorphism network approach

Prediction of the interactions between small molecules and their targets play important roles in various applications of drug development, such as lead discovery, drug repurposing and elucidation of potential drug side effects. Therefore, a variety of machine learning-based models have been developed to predict these interactions. In this study, a model called auxiliary multi-task graph isomorphism network with uncertainty weighting (AMGU) was developed to predict the inhibitory activities of small molecules against 204 different kinases based on the multi-task Graph Isomorphism Network (MT-GIN) with the auxiliary learning and uncertainty weighting strategy. The calculation results illustrate that the AMGU model outperformed the descriptor-based models and state-of-the-art graph neural networks (GNN) models on the internal test set. Furthermore, it also exhibited much better performance on two external test sets, suggesting that the AMGU model has enhanced generalizability due to its great transfer learning capacity. Then, a naïve model-agnostic interpretable method for GNN called edges masking was devised to explain the underlying predictive mechanisms, and the consistency of the interpretability results for 5 typical epidermal growth factor receptor (EGFR) inhibitors with their structure‒activity relationships could be observed. Finally, a free online web server called KIP was developed to predict the kinome-wide polypharmacology effects of small molecules (http://cadd.zju.edu.cn/kip).

Calcium decoders and their targets: The holy alliance that regulate cellular responses in stress signaling

Calcium (Ca²⁺) signaling is versatile communication network in the cell. Stimuli perceived by cells are transposed through Ca²⁺-signature, and are decoded by plethora of Ca²⁺ sensors present in the cell. Calmodulin, calmodulin-like proteins, Ca²⁺-dependent protein kinases and calcineurin B-like proteins are major classes of proteins that decode the Ca²⁺ signature and serve in the propagation of signals to different parts of cells by targeting downstream proteins. These decoders and their targets work together to elicit responses against diverse stress stimuli. Over a period of time, significant attempts have been made to characterize as well as summarize elements of this signaling machinery. We begin with a structural overview and amalgamate the newly identified Ca²⁺ sensor protein in plants. Their ability to bind Ca²⁺, undergo conformational changes, and how it facilitates binding to a wide variety of targets is further embedded. Subsequently, we summarize the recent progress made on the functional characterization of Ca²⁺ sensing machinery and in particular their target proteins in stress signaling. We have focused on the physiological role of Ca²⁺, the Ca²⁺ sensing machinery, and the mode of regulation on their target proteins during plant stress adaptation. Additionally, we also discuss the role of these decoders and their mode of regulation on the target proteins during abiotic, hormone signaling and biotic stress responses in plants. Finally, here, we have enumerated the limitations and challenges in the Ca²⁺ signaling. This article will greatly enable in understanding the current picture of plant response and adaptation during diverse stimuli through the lens of Ca²⁺ signaling.

Recent Trends in Rationally Designed Molecules as Kinase Inhibitors

Protein kinases modulate the structure and function of proteins by adding phosphate groups to threonine, tyrosine, and serine residues. The phosphorylation process mediated by the kinases regulates several physiological processes, while their overexpression results in the development of chronic diseases, including cancer. Targeting of receptor tyrosine kinase pathways results in the inhibition of angiogenesis and cell proliferation that validates kinases as a key target in the management of aggressive cancers. As such, the identification of protein kinase inhibitors revolutionized the contemporary anticancer therapy by inducing a paradigm shift in the management of disease pathogenesis. Contemporary drug design programs focus on a broad range of kinase targets for the development of novel pharmacophores to manage the overexpression of kinases and their pathophysiology in cancer pathogenesis. In this review, we present the emerging trends in the development of rationally designed molecular inhibitors of kinases over the last five years (2016-2021) and their incipient role in the development of impending anticancer pharmaceuticals.

Phosphoproteomics data-driven signalling network inference: Does it work?

The advent of global phosphoproteome profiling has led to wide phosphosite coverage and therefore the opportunity to predict kinase-substrate associations from these datasets. However, the regulatory kinase is unknown for most substrates, due to biased and incomplete database annotations. In this study we compare the performance of six pairwise measures to predict kinase-substrate associations using a data driven approach on publicly available time resolved and perturbation mass spectrometry-based phosphoproteome data. First, we validated the performance of these measures using as a reference both a literature-based phosphosite-specific protein interaction network and a predicted kinase-substrate (KS) interactions set. The overall performance in predicting kinase-substrate associations using pairwise measures across both these reference sets was poor. To expand into the wider interactome space, we applied the approach on a network comprising pairs of substrates regulated by the same kinase (substrate-substrate associations) but found the performance to be equally poor. However, the addition of a sequence similarity filter for substrate-substrate associations led to a significant boost in performance. Our findings imply that the use of a filter to reduce the search space, such as a sequence similarity filter, can be used prior to the application of network inference methods to reduce noise and boost the signal. We also find that the current gold standard for reference sets is not adequate for evaluation as it is limited and context-agnostic. Therefore, there is a need for additional evaluation methods that have increased coverage and take into consideration the context-specific nature of kinase-substrate associations.

Repurposing of a human antibody-based microarray to explore conserved components of the signalome of the parasitic nematode Haemonchus contortus

BACKGROUND

Gaining insight into molecular signalling pathways of socioeconomically important parasitic nematodes has implications for understanding their molecular biology and for developing novel anthelmintic interventions.

METHODS

Here, we evaluated the use of a human antibody-based microarray to explore conserved elements of the signalome in the barber's pole worm Haemonchus contortus. To do this, we prepared extracts from mixed-sex (female and male) adult worms and third-stage larvae (L3s), incubated these extracts on the antibody microarray and then measured the amounts of antibody-bound proteins ('signal intensity').

RESULTS

In total, 878 signals were classified into two distinct categories: signals that were higher for adults than for larvae of H. contortus (n = 376), and signals that were higher for larvae than for adults of this species (n = 502). Following a data-filtering step, high confidence ('specific') signals were obtained for subsequent analyses. In total, 39 pan-specific signals (linked to antibodies that recognise target proteins irrespective of their phosphorylation status) and 65 phosphorylation-specific signals were higher in the adult stage, and 82 pan-specific signals and 183 phosphorylation-specific signals were higher in L3s. Thus, notably more signals were higher in L3s than in the adult worms. Using publicly available information, we then inferred H. contortus proteins that were detected (with high confidence) by specific antibodies directed against human homologues, and revealed relatively high structural conservation between the two species, with some variability for select proteins. We also in silico-matched 763 compound structures (listed in the DrugBank and Kinase SARfari public databases) to four H. contortus proteins (designated HCON_00005760, HCON_00079680, HCON_00013590 and HCON_00105100).

CONCLUSIONS

We conclude that the present antibody-based microarray provides a useful tool for comparative analyses of signalling pathways between/among developmental stages and/or species, as well as opportunities to explore nematocidal target candidates in H. contortus and related parasites.

Transcriptomic responses under combined bacterial blight and drought stress in rice reveal potential genes to improve multi-stress tolerance

BACKGROUND

The unprecedented drought and frequent occurrence of pathogen infection in rice is becoming more due to climate change. Simultaneous occurrence of stresses lead to more crop loss. To cope up multiple stresses, the durable resistant cultivars needs to be developed, by identifying relevant genes from combined biotic and abiotic stress exposed plants.

RESULTS

We studied the effect of drought stress, bacterial leaf blight disease causing Xanthomonas oryzae pv. oryzae (Xoo) pathogen infection and combined stress in contrasting BPT5204 and TN1 rice genotypes. Mild drought stress increased Xoo infection irrespective of the genotype. To identify relevant genes that could be used to develop multi-stress tolerant rice, RNA sequencing from individual drought, pathogen and combined stresses in contrasting genotypes has been developed. Many important genes are identified from resistant genotype and diverse group of genes are differentially expressed in contrasting genotypes under combined stress. Further, a meta-analysis from individual drought and Xoo pathogen stress from public domain data sets narrowed- down candidate differentially expressed genes. Many translation associated genes are differentially expressed suggesting their extra-ribosomal function in multi-stress adaptation. Overexpression of many of these genes showed their relevance in improving stress tolerance in rice by different scientific groups. In combined stress, many downregulated genes also showed their relevance in stress adaptation when they were over-expressed.

CONCLUSIONS

Our study identifies many important genes, which can be used as molecular markers and targets for genetic manipulation to develop durable resistant rice cultivars. Strategies should be developed to activate downregulated genes, to improve multi-stress tolerance in plants.

Dysregulated Protein Phosphorylation in a Mouse Model of FTLD-Tau

The neocortex of P301S mice, used as a model of fronto-temporal lobar degeneration linked to tau mutation (FTLD-tau), and wild-type mice, both aged 9 months, were analyzed with conventional label-free phosphoproteomics and SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry) to assess the (phospho)proteomes. The total number of identified dysregulated phosphoproteins was 328 corresponding to 524 phosphorylation sites. The majority of dysregulated phosphoproteins, most of them hyperphosphorylated, were proteins of the membranes, synapses, membrane trafficking, membrane vesicles linked to endo- and exocytosis, cytoplasmic vesicles, and cytoskeleton. Another group was composed of kinases. In contrast, proteins linked to DNA, RNA metabolism, RNA splicing, and protein synthesis were hypophosphorylated. Other pathways modulating energy metabolism, cell signaling, Golgi apparatus, carbohydrates, and lipids are also targets of dysregulated protein phosphorylation in P301S mice. The present results, together with accompanying immunohistochemical and Western-blotting studies, show widespread abnormal phosphorylation of proteins, in addition to protein tau, in P301S mice. These observations point to dysregulated protein phosphorylation as a relevant contributory pathogenic component of tauopathies.

Electrochemical biosensors based on peptide-kinase interactions at the kinase docking site

Kinases are important cancer biomarkers and are conventionally detected based on their catalytic activity. Kinases regulate cellular activities by phosphorylation of motif-specific multiple substrate proteins, resulting in a lack of selectivity of activity-based kinase biosensors. We present an alternative approach of sensing kinases based on the interactions of their allosteric docking sites with a specific partner protein. The new approach was demonstrated for the ERK2 kinase and its substrate ELK-1. A peptide derived from ELK-1 was bound to a gold electrode and ERK2 sensing was performed by electrochemical impedance spectroscopy. We performed a detailed analysis of the interaction between the ELK-1 peptide and the kinase on gold surfaces. Atomic force microscopy, variable angle spectroscopic ellipsometry, X-ray Photoelectron Spectroscopy, and polarization modulation IR reflection-absorption spectroscopy analysis of the gold surface revealed the adsorbed layer of the ERK2 on the peptide monolayer. The sensors showed a high level of target selectivity for ERK2 compared to the p38γ kinase and BSA. ERK2 was detected in its cellular concentration range, 0.5-2.0 μM, and the limit of detection was calculated to be 0.35 μM. Using the flexibility of peptide design, our method is generic for developing sensitive and substrate-specific biosensors and other disease-related enzymes based on their interactions.

Heat shock proteins in cell signaling and cancer

Heat Shock Proteins (HSPs) and their co-chaperones have well-established roles in regulating proteostasis within the cell, the nature of which continues to emerge with further study. To date, HSPs have been shown to be integral to protein folding and re-folding, protein transport, avoidance of protein aggregation, and modulation of protein degradation. Many cell signaling events are mediated by the chemical modification of proteins post-translationally that can alter protein conformation and activity, although it is not yet known whether the changes in protein conformation induced by post-translational modifications (PTMs) are also dependent upon HSPs and their co-chaperones for subsequent protein re-folding. We discuss what is known regarding roles for HSPs and other molecular chaperones in cell signaling events with a focus on oncogenic signaling. We also propose a hypothesis by which Hsp70 and Hsp90 may co-operate to facilitate cell signaling events that may link PTMs with the cellular protein folding machinery.

1-(7-Chloroquinolin-4-yl)-N-(4-Methoxybenzyl)-5-Methyl-1H-1,2, 3-Triazole-4- carboxamide Reduces Aβ Formation and Tau Phosphorylation in Cellular Models of Alzheimer's Disease

1-(7-Chloroquinolin-4-yl)-N-(4-methoxybenzyl)-5-methyl-1H-1,2,3-triazole-4- carboxamide (QTC-4-MeOBnE) is a new multi-target directed ligand (MTDL) rationally designed to have affinity with β-secretase (BACE), Glycogen Synthase Kinase 3β (GSK3β) and acetylcholinesterase, which are considered promising targets on the development of disease-modifying therapies against Alzheimer's Disease (AD). Previously, QTC-4-MeOBnE treatment showed beneficial effects in preclinical AD-like models by influencing in vivo neurogenesis, oxidative and inflammatory pathways. However, the biological effect and mechanism of action exerted by QTC-4-MeOBnE in AD cellular models have not been elucidated yet. Hereby we investigate the acute effect of QTC-4-MeOBnE on neuronal cells overexpressing Amyloid Protein Precursor (APP) or human tau protein, the two main features of the AD pathophysiology. When compared to the control group, QTC-4-MeOBnE treatment prevented amyloid beta (Aβ) formation through the downregulation of APP and BACE levels in APPswe-expressing cells. Furthermore, in N2a cells overexpressing human tau, QTC-4-MeOBnE reduced the levels of phosphorylated forms of tau via the modulation of the GSK3β pathway. Taken together, our findings provide new insights into the mechanism of action exerted by QTC-4-MeOBnE in AD cellular models, and further support its potential as an interesting therapeutic strategy against AD.

Transcription by RNA polymerase II and the CTD-chromatin crosstalk

The epigenetic phenomenon is known to derive the phenotypic variation of an organism through an interconnected cellular network of histone modifications, DNA methylation and RNA regulatory network. Transcription for protein coding genes is a highly regulated process and carried out by a large multi-complex RNA Polymerase II. The carboxy terminal domain (CTD) of the largest subunit of RNA Polymerase II consists of a conserved and highly repetitive heptad sequence Tyr₁-Ser₂-Pro₃-Thr₄-Ser₅-Pro₆-Ser₇. The epigenetically modified CTD is thought to selectively bind different protein complexes that participate in mRNA biogenesis and export. The CTD and chromatin appears to have a spatial relationship during the transcription cycle, where the epigenetic modifications of CTD not only influence the state of histone modification but also mediates CTD-chromatin crosstalk. In this mini review, we have surveyed and discussed current developments of RNA Polymerase II CTD and its new emerging crosstalk with chromatin, during the stage specific progression of RNA Polymerase II in transcription cycle. This review is mainly focussed on the insights in budding yeast.

Dysregulated protein kinase/phosphatase networks in SLE T cells

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease associated with multiple phenotypic and functional aberrations in T lymphocytes. Among these, altered expression and/or activity of several protein kinases and phosphatases has been consistently documented in T cells obtained from patients with SLE. In this review, we describe and contextualize some of the kinase and phosphatase defects reported in T cells from patients with SLE, highlighting their relevance and possible consequences. Additionally, we discuss the origin of the defects and its significance for disease development and expression.

Kinases and therapeutics in pathogen mediated gastric cancer

INTRODUCTION

Many pathogens have coexisted with humans for millennia and can cause chronic inflammation which is the cause of gastritis. Gastric cancer (GC) is associated with 8.8% of cancer related deaths, making it one of the leading causes of cancer related deaths worldwide. This review is intended to give brief information about Helicobacter pylori (H. pylori), Epstein-Barr virus (EBV), human cytomegalovirus (HCMV) role in GC and associated kinases. These organisms can trigger multiple cellular pathways aiming for unnatural cellular proliferation, apoptosis, migration and inflammatory response. Kinases also can activate and deactivate the signalling leading to aforementioned pathways. Therefore, studying kinases is inevitable.

MATERIAL AND METHODS

This review is the comprehensive collection of information from different data sources such as journals, book, book chapters and verified online information.

CONCLUSION

Kinase amplifications could be used as diagnostic, prognostic, and predictive biomarkers in various cancer types. Hence targeting kinase and related signalling molecules could be considered as a potential approach to prevent cancer through these organisms. Here we summarize the brief information about the role of kinases, signalling and their therapeutics in GC concerning H. pylori, EBV and HCMV.

Medicinal chemistry updates of novel HDACs inhibitors (2020 to present)

Epigentic enzymes histone deacetylases (HDACs) catalyze the removal of acetyl groups from the ε-N-acetylated lysine residues of various protein substrates including both histone and non-histone proteins. Different HDACs have distinct biological functions and are recruited to specific regions of the genome. Due to their important biological functions, HDACs have been validated in clinics for anticancer therapy, and are being explored for potential treatment of several other diseases such as Alzheimer disease (AD), metabolic disease, viral infection, and multiple sclerosis, etc. Besides five approved drugs, there are more than thirty HDACs inhibitors currently being investigated in clinical trials. Centering on the advances of drug discovery programs in this field since 2020, this review discusses HDACs inhibitors from the aspects of the structure-based rational design, isoform selectivity, pharmacology, and toxicology of the compounds of interest. The hope is to provide the medicinal chemistry community with up-to-date information and to accelerate the drug discovery programs in this area.

Using Optical Tweezers to Dissect Allosteric Communication Networks in Protein Kinases

Mutations in protein kinases are often associated with the development of cancer, and application of mutant-specific inhibitors as therapeutic measures have shown a remarkable improvement in prolonging patient survival. However, it has also been observed that tumors bearing certain mutation types are more resistant to current approved drugs. Importantly, many resistant mutations are located in regions outside substrate or inhibitor binding sites, indicating allosteric effects. Understanding how mutations trigger effects over a distant site of the protein requires a deeper investigation of the molecular origin of allosteric regulation networks in kinases. In this chapter, we show the application of single-molecule optical tweezers to selectively manipulate specific regions of proteins to trace allosteric signals, thereby allowing the elucidation of allosteric communication networks. We illustrate this approach using as model system the regulatory subunit of protein kinase A. This single-molecule optical tweezers approach, however, can be readily applicable to study other kinases, and can be further expanded to screen potential allosteric drugs for future therapeutics.

Development of potent dual PDK1/AurA kinase inhibitors for cancer therapy: Lead-optimization, structural insights, and ADME-Tox profile

We report the synthesis of novel first-in-class 2-oxindole-based derivatives as dual PDK1-AurA kinase inhibitors as a novel strategy to treat Ewing sarcoma. The most potent compound 12 is suitable for progression to in vivo studies. The specific attributes of 12 included nanomolar inhibitory potency against both phosphoinositide-dependent kinase-1 (PDK1) and Aurora A (AurA) kinase, with acceptable in vitro ADME-Tox properties (cytotoxicity in 2 healthy and 14 hematological and solid cancer cell-lines; inhibition of PDE4C1, SIRT7, HDAC4, HDAC6, HDAC8, HDAC9, AurB, CYP1A2, CYP2C9, CYP2C19, CYP2D6, and hERG). X-ray crystallography and docking studies led to the identification of the key AurA and PDK1/12 interactions. Finally, in vitro drug-intake kinetics and in vivo PK appear to indicate that these compounds are attractive lead-structures for the design and synthesis of PDK1/AurA dual-target molecules to further investigate the in vivo efficacy against Ewing Sarcoma.

Protein phosphatase 2A in the healthy and failing heart: New insights and therapeutic opportunities

Protein phosphatases have emerged as critical regulators of phosphoprotein homeostasis in settings of health and disease. Protein phosphatase 2A (PP2A) encompasses a large subfamily of enzymes that remove phosphate groups from serine/threonine residues within phosphoproteins. The heterogeneity in PP2A structure, which arises from the grouping of different catalytic, scaffolding and regulatory subunit isoforms, creates distinct populations of catalytically active enzymes (i.e. holoenzymes) that localise to different parts of the cell. This structural complexity, combined with other regulatory mechanisms, such as interaction of PP2A heterotrimers with accessory proteins and post-translational modification of the catalytic and/or regulatory subunits, enables PP2A holoenzymes to target phosphoprotein substrates in a highly specific manner. In this review, we summarise the roles of PP2A in cardiac physiology and disease. PP2A modulates numerous processes that are vital for heart function including calcium handling, contractility, β-adrenergic signalling, metabolism and transcription. Dysregulation of PP2A has been observed in human cardiac disease settings, including heart failure and atrial fibrillation. Efforts are underway, particularly in the cancer field, to develop therapeutics targeting PP2A activity. The development of small molecule activators of PP2A (SMAPs) and other compounds that selectively target specific PP2A holoenzymes (e.g. PP2A/B56α and PP2A/B56ε) will improve understanding of the function of different PP2A species in the heart, and may lead to the development of therapeutics for normalising aberrant protein phosphorylation in settings of cardiac remodelling and dysfunction.

Vitamin E research: Past, now and future

The early history of vitamin E from its discovery by Herbert M. Evans and Katharine J. S. Bishop in 1922 up to its chemical synthesis by Paul Karrer and coworkers in 1938 and the development of the concept that vitamin E acts as an antioxidant in vivo are recalled. Some more recent results shedding doubt on this hypothesis are reviewed. They comprise influence of vitamin E on enzyme activities, signaling cascades, gene expression and bio-membrane structure. The overall conclusion is that our knowledge of the vitamin's mechanism of action still remains fragmentary. The metabolism of tocopherols and tocotrienols is presented and discussed in respect to bioactivity of the metabolites, interference with drug metabolism and the future design of clinical trials. Some strategies are recommended how to reach the final goal: the identification of the primary vitamin E target(s) and the analysis of the downstream events up to the physiological phenomena.

Capillary electrophoresis for enzyme-based studies: Applications to lipases and kinases

Capillary electrophoresis (CE) is a powerful technique continuously expanding into new application fields. One of these applications involves the study of enzymes, their catalytic activities and the alteration of this activity by specific ligands. In this review, two model enzymes, lipases and kinases, will be used since they differ substantially in their modes of action, reaction requirements and applications making them perfect subjects to demonstrate the advantages and limitations of CE-based enzymatic assays. Indeed, the ability to run CE in various operation modes and hyphenation to different detectors is essential for lipase-based studies. Additionally, the low sample consumption provided by CE promotes it as a promising technique to assay human and viral nucleoside kinases. Undeniably, these are rarely commercially available enzymes and must be frequently produced in the laboratory, a process which requires special sets of skills. CE-based lipase and kinase reactions can be performed outside the capillary (pre-capillary) where the reactants are mixed in a vial prior to their separation or, inside the capillary (in-capillary) where the reactants are mixed before the electrophoretic analysis. These enzyme-based applications of CE will be compared to those of liquid chromatography-based applications in terms of advantages and limitations. Binding assays based on affinity CE and the compelling microscale thermophoresis (MST) will be briefly presented as they allow a broad understanding of the molecular mechanism behind ligand binding and of the resulting modulation in activity.

With no lysine kinases: the key regulatory networks and phytohormone cross talk in plant growth, development and stress response

With No Lysine kinases (WNKs) are a distinct family of Serine/Threonine protein kinase with unique arrangement of catalytic residues in kinase domain. In WNK, an essential catalytic lysine requisite for attaching ATP and phosphorylation reaction is located in subdomain I, instead of subdomain II, which is essentially a typical feature of other Ser/Thr kinases. WNKs are identified in diverse organisms including multicellular and unicellular organisms. Mammalian WNKs are well characterized at structural and functional level, while plant WNKs are not explored much except few recent studies. Plant WNKs role in various physiological processes viz. ion maintenance, osmotic stress, pH homeostasis, circadian rhythms, regulation of flowering time, proliferation and organ development, and abiotic stresses are known, but the mechanisms involved are unclear. Plant WNKs are known to be involved in enhanced drought and salt stress response via ABA-signaling pathway, but the complete signaling cascade is yet to be elucidated. The current review will discuss the interplay between WNKs and growth regulators and their cross talks in plant growth and development. We have also highlighted the link between the stress phytohormones and WNK members in regulating abiotic stress responses in plants. The present review will provide an overall known mechanism on the involvement of WNKs in plant growth and development and abiotic stress response and highlight its role/applications in the development of stress-tolerant plants.

A holistic view on c-Kit in cancer: Structure, signaling, pathophysiology and its inhibitors

Receptor tyrosine kinases play an important role in many cellular processes, and their dysregulation leads to diseases, most importantly cancer. One such receptor tyrosine kinase is c-Kit, a type-III receptor tyrosine kinase, which is involved in various intracellular signaling pathways. The role of different mutant isoforms of c-Kit has been established in several types of cancers. Accordingly, promising c-Kit inhibition results have been reported for the treatment of different cancers (e.g., gastrointestinal stromal tumors, melanoma, acute myeloid leukemia, and other tumors). Therefore, lots of effort has been put to target c-Kit for the treatment of cancer. Here, we provide a comprehensive compilation to provide an insight into c-Kit inhibitor discovery. This compilation provides key information regarding the structure, signaling pathways related to c-Kit, and, more importantly, pharmacophores, binding modes, and SAR analysis for almost all small-molecule heterocycles reported for their c-Kit inhibitory activity. This work could be used as a guide in understanding the basic requirements for targeting c-Kit, and how the selectivity and efficacy of the molecules have been achieved till today.

Phosphatase and Kinase Substrate Specificity Profiling with Pooled Synthetic Peptides and Mass Spectrometry

Reversible phosphorylation is a pervasive regulatory event in cellular physiology controlled by reciprocal actions of protein kinases and phosphatases. Determining the inherent substrate specificity of kinases and phosphatases is essential for understanding their cellular roles. Synthetic peptides have long served as substrate proxies for defining intrinsic kinase and phosphatase specificities. Here, we describe a high throughput protocol to simultaneously measure specificity constants (k_cat/K_M) of many synthetic peptide substrates in a single pool using label-free quantitative mass spectrometry. The generation of specificity constants from a single pooled reaction provides a rigorous and rapid comparison of substrate variants to help define an enzyme's specificity. Equally applicable to kinases and phosphatases, as well as other enzyme classes, the protocol consists of three general steps: (1) reaction of enzyme with pooled peptide substrates, each ideally with a unique mass and at concentrations well below K_M, (2) analysis of reaction products using liquid chromatography-coupled mass spectrometry (LC-MS), and (3) automated extraction and integration of elution peaks for each substrate/product pair. We incorporate an ionization correction strategy allowing direct calculation of reaction progress, and subsequently k_cat/K_M, from substrate and product peak areas in a single sample, obviating the need for stable isotope labeling. Peptide consumption is minimal, and high peptide purity and accurate concentrations are not required. Access to a high-resolution LC-MS system is the only nonstandard equipment need. We present an analysis pipeline consisting entirely of established open-source software tools, and demonstrate proof of principle with the highly selective cell cycle phosphatase Cdc14 from Saccharomyces cerevisiae.

Precision medicine and phosphoproteomics for the identification of novel targeted therapeutic avenues in sarcomas

Rapid advances in genomic technologies have enabled in-depth interrogation of cancer genomes, revealing novel and unexpected therapeutic targets in many cancer types. Identifying actionable dependencies in the diverse and heterogeneous group of sarcomas, particularly those that occur in children or adolescents and young adults (AYAs), remains especially challenging. These patients rarely harbor actionable genomic aberrations, no targeted agent is approved, and outcomes have remained poor for the past decades. This underlines a clear need to refine our methods for target identification. Phosphoproteomics studies in sarcoma showed the power of such analyses to capture novel actionable drivers that are not accompanied by mutational events or gene amplifications. This Review makes the case that incorporating phosphoproteomic molecular profiling alongside (functional) genomics technologies can significantly expand therapeutic target identification, and pinpoint drug mechanisms of action, in pediatric and AYA sarcoma patients. We explore the utility and prospects of phosphoproteomics in personalized medicine.

Protein kinase and phosphatase control of plant temperature responses

Plants must cope with ever-changing temperature conditions in their environment. Suboptimal high and low temperatures, and stressful extreme temperatures, induce adaptive mechanisms that allow optimal performance and survival, respectively. These processes have been extensively studied at the physiological, transcriptional and (epi)genetic level. Cellular temperature signalling cascades and tolerance mechanisms also involve post-translational modifications (PTMs), particularly protein phosphorylation. Many protein kinases are known to be involved in cold acclimation and heat stress responsiveness but research on the role and importance of kinases and phosphatases in triggering responses to mild changes in temperature such as thermomorphogenesis is inadequately understood. In this review, we summarize the current knowledge on the roles of kinases and phosphatases in plant temperature responses. We discuss how kinases can function over a range of temperatures in different signalling pathways and provide an outlook to the application of PTM-modifying factors for the development of thermotolerant crops.

Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis

Background

Multiple sclerosis (MS) is a major health problem, leading to a significant disability and patient suffering. Although chronic activation of the immune system is a hallmark of the disease, its pathogenesis is poorly understood, while current treatments only ameliorate the disease and may produce severe side effects.

Methods

Here, we applied a network-based modeling approach based on phosphoproteomic data to uncover the differential activation in signaling wiring between healthy donors, untreated patients, and those under different treatments. Based in the patient-specific networks, we aimed to create a new approach to identify drug combinations that revert signaling to a healthy-like state. We performed ex vivo multiplexed phosphoproteomic assays upon perturbations with multiple drugs and ligands in primary immune cells from 169 subjects (MS patients, n=129 and matched healthy controls, n=40). Patients were either untreated or treated with fingolimod, natalizumab, interferon-β, glatiramer acetate, or the experimental therapy epigallocatechin gallate (EGCG). We generated for each donor a dynamic logic model by fitting a bespoke literature-derived network of MS-related pathways to the perturbation data. Last, we developed an approach based on network topology to identify deregulated interactions whose activity could be reverted to a “healthy-like” status by combination therapy. The experimental autoimmune encephalomyelitis (EAE) mouse model of MS was used to validate the prediction of combination therapies.

Results

Analysis of the models uncovered features of healthy-, disease-, and drug-specific signaling networks. We predicted several combinations with approved MS drugs that could revert signaling to a healthy-like state. Specifically, TGF-β activated kinase 1 (TAK1) kinase, involved in Transforming growth factor β-1 proprotein (TGF-β), Toll-like receptor, B cell receptor, and response to inflammation pathways, was found to be highly deregulated and co-druggable with all MS drugs studied. One of these predicted combinations, fingolimod with a TAK1 inhibitor, was validated in an animal model of MS.

Conclusions

Our approach based on donor-specific signaling networks enables prediction of targets for combination therapy for MS and other complex diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00925-8.

Next-Generation Kinase Inhibitors Targeting Specific Biomarkers in Non-Small Cell Lung Cancer (NSCLC): A Recent Overview

Lung cancer causes many deaths globally. Mutations in regulatory genes, irregularities in specific signal transduction events, or alterations of signalling pathways are observed in cases of non-small cell lung cancer (NSCLC). Over the past two decades, a few kinases have been identified, validated, and studied as biomarkers for NSCLC. Among them, EGFR, ALK, ROS1, MET, RET, NTRK, and BRAF are regarded as targetable biomarkers to cure and/or control the disease. In recent years, the US Food and Drug Administration (FDA) approved more than 15 kinase inhibitors targeting these NSCLC biomarkers. The kinase inhibitors significantly improved the progression-free survival (PFS) of NSCLC patients. Challenges still remain for metastatic diseases and advanced NSCLC cases. New discoveries of potent kinase inhibitors and rapid development of modern medical technologies will help to control NSCLC cases. This article provides an overview of the discoveries of various types of kinase inhibitors against NSCLC, along with medicinal chemistry aspects and related developments in next-generation kinase inhibitors that have been reported in recent years.