Modulation Of Kinase Activity Research Articles

Viral dissemination and immune activation modulate antiretroviral drug levels in lymph nodes of SIV-infected rhesus macaques.

To understand the relationship between immunovirological factors and antiretroviral (ARV) drug levels in lymph nodes (LN) in HIV therapy, we analyzed drug levels in twenty-one SIV-infected rhesus macaques subcutaneously treated with daily tenofovir (TFV) and emtricitabine (FTC) for three months. The intracellular active drug-metabolite (IADM) levels (TFV-dp and FTC-tp) in lymph node mononuclear cells (LNMC) were significantly lower than in peripheral blood mononuclear cells (PBMC) (P≤0.005). Between Month 1 and Month 3, IADM levels increased in both LNMC (P≤0.001) and PBMC (P≤0.01), with a steeper increase in LNMC (P≤0.01). The viral dissemination in plasma, LN, and rectal tissue at ART initiation correlated negatively with IADM levels at Month 1. Physiologically-based pharmacokinetic model simulations suggest that, following subcutaneous ARV administration, ART-induced reduction of immune activation improves the formation of active drug-metabolites through modulation of kinase activity and/or through improved parent drug accessibility to LN cellular compartments. These observations have broad implications for drugs that need to phosphorylate to exert their pharmacological activity, especially in the settings of the pre-/post-exposure prophylaxis and efficacy of antiviral therapies targeting pathogenic viruses such as HIV or SARS-CoV-2 replicating in highly inflammatory anatomic compartments.

Modulation of Kinase Activities In Vitro by Hepatitis C Virus Protease NS3/NS4A Mediated-Cleavage of Key Immune Modulator Kinases

Hepatitis C Virus NS3/NS4A, a serine protease complex, has been found to interact with many host proteins and cause various adverse effects on cellular function and immune response. For example, the cleavage of important immune factors by NS3/NS4A has been suggested as a mechanism for the hepatitis C virus to evade innate immunity. The spectrum of susceptible substrates for NS3/NS4A cleavage certainly includes important immune modulator kinases such as IKKα, IKKβ, IKKε, and TBK1, as demonstrated in this paper. We show that the kinase activities of these four host kinases were transformed in unexpected ways by NS3/NS4A. Treatment with NS3/NS4A caused a significant reduction in the kinase activities of both IKKα and IKKβ, suggesting that HCV might use its NS3/NS4A protease activity to deactivate the NF-κB-associated innate immune responses. In contrast, the kinase activities of both IKKε and TBK1 were enhanced after NS3/NS4A treatment, and more strikingly, the enhancement was more than 10-fold within 20 min of treatment. Our mass spectroscopic results suggested that the cleavage after Cys89 in the kinase domain of IKKε by NS3/NS4A led to their higher kinase activities, and three potential mechanisms were discussed. The observed kinase activity enhancement might facilitate the activation of both IKKε- and TBK1-dependent cellular antiviral pathways, likely contributing to spontaneous clearance of the virus and observed acute HCV infection. After longer than 20 min cleavage, both IKKε- and TBK1 gradually lost their kinase activities and the relevant antiviral pathways were expected to be inactivated, facilitating the establishment of chronic HCV infection.

Probing conformational landscapes and mechanisms of allosteric communication in the functional states of the ABL kinase domain using multiscale simulations and network-based mutational profiling of allosteric residue potentials.

In the current study, multiscale simulation approaches and dynamic network methods are employed to examine the dynamic and energetic details of conformational landscapes and allosteric interactions in the ABL kinase domain that determine the kinase functions. Using a plethora of synergistic computational approaches, we elucidate how conformational transitions between the active and inactive ABL states can employ allosteric regulatory switches to modulate intramolecular communication networks between the ATP site, the substrate binding region, and the allosteric binding pocket. A perturbation-based network approach that implements mutational profiling of allosteric residue propensities and communications in the ABL states is proposed. Consistent with biophysical experiments, the results reveal functionally significant shifts of the allosteric interaction networks in which preferential communication paths between the ATP binding site and substrate regions in the active ABL state become suppressed in the closed inactive ABL form, which in turn features favorable allosteric coupling between the ATP site and the allosteric binding pocket. By integrating the results of atomistic simulations with dimensionality reduction methods and Markov state models, we analyze the mechanistic role of macrostates and characterize kinetic transitions between the ABL conformational states. Using network-based mutational scanning of allosteric residue propensities, this study provides a comprehensive computational analysis of long-range communications in the ABL kinase domain and identifies conserved regulatory hotspots that modulate kinase activity and allosteric crosstalk between the allosteric pocket, ATP binding site, and substrate binding regions.

Abstract WMP110: Cerebral Ischemia-Reperfusion Alters Postsynaptic Kinase Activities Through Ubiquitination

Background: Aberrant activity of the postsynaptic density (PSD)-associated kinases CaMKII, PKC, Pyk2 and Cdk5 contributes to post-ischemic neuronal death. However, the mechanism(s) leading to altered activity after ischemia have not been discovered. We investigated the role of ubiquitination in post-ischemic PSD kinase activity regulation. Methods: Cerebral ischemia was induced in male C57BL6 mice by middle cerebral artery occlusion (MCAO), followed by 1-hour reperfusion. Ubiquitinated and phosphorylated proteins in the ischemic neocortex were identified by nanoLC-MS/MS and analyzed for GO enrichment. PSD isolation was carried out by detergent extraction. Kinase ubiquitination was confirmed by co-immunoprecipitation with ubiquitin. Protein phosphorylation was assessed with phospho-specific antibodies and kinase activities were measured by transfer of γ 32 P to peptide substrates. Removal of ubiquitin from PSD lysates was achieved by addition of USP2 deubiquitinase. Results: MS analysis revealed that MCAO increases ubiquitination of proteins associated with the PSD (p=5.14x10 -33 , n=60/group). This is also evidenced by biochemical detection of ubiquitin at the synapse and PSD but not cytosol of cortical MCAO extracts (p<0.001, n=6/group). Interestingly, a significant number of ubiquitinated PSD proteins exhibit kinase activity (p=1.02x10 -23 , n=60/group) and include the kinases CaMKII, PKC, Pyk2 and Cdk5, which were biochemically verified (n=3/group). Concurrent with ubiquitination, MCAO also changes the phosphorylation state of PSD-associated proteins (p=3.66x10 -13 , n=60/group). Pyk2 and Cdk5 target sites are hyper-phosphorylated in post-ischemic PSD extracts, while CaMKII and PKC targets show decreased phosphorylation (p<0.05, n=5/group). In line with this, post-ischemic CaMKII (-69±6% of sham, p<0.001, n=9/group) and PKC (-63±8% of sham, p<0.001, n=6/group) activities are severely suppressed at the PSD, which is restored by de-ubiquitination (CaMKII: 105.8±23% of sham, n=6/group; PKC: 101.4±11% of sham, n=4/group). Conclusions: Ubiquitination is a potent and reversible modulator of kinase activity at the PSD that could impact tissue outcome and, as such, may open new avenues for the treatment of ischemic stroke.

The copper chaperone CCS facilitates copper binding to MEK1/2 to promote kinase activation

Normal physiology relies on the precise coordination of intracellular signaling pathways that respond to nutrient availability to balance cell growth and cell death. The canonical mitogen-activated protein kinase pathway consists of the RAF-MEK-ERK signaling cascade and represents one of the most well-defined axes within eukaryotic cells to promote cell proliferation, which underscores its frequent mutational activation in human cancers. Our recent studies illuminated a function for the redox-active micronutrient copper (Cu) as an intracellular mediator of signaling by connecting Cu to the amplitude of mitogen-activated protein kinase signalingviaa direct interaction between Cu and the kinases MEK1 and MEK2. Given the large quantities of molecules such as glutathione and metallothionein that limit cellular toxicity from free Cu ions, evolutionarily conserved Cu chaperones facilitate efficient delivery of Cu to cuproenzymes. Thus, a dedicated cellular delivery mechanism of Cu to MEK1/2 likely exists. Using surface plasmon resonance and proximity-dependent biotin ligase studies, we report here that the Cu chaperone for superoxide dismutase (CCS) selectively bound to and facilitated Cu transfer to MEK1. Mutants of CCS that disrupt Cu(I) acquisition and exchange or a CCS small-molecule inhibitor were used and resulted in reduced Cu-stimulated MEK1 kinase activity. Our findings indicate that the Cu chaperone CCS provides fidelity within a complex biological system to achieve appropriate installation of Cu within the MEK1 kinase active site that in turn modulates kinase activity and supports thedevelopment of novel MEK1/2 inhibitors that target the Custructural interface or blunt dedicated Cu delivery mechanismsviaCCS.

Sustained O‐GlcNAcylation causes ERK Signal and APP Amplification

Activation of ERK (Extra-cellular Regulated Kinase) signal plays a major role in metabolic diseases such as cancer and Alzheimer's. Ingenuity Pathway Analysis (IPA) of RNA-Seq data from long-term O-GlcNAcase (OGA) enzyme inhibitor- Thiamet-G (TMG) treated SH-SY5Y (neuroblastoma) cells, which elevates O-GlcNAc levels, indicated ERK Signaling as a top upregulated pathway. O-GlcNAcylation consists of the addition of a single N-acetyl-glucosamine residue (GlcNAc) to specific serine/threonine residues of proteins by the enzyme OGT (O-GlcNAc Transferase) and the removal of O-GlcNAc is catalyzed by the enzyme OGA. O-GlcNAc is highly abundant and is known to modulate kinase activity. Thus, to further investigate the mechanism by which O-GlcNAcylation activates ERK, we did a serum reactivation time-course and found that there is an amplification in ERK phosphorylation after long-term TMG treatment in HeLa and SH-SY5Y cells. Next, TGF-β stimulation that specifically activates ERK signaling also indicated an increase in ERK phosphorylation with long-term TMG treatment, confirming a robust ERK activation with TMG treatment. ERK phosphorylation oscillates with time after mitogen activation; therefore, we wanted to see if TMG treatment influenced ERK oscillation for a period of 24 hours. Serum reactivation revealed an oscillation in phosphorylated-ERK expression within a 24-hour period, where it reaches a maximum at 4 hours and slowly decreases at 8,12 and 24 hours upon long-term TMG treatment. Next, we wanted to further evaluate the mechanism by which TMG treatment increases ERK phosphorylation. Of note, we did not measure any O-GlcNAcylation on ERK; hence, we probed the expression of activated mitogen activated protein kinase-kinase (phosphorylated MEK) which phosphorylates ERK and Dual specificity phosphatases (DUSPs), which dephosphorylate ERK. Interestingly, serum reactivation time course showed an increase in both phosphorylated-MEK and total DUSP4 with TMG treatment. In addition to the use of pharmacological OGA inhibitor, we measured the effect of OGT knock-down (KD) and OGA KD on ERK signaling in SH-SY5Y and HeLa cells. There was amplification in ERK phosphorylation even after OGT knock-down (OGT KD) which lowers the level of O-GlcNAcylation, in contrast to long-term TMG treatment which increases O-GlcNAcylation. These data suggest that the cycling of the modification on and off substrates is key to ERK pathway regulation. Recent research also shows APOE4 stimulates the transcription of amyloid precursor protein (APP) via a non-canonical ERK signaling pathway, leading to increased amyloid-beta secretion in Alzheimer's disease pathogenesis. Therefore, we wanted to see if there is an increase in the expression of APP in the long-term TMG treated SH-SY5Y cells after serum reactivation, and we saw an increase in APP expression correlating with amplification of ERK signaling. Further evaluation of these molecular mechanisms to elucidate how O-GlcNAcylation amplifies ERK signaling and understand if O-GlcNAcylation and ERK activation work together to increase the transcription of APP are necessary.

Contribution of dsRBD2 to PKR Activation.

Protein kinase R (PKR) is a key pattern recognition receptor of the innate immune pathway. PKR is activated by double-stranded RNA (dsRNA) that is often produced during viral genome replication and transcription. PKR contains two tandem double-stranded RNA binding domains at the N-terminus, dsRBD1 and dsRBD2, and a C-terminal kinase domain. In the canonical model for activation, RNAs that bind multiple PKRs induce dimerization of the kinase domain that promotes an active conformation. However, there is evidence that dimerization of the kinase domain is not sufficient to mediate activation and PKR activation is modulated by the RNA-binding mode. dsRBD2 lacks most of the consensus RNA-binding residues, and it has been suggested to function as a modulator of PKR activation. Here, we demonstrate that dsRBD2 regulates PKR activation and identify the N-terminal helix as a critical region for modulating kinase activity. Mutations in dsRBD2 that have minor effects on overall dsRNA-binding affinity strongly inhibit the activation of PKR by dsRNA. These mutations also inhibit RNA-independent PKR activation. These data support a model where dsRBD2 has evolved to function as a regulator of the kinase.

Chemical Space Exploration of Oxetanes.

This paper focuses on new derivatives bearing an oxetane group to extend accessible chemical space for further identification of kinase inhibitors. The ability to modulate kinase activity represents an important therapeutic strategy for the treatment of human illnesses. Known as a nonclassical isoster of the carbonyl group, due to its high polarity and great ability to function as an acceptor of hydrogen bond, oxetane seems to be an attractive and underexplored structural motif in medicinal chemistry.

Abstract NG16: Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

Abstract NG16: Double <i>PIK3CA</i> mutations in <i>cis</i> increase oncogenicity and sensitivity to PI3Kα inhibitors

P019 Colonic mucosal kinase activity, cytokine and chemokine profiles in inflammatory bowel disease

Abstract Background With the approval of tofacitinib, an oral Janus Kinase (JAK) inhibitor, modulation of kinase activity has been added to the therapeutic armamentarium of inflammatory bowel disease (IBD). Despite its established efficacy, at least a third of patients will not respond to this or other therapeutic options such as anti-tumour necrosis factor (TNF), anti-interleukin (IL)23/IL12 compounds or vedolizumab. A better understanding of the inflammatory profile could aid in tailoring drugs to individual patients. We therefore explored mucosal cytokine, chemokine and kinase activity profiles in IBD. Methods Colonic mucosal biopsies were collected from (1) patients with Crohn’s disease (CD, N = 8), (2) patients with ulcerative colitis (UC, N = 8) and (3) healthy controls (N = 4). IBD samples were collected both from inflamed and non-inflamed tissue from the same patients. All IBD patients were biological-naïve and had not used corticosteroids in the past 3 months. Biopsies were snap frozen for later kinase activity determination or directly used in a 24-h explant culture. Whole biopsy kinase activity (tyrosine, serine and threonine kinases) was assessed using the Pamgene platform. A 64-analyte panel was examined in the supernatant of the cultured biopsies employing a multiplex assay (Luminex). Results Whole-biopsy kinase activity differed between inflamed and non-inflamed mucosa of IBD patients, with more overall tyrosine kinase activity in inflamed mucosa in UC, and serine/threonine kinase activity in inflamed mucosa in CD as compared with non-inflamed mucosa (Figure 1). The kinase activity profile of non-inflamed mucosa of CD and UC patients was similarly different from mucosa of healthy control participants (Figure 2). The cytokine and chemokine profile of inflamed biopsies differed from non-inflamed IBD biopsies and healthy control biopsies, with higher levels of S100A8, TNFα, IL-6, oncostatin M (OSM) and triggering receptor expressed on myeloid cells-1 (TREM-1), amongst others (Figure 3). Conclusion In IBD, inflammation in the mucosa can be characterised both by explant-culture and kinase activity assessment. The difference in kinase activity between non-inflamed IBD mucosa and healthy control mucosa suggests the presence of sub-clinical alterations in cell signalling. The observed differences in the kinase, cytokine and chemokine profiles underscore the importance of this approach in the elucidation of the pathophysiology in IBD.

A High-Throughput BRET Cellular Target Engagement Assay Links Biochemical to Cellular Activity for Bruton's Tyrosine Kinase.

Protein kinases are intensely studied mediators of cellular signaling. While traditional biochemical screens are capable of identifying compounds that modulate kinase activity, these assays are limited in their capability of predicting compound behavior in a cellular environment. Here, we aim to bridge target engagement and compound-cellular phenotypic behavior by utilizing a bioluminescence resonance energy transfer (BRET) assay to characterize target occupancy within living cells for Bruton's tyrosine kinase (BTK). Using a diverse chemical set of BTK inhibitors, we determine intracellular engagement affinity profiles and successfully correlate these measurements with BTK cellular functional readouts. In addition, we leveraged the kinetic capability of this technology to gain insight into in-cell target residence time and the duration of target engagement, and to explore a structural hypothesis.

Selective downregulation of distinct circRNAs in the tissues and plasma of patients with primary hepatic carcinoma.

Multiple studies have indicated that circular RNAs (circRNAs) are closely associated with malignant tumor development and metastasis. However, the significance of circRNAs in primary hepatic carcinoma (PHC), particularly in the plasma, remains largely undetermined. In the current study, circRNA expression profiles in three pairs of tumor and adjacent normal samples from patients with PHC, were examined using circRNA chip screening. A total of 80 circRNAs were upregulated, while 75 circRNAs were downregulated in PHC tissues, relative to para-tumor tissues (fold change, ≥1.5). A total of two upregulated circRNAs and three downregulated circRNAs were selected as candidates for further validation of their differential expression. This was performed using reverse transcription-quantitative PCR with 11 pairs of PHC tissues and para-tumor tissues. The results indicated that hsa_circ_0003056 exhibited reduced expression in PHC tissues. Moreover, hsa_circ_0003056 and hsa_circ_0067127 were quantified in the plasma samples of 35 PHC patients and 32 healthy donors. The results revealed that hsa_circ_0067127 was significantly downregulated in the patients' plasma. Finally, a competing endogenous RNA network was constructed, which consisted of one circRNA (hsa_circ_0003056 or has_circ_0067127), five miRNAs and miRNA-targeted genes (mRNAs). Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that differentially expressed (DE) genes were significantly enriched in the pathway associated with ‘regulation of the pluripotency of stem cells’ for hsa_circ_0003056, and ‘ubiquitin-mediated proteolysis’ and ‘prostate cancer’ for hsa_circ_0067127. Gene ontology analysis revealed that DE genes were primarily associated with the ‘modulation of kinase activity’ and ‘intracellular and transmembrane-ephrin receptor activity’ for hsa_circ_0003056, ‘artery morphogenesis activity’, ‘HOPS complex and transferase activity’ and in ‘transferring acyl groups’ for hsa_circ_0067127. This approach indicated that hsa_circ_0003056 in PHC tissue, and hsa_circ_0067127 in PHC plasma, are downregulated and may be implicated in the tumorigenesis of PHC.

The kinase domain of CK1δ can be phosphorylated by Chk1.

Members of the casein kinase 1 (CK1) family are key regulators in numerous cellular signal transduction pathways and in order to prevent the development of certain diseases, CK1 kinase activity needs to be tightly regulated. Modulation of kinase activity by site-specific phosphorylation within the C-terminal regulatory domain of CK1δ has already been shown for several cellular kinases. By using biochemical methods, we now identified residues T161, T174, T176, and S181 within the kinase domain of CK1δ as target sites for checkpoint kinase 1 (Chk1). At least residues T176 and S181 show full conservation among CK1δ orthologues from different eukaryotic species. Enzyme kinetic analysis furthermore led to the hypothesis that site-specific phosphorylation within the kinase domain finally contributes to fine-tuning of CK1δ kinase activity. These data provide a basis for the extension of our knowledge about the role of site-specific phosphorylation for regulation of CK1δ and associated signal transduction pathways.

On‐Command Regulation of Kinase Activity using Photonic Stimuli

AbstractThe underlying role that many kinases play in complex cellular pathways as well as disease remains unclear. To better understand the role that kinases play in both health and disease states, the use of light as an external stimulus to modulate kinase activity with high spatiotemporal resolution has gained increasing interest over the years. Herein we highlight the progress made towards the development of light‐responsive kinase enzymes and small molecule inhibitors. In these examples, photolabile caging groups and photoswitchable entities have been utilised to modulate either kinase activation or inhibition in a light‐controlled manner.

Hyaluronic acid-induced capacitation involves protein kinase C and tyrosine kinase activity modulation with a lower oxidative metabolism in cryopreserved bull sperm

Hyaluronic acid is a glycosaminoglycan present in uterine and oviductal fluids in female ruminants, which has been used as a sperm capacitation inducer prior to in vitro fertilization in several species. CD44 is a specific hyaluronic acid receptor, present in the sperm plasma membrane, but its signaling transduction system has not been elucidated yet. Our aim was to study protein kinase C and tyrosine kinase participation in intracellular signaling and oxidative metabolism in hyaluronic acid-induced capacitation of cryopreserved bull spermatozoa. Sperm capacitation was induced with hyaluronic acid or heparin. GF-109203× and genistein were used as protein kinase C and tyrosine kinase inhibitors, respectively. Capacitation, sperm plasma membrane and acrosome integrity were studied using CTC and trypan blue – DIC, while variations in enzymatic activities were determined by spectrophotometry. The inhibition of protein kinase C and tyrosine kinase blocked hyaluronic acid and heparin induced capacitation. Metabolic enzymes such as NADP-dependent isocitrate and malate dehydrogenases participate in hyaluronic acid capacitation, in coincidence with a lower mitochondrial metabolism compared with heparin. On the other hand, NAD-dependent isocitrate and malate dehydrogenase were not modified by hyaluronic acid induction. These dehydrogenases were also modulated by protein kinase C and tyrosine kinase in the capacitation induced by heparin or hyaluronic acid. In conclusion, hyaluronic acid intracellular signal system involves protein kinase C and tyrosine kinase activities, which may modulate capacitation in cryopreserved bull sperm with a lower oxidative metabolism than heparin.

Abstract 252: Prostate carcinogenesis inhibition through AKT-PKCα signaling pathway by diosmetin

Abstract Mammalian target of rapamycin (mTOR) integrates nutrient and mitogen signals to regulate cell growth (increased cell mass and cell size) and cell division. mTOR protein kinase have two different complexes; complex-I contains major component raptor, whereas complex II (insensitive to rapamycin), has major component rictor. Rictor plays a critical role in AKT (Ser-473 phosphorylation), which facilitates phosphorylation of AKT on Thr-308 by PDK1 for full activation. When we genetically disrupted Rictor, it decreased AKT phosphorylation (Ser-473) and impaired PKCα (Ser-657) expressions. Growth factors viz., IGF-1 and IL-6 are the major player in prostate cancers, these increases Rictor expression. We need to have an agent that can modulate kinase activity of AKT and PKCα to inhibit prostate cancer cell growth. Diosmetin (5, 7-Trihydroxy-4′-methoxyflavone) could be such an agent. Diosmetin, a natural flavone present in plant legumes, has anti-mutagenic and anti-allergic properties. Diosmetin inhibited IGF-1 and IL-6 induced rictor expression in LNCaP and PC-3 prostate cancer cells. Diosmetin dose response treatment to these cells inhibited cell growth and induced apoptosis with no significant growth inhibition in normal prostate epithelial cells (RWPE1). Diosmetin treatment to prostate cancer cells modulated cell survival machinery by down regulating key molecules viz., c-Myc, Survivin and XIAP (X-Linked Inhibitor of Apoptosis). Similarly diosmetin (20 and 50μg/animal/day) feeding to nude mice models, which were orthotopically implanted with luciferase tag PC-3 cells in ventral prostate represented significant decrease in tumor volume than control mice. Diosmetin fed tumor bearing mice reduced phosphorylation of Rictor, (Thr-1135), AKT (Ser-473) and PKCα (Ser-657) expressions to inhibit tumor growth significantly. Moreover, luciferase activity of implanted tumor decreased after diosmetin dose response feeding than control mice. Additionally bone radiographic images suggested that diosmetin treatment inhibited homing of PC-3 cells in the bone. These effects were associated with decrease in cyclin D1 expression and their activating partner, cyclin-dependent kinase (cdk) 2 and 4 with concomitant upregulation of p27/KIP1. Further diosmetin treatment induced apoptosis which was evident by increased expression of cleaved caspase-3. We are documenting these evidences for the first time in animal model system that diosmetin acts against potential molecular targets to alter cellular events to elicit anticancer effects in prostate cancer. Citation Format: Rebecca Pakradooni, Ahmad Khalifa, Ilaha Isali, Sanjeev Shukla. Prostate carcinogenesis inhibition through AKT-PKCα signaling pathway by diosmetin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 252.

Characterization of two potential immunotherapeutics in tumor infiltrating lymphocytes (TILs) using flow cytometry and Meso Scale Discovery.

e15052 Background: Inter-K Peptide Therapeutics has developed two synthetic compounds that modulate kinase activity. To investigate the potential of these compounds as cancer immunotherapeutics, a flow cytometric intracellular cytokine staining (ICS) assay was developed to investigate the effect of the compounds on immune cells isolated from tumors from subjects with non-small cell lung cancer (NSCLC). In addition, the concentration of various cytokines was measured in cell culture supernatant after treatment with the compounds. Methods: After optimizing the assays in PBMC from healthy donors, the assay was used for clinical specimens. Tumor infiltrating lymphocytes (TILs) were isolated from two resected tumors by mechanical disaggregation. TILs were stimulated with or without anti-CD3/CD28 antibodies with and without Inter-K Compound A or Compound B for 72 hours. Following stimulation, cell culture supernatants were analyzed for 10 proinflammatory-related cytokines using the Meso Scale Discovery (MSD) assay. TILs were analyzed by flow cytometry with a 10-color immunophenotyping panel to measure the expression of functional markers CD25, IL-2, IFNg and Ki67 in NK, NKT, CD4 T and CD8 T cells. Results: Immunomodulation induced by Compound A treatment included an over two-fold increase in CD25 expression in CD4 T cells, statistically significant increases in IL-6 and IL-8 production while a decrease in Ki67 expression in CD8 T cells and a reduction in IL-2, IFNg, TNFa, IL-4, IL-10 and IL-13 production was observed. Compound B did not appear to have immunomodulatory properties. Conclusions: This work provides an example of the utility of flow cytometry in compound evaluation. In this case, preliminary data suggests that Compound A but not B was able to modulate the response in TIL samples in vitro, and supports the continued investigation of Compound A as an immunotherapeutic. Although TIL specimens are challenging to work with due to tumor availability and low cellular recovery, as the target for the immunotherapy, it is important that compound characterization be conducted in TIL in addition to healthy donor PBMC and cell lines.

CDC42 binds PAK4 via an extended GTPase-effector interface

The p21-activated kinase (PAK) group of serine/threonine kinases are downstream effectors of RHO GTPases and play important roles in regulation of the actin cytoskeleton, cell growth, survival, polarity, and development. Here we probe the interaction of the type II PAK, PAK4, with RHO GTPases. Using solution scattering we find that the full-length PAK4 heterodimer with CDC42 adopts primarily a compact organization. X-ray crystallography reveals the molecular nature of the interaction between PAK4 and CDC42 and shows that in addition to the canonical PAK4 CDC42/RAC interactive binding (CRIB) domain binding to CDC42 there are unexpected contacts involving the PAK4 kinase C-lobe, CDC42, and the PAK4 polybasic region. These additional interactions modulate kinase activity and increase the binding affinity of CDC42 for full-length PAK4 compared with the CRIB domain alone. We therefore show that the interaction of CDC42 with PAK4 can influence kinase activity in a previously unappreciated manner.

Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone.

The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.

Gene expression profiles and signaling mechanisms in \u03b12B-adrenoceptor-evoked proliferation of vascular smooth muscle cells

Backgroundα2-adrenoceptors are important regulators of vascular tone and blood pressure. Regulation of cell proliferation is a less well investigated consequence of α2-adrenoceptor activation. We have previously shown that α2B-adrenoceptor activation stimulates proliferation of vascular smooth muscle cells (VSMCs). This may be important for blood vessel development and plasticity and for the pathology and therapeutics of cardiovascular disorders. The underlying cellular mechanisms have remained mostly unknown. This study explored pathways of regulation of gene expression and intracellular signaling related to α2B-adrenoceptor-evoked VSMC proliferation.ResultsThe cellular mechanisms and signaling pathways of α2B-adrenoceptor-evoked proliferation of VSMCs are complex and include redundancy. Functional enrichment analysis and pathway analysis identified differentially expressed genes associated with α2B-adrenoceptor-regulated VSMC proliferation. They included the upregulated genes Egr1, F3, Ptgs2 and Serpine1 and the downregulated genes Cx3cl1, Cav1, Rhoa, Nppb and Prrx1. The most highly upregulated gene, Lypd8, represents a novel finding in the VSMC context. Inhibitor library screening and kinase activity profiling were applied to identify kinases in the involved signaling pathways. Putative upstream kinases identified by two different screens included PKC, Raf-1, Src, the MAP kinases p38 and JNK and the receptor tyrosine kinases EGFR and HGF/HGFR. As a novel finding, the Src family kinase Lyn was also identified as a putative upstream kinase.Conclusionsα2B-adrenoceptors may mediate their pro-proliferative effects in VSMCs by promoting the activity of bFGF and PDGF and the growth factor receptors EGFR, HGFR and VEGFR-1/2. The Src family kinase Lyn was also identified as a putative upstream kinase. Lyn is known to be expressed in VSMCs and has been identified as an important regulator of GPCR trafficking and GPCR effects on cell proliferation. Identified Ser/Thr kinases included several PKC isoforms and the β-adrenoceptor kinases 1 and 2. Cross-talk between the signaling mechanisms involved in α2B-adrenoceptor-evoked VSMC proliferation thus appears to involve PKC activation, subsequent changes in gene expression, transactivation of EGFR, and modulation of kinase activities and growth factor-mediated signaling. While many of the identified individual signals were relatively small in terms of effect size, many of them were validated by combining pathway analysis and our integrated screening approach.