Protein-ligand binding and protein allostery play a crucial role in cell signaling, cell regulation, and modern drug discovery. In recent years, experimental studies of protein structures including crystallography, NMR, and Cryo-EM are widely used to investigate the functional and inhibitory properties of a protein. On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role in depicting the general figures of the conformational landscape of those proteins. On the other hand, free energy calculations which include the conformational and binding free energy calculation, which provides the thermodynamics basis of protein allostery and inhibitor binding, have proven its ability to guide new inhibitor discovery and protein functional studies. In this dissertation, I have used multiple different analysis and free energy methods to understand the significance of the conformational and binding free energy landscapes of protein kinases and other disease-related proteins and developed a novel alchemical-based free energy method, restrain free energy release (R-FEP-R) to overcome the difficulties in choosing appropriate collective variables and pathways in conformational free energy methods like umbrella sampling and metadynamics. / Chemistry

Platelets are crucial components of the hemostatic machinery of the body. When the endothelial continuity is disrupted due to injury or atherosclerotic plaque rupture, one of the earliest responses to arrest the bleeding is the adhesion of circulating platelets to the exposed subendothelial collagen matrix. Subsequent intracellular signaling mediated downstream of various receptor systems leads to alpha IIb beta 3 activation, thromboxane generation, ADP release, etc., culminating in platelet clot or thrombus formation. The protein kinase family of enzymes mediates a significant number of these intracellular signaling events that culminate in platelet activation. These enzymes can be broadly classified into two classes- tyrosine kinases and serine/threonine kinases. Syk (spleen tyrosine kinase) is an important non-receptor tyrosine kinase present in platelets and plays an important role downstream of GPVI-FcR gamma chain receptor complex activation. We studied the effects of curcumin (diferuloylmethane), which is the active ingredient found in the herbal remedy and food spice turmeric, on the GPVI-mediated platelet activation. We have found that it significantly inhibits the kinase activity of Syk without affecting its phosphorylation. Pre-incubating the platelets with curcumin for only a minute resulted in a concentration-dependent inhibition of aggregation and secretion, with approximately 75% inhibition observed at 50 mM curcumin. Additionally, the activation-dependent phosphorylation of tyrosines 753/759 on PLC gamma2 and phosphorylation of tyrosine 191 on the transmembrane scaffold protein LAT, were inhibited (p<0.05). However, the phosphorylation of the activation loop tyrosines 525/526 on Syk and of the tyrosine 145 on intracellular adaptor molecule SLP-76 were not significantly affected. Furthermore, the inhibitory action of curcumin on the catalytic activity of Syk was independent of any of its effects on the thromboxane generation because all our studies were performed using aspirin-treated platelets. PKC zeta is an atypical member of the PKC family of serine/threonine kinases. In this study, we have confirmed that it is expressed in human platelets and is constitutively phosphorylated at the activation loop threonine 410 as well as the turn motif threonine 560, which is an autophosphorylation site. Phosphorylation at these two residues has been shown to be important for its kinase activity. Furthermore, agonist-mediated platelet aggregation under stirring condition results in dephosphorylation of the Thr410 residue, which can be prevented by blocking integrin alpha IIb beta 3 by its antagonist SC-57101 (p<0.01). The dephosphorylation of Thr410 can also be prevented by okadaic acid, a Ser/Thr protein phosphatase inhibitor, at concentrations above 100 nM. However, in PP1c gamma null mice, we did not observe any effect on the dephosphorylation, suggesting that other isoforms of PP1 or other classes of the phosphatases could be responsible for this phenomenon, at least in these knockout mice. The basal phosphorylation of Thr560, however, remained unaffected by agonist stimulation, integrin activation, integrin blockade, okadaic acid treatment and in the PP1c gamma null mice. It can be speculated that PKC zeta may be constitutively active under basal resting conditions and acts as a negative regulator of platelet activation or functional responses. The Thr560 autophosphorylation signal alone may not be sufficient to sustain its full enzymatic activity. / Physiology

Cardiovascular disease remains the leading cause of morbidity and mortality worldwide and Myocardial Infarction (MI) and subsequent heart failure remains the leading cause for death. Despite the improvement in prognosis and treatment of acute MI patients, the underlying causes including loss of cardiomyocytes and microvasculature remain potential risk and lack proper and efficient solutions. Stem cell-based therapies for repair and regeneration have evolved and have been applied in clinical trials. Different types of stem cells, including Endothelial progenitor cell (EPC), Mesenchymal Stem Cell (MSC), induced Pluripotent Stem Cell (iPSC) and cardiac progenitor cells etc. have been used for potential long term recovery and cardiac regeneration. However, results from the clinical trials have been largely disappointing and improvement in cardiac functions have been modest likely due to the limitations of cell therapy including low integration in myocardium, poor survival, cellular dysfunction and limited differentiation ability. It is therefore necessary and urgent to develop cell free alternatives as next generation regenerative therapies. There is a consensus that the beneficial effect of stem cell therapy is largely due to paracrine effects. Exosomes have recently emerged as important functional units mediating stem cell paracrine effects. Exosomes are the family of extracellular vesicles (EV) which are 30-150nm in size, secreted by almost all types of cells and responsible for cell-cell communication via delivering their cargo including RNAs and proteins to host cells. Studies from our and other labs have shown that exosomes mimic parental stem cell in improving post-MI functions. The essential feature of exosome is decided by their cargo including RNA and protein, which are subject to dynamic changes depending on the environment of parental cells. Our studies were focused on Endothelial Progenitor Cell (EPC)-derived exosomes. EPCs are generated in bone marrow, and home to the site of tissue injury and orchestrate neovascularization and tissue repair. Patients with ischemic heart disease, are usually accompanied with comorbidities such as systemic inflammation, aging, diabetes, etc. which are known to compromise EPC functions. We hypothesized that EPCs under inflammatory stress produce dysfunctional exosomes with altered RNA and protein content, leading to impaired cardiac reparative properties. We chose interleukin-10 knockout (IL-10KO) mice as a model of systemic inflammation. EPCs were isolated from IL-10KO and wild-type (WT) mice, and their exosomes (Exo) were compared for their reparative properties both in vitro and in vivo. Our in vitro studies showed WT-EPC-Exo treatment attenuated recipient cell apoptosis, enhanced cell mobilization and tube formation, whereas IL-10KO-EPC-Exo were functionally deficient or even had detrimental effects. We used MI mouse model to compare the in vivo function of two groups of exosomes and found WT-EPC-Exo treatment significantly improved left ventricular (LV) cardiac function, inhibited cell death, promoted angiogenesis and attenuated cardiac remodeling; while these cardioprotective effects were lost in IL-10KO-EPC-Exo treated group. Both in vitro and in vivo studies proved that even the same progenitor cell type (EPCs), under inflammatory stimulus (IL-10KO), secretes exosomes with different reparative properties. Next, we explored whether the observed difference in exosome function is caused by altered exosome content. Using Next Generation RNA Sequencing (NGS RNAseq) and mass spectrometry we found RNA and protein expression patterns were drastically different in wild type and IL-10 knockout EPC derived exosomes. This evidence leads to the conclusion that alteration in exosome content is fundamental for exosome function. We picked two candidates that are highly enriched in IL-10KO-EPC-Exo for further study, miR-375 and Integrin-Linked Kinase (ILK). We treated IL-10KO-EPC with anti-miR against miR-375 and siRNA against ILK separately, and successfully decreased the expression of miR-375 and ILK in both EPCs and EPC derived exosomes. Then we explored the function of those miR and protein ‘modified exosomes’ with similar in vitro and in vivo experiments as previously described. Compared to IL-10KO-EPC-Exo, miR-375 knockdown exosomes showed enhanced angiogenesis and inhibited cell apoptosis, while ILK knockdown in exosomes rescued functions in both in vitro and in vivo experiments. These results suggested the possibility that exosome manipulation of identified factors may partially rescue their reparative functionality. In summary, our studies revealed that stem cell derived exosomes are capable for independent cardiac repair in ischemic heart disease, however, parental stem cells under pathological stimulus secrete dysfunctional exosomes with altered RNA and protein content. Exosome function can be rescued or enhanced through RNA and protein content modification. / Biomedical Sciences

Cholesterol and fatty acid homeostasis is maintained by a complex network of regulatory mechanisms that control the biosynthesis and deposition of lipids over diverse physiological conditions. However, these processes can become dysregulated and uncoupled from energy metabolism by metabolic stress such as a hyper-caloric diet and physical inactivity; eventually manifesting as risk factors associated with atherosclerotic cardiovascular disease (ASCVD), Type 2 diabetes (T2D), and/or non-alcoholic fatty liver disease (NAFLD). AMP-activated protein kinase (AMPK) is a sensor of cellular energy status that promotes metabolic homeostasis by mediating effects on multiple cellular processes including cholesterol and fatty acid synthesis biosynthesis. However, the mechanisms linking AMPK to lipid metabolism under normal and pathological conditions, remain undefined. In these studies, we identify a novel nutrient sensing mechanism whereby the coenzyme A (CoA) activated esters of long-chain fatty acids (LCFA-CoA) directly activate AMPK via specific interactions within the β1-regulatory subunit involving a Ser108 residue previously shown only with synthetic activators. We demonstrate the physiological relevance for this mechanism in an acute setting by showing that fatty acid oxidation was attenuated in mice harboring an AMPKβ1-S108A knock-in mutation compared to WT mice. We then demonstrated that β1-selctive AMPK activation is mimicked by the CoA conjugated form of bempedoic acid, a synthetic small molecule lipid synthesis inhibitor in clinical development for lowering elevated levels of low-density lipoprotein cholesterol (LDL-C). The importance of this mechanism was determined by assessing multiple disease outcomes in Ampkβ1-/-/Apoe-/- double knockout (DKO) mice fed a high fat-high cholesterol (HFHC) diet ± bempedoic acid. In these studies, bempedoic acid treatment reduced plasma LDL-C and atherosclerosis in both Apoe-/- and DKO mice, while no differences in disease outcomes was detected between the two genotypes in response to HFHC feeding. Further mechanistic investigations in rodent and primary human hepatocytes, revealed that the CoA conjugate of bempedoic acid suppressed lipid synthesis via competitive inhibition of ATP-citrate lyase (ACL), which promoted LDL receptor upregulation and associated reductions in LDL-C. We then integrate these findings with published literature in a written synthesis aimed to evaluate the role of ACL in metabolism, and its potential utility as a therapeutic target to treat ASCVD and metabolic disorders in humans. Although several questions remain regarding the metabolic role of AMPK activation by LCFA-CoAs, these studies have expanded our understanding of how cells acutely integrate lipid and energy signals to maintain lipid homeostasis, and identified ACL as a promising strategy to treat hypercholesterolemia, ASCVD, and associated metabolic disorders. / Thesis / Doctor of Philosophy (PhD) / The dysregulation of cholesterol and triglyceride metabolism can manifest as risk factors for life-threating diseases such as atherosclerotic cardiovascular diseases (ASCVD), Type-2 diabetes (T2D), and nonalcoholic fatty liver disease (NAFLD). However, the underlying mechanisms controlling lipid homeoastasis in health and disease are not completely understood. ATP-citrate lyase (ACL) and AMP-activated protein kinase (AMPK) are emerging as key nodes in metabolism that integrate lipid metabolism with signals of nutrient availability and cellular energy status, respectively. These strategic positions in metabolism suggest that both these enzymes could play an important role in the underlying pathophysiology of lipid-related diseases, and are therefore, prime candidates for therapeutic intervention. In these studies, we expand our understanding of the role of AMPK in metabolism beyond energy sensing by identifying specific lipid metabolites as direct allosteric activators of kinase activity. We also evaluate the therapeutic utility of targeting both AMPK and ACL in novel models of hypercholesterolemia and metabolic disease, and demonstrate that ACL inhibition offers a promising strategy to address multiple unmet medical needs.

No description available.

This study was designed to examine the effect of genistein, a botanical derived primarily from legumes, on pancreatic β-cell proliferation and the related molecular mechanisms. Diabetes mellitus is a major and growing public health problem worldwide. Both in type 1 (T1D) and type 2 diabetes (T2D), the deterioration of glycemic control over time is primarily caused by an inadequate mass and progressive dysfunction of β-cells. Therefore, the search for novel, safe and cost-effective agents that can enhance islet β-cell proliferation, thereby preserving β-cell mass, could be one of the essential strategies to prevent diabetes, given that β-cells have the potential to regenerate by proliferation of pre-existing b-cells in both physiological condition and after onset of diabetes. Genistein has various biological actions. However, studies on whether genistein has an effect on pancreatic β-cell function are very limited. Our laboratory recently found that genistein activates cAMP/protein kinase A (PKA) signaling in both clonal β-cells and mouse islets. Here I present evidence that genistein induced cellular proliferation of clonal rat pancreatic β-cells (INS1) and human islets following 24 h of incubation. This effect was dose-dependent with 5 µM genistein inducing a maximal 41% increase. The effect of genistein on cell proliferation was not dependent on estrogen receptors because this effect was not blocked by the estrogen receptor inhibitor ICI182,780. In addition, the genistein effect on β-cell proliferation was not shared by 17-β-estradiol or a host of structurally related flavonoid compounds, suggesting that this genistein action is structure-specific. Pharmacological or molecular intervention of PKA or MEK1/2, the upstream kinase of p42/44 mitogen activated protein kinases (ERK1/2), completely abolished the genistein-stimulated proliferation of INS1 cells and human islets, suggesting that both molecules are essential for genistein action. Consistent with its effect on cell proliferation, genistein increased intracellular cAMP and subsequently activated PKA in human islets. Genistein also caused a rapid and sustained phosphorylation of ERK1/2 with a maximal increase of 185% at 5 µM genistein. The genistein-induced ERK1/2 activation was completely ablated by inhibition of PKA in INS1 cells and human islets. Furthermore, I found that genistein induced protein expression of cyclin D1, a nuclear target of PKA and ERK1/2 activation and a major cell-cycle regulator essential for ï ¢-cell growth. These findings demonstrated that genistein may be a plant-derived growth factor for pancreatic β-cells involving induction of cyclin D1 via activation of the cAMP/PKA-dependent ERK1/2 signaling pathway, thereby providing a novel role for genistein in the regulation of pancreatic β-cell function. / Master of Science

京都大学 / 新制・課程博士 / 博士(医学) / 甲第25000号 / 医博第5034号 / 新制||医||1070(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 長船 健二, 教授 尾野 亘, 教授 江藤 浩之 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

No / Background: The molecular regulation of endothelial nitric oxide synthase (eNOS) in blood platelets and the signalling events induced by platelet-derived NO are poorly defined. In particular, the ability of von Willebrand factor (VWF) to stimulate cyclic guanosine monophosphate (cGMP) formation in platelets has produced conflicting data. Objectives: To determine the mechanisms leading to eNOS activation and clarify the downstream signaling pathways activated by platelet-derived NO in response to VWF. Methods: We used three independent markers of NO signaling, [3H] l-citrulline production, cGMP accrual and immunoblotting of vasodilator¿stimulated phosphoprotein (VASP) to examine the NO signaling cascade in response to VWF. Results: VWF increased NO synthesis and bioavailability, as evidenced by increased [3H] l-citrulline production and cGMP accrual, respectively. VWF-induced eNOS activation was GPIb-IX-dependent and independent of integrin ¿IIbß3. cGMP formation in response to VWF required Ca2+ mobilization, Src family kinases, phosphatidylinositol 3-kinase and phospholipase C, but not protein kinase C. This suggests that a cross-talk between the signaling mechanisms regulates platelet activation and NO synthesis. VWF-induced cGMP accrual was completely blocked by apyrase and indomethacin, demonstrating an essential role for platelet-derived ADP and thromboxane A2 (TxA2). Elevated cGMP levels led to increased VASP phosphorylation at serine239 that was both protein kinase G (PKG)- and protein kinase A (PKA)-dependent. Conclusions: We demonstrate that VWF activates eNOS through a specific Ca2+-dependent GPIb receptor-signaling cascade that relies on the generation of platelet-derived ADP and TxA2. Furthermore, we provide the first evidence to suggest that platelet derived-NO/cGMP activates PKA in addition to PKG.

Yes / Group I metabotropic glutamate receptor (mGluR) dependent long-term depression (LTD) is a major form of synaptic plasticity underlying learning and memory. The molecular mechanisms involved in mGluR-LTD have been investigated intensively for the last two decades. In this 60th anniversary special issue article, we review the recent advances in determining the mechanisms that regulate the induction, transduction and expression of mGluR-LTD in the hippocampus, with a focus on the mitogen-activated protein kinase (MAPK) pathways. In particular we discuss the requirement of p38 MAPK and extracellular signal-regulated kinase 1/2 (ERK 1/2) activation. The recent advances in understanding the signaling cascades regulating mGluR-LTD are then related to the cognitive impairments observed in neurological disorders, such as fragile X syndrome and Alzheimer's disease.

Yes / The key metabolic regulator, AMP-activated protein kinase (AMPK) is reported to be downregulated in metabolic disorders, but the mechanisms are poorly characterised. Recent studies have identified phosphorylation of the AMPKα1/α2 catalytic subunit isoforms at Ser487/491 respectively as an inhibitory regulation mechanism. Vascular endothelial growth factor (VEGF) stimulates AMPK and protein kinase B (Akt) in cultured human endothelial cells. As Akt has been demonstrated to be an AMPKα1 Ser487 kinase, the effect of VEGF on inhibitory AMPK phosphorylation in cultured primary human endothelial cells was examined. Stimulation of endothelial cells with VEGF rapidly increased AMPKα1 Ser487 phosphorylation in an Akt-independent manner, without altering AMPKα2 Ser491 phosphorylation. In contrast, VEGF-stimulated AMPKα1 Ser487 phosphorylation was sensitive to inhibitors of protein kinase C (PKC) and PKC activation using phorbol esters or overexpression of PKC stimulated AMPKα1 Ser487 phosphorylation. Purified PKC and Akt both phosphorylated AMPKα1 Ser487 in vitro with similar efficiency. PKC activation was associated with reduced AMPK activity, as inhibition of PKC increased AMPK activity and phorbol esters inhibited AMPK, an effect lost in cells expressing mutant AMPKα1 Ser487Ala. Consistent with a pathophysiological role for this modification, AMPKα1 Ser487 phosphorylation was inversely correlated with insulin sensitivity in human muscle. These data indicate a novel regulatory role of PKC to inhibit AMPKα1 in human cells. As PKC activation is associated with insulin resistance and obesity, PKC may underlie the reduced AMPK activity reported in response to overnutrition in insulin-resistant metabolic and vascular tissues.