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Sepsis is generally considered as a severe condition of inflammation that leads to lymphocyte apoptosis and multiple organ dysfunction. Hydroxysafflor yellow A (HSYA) exerts anti-inflammatory and anti-apoptotic effects in infectious diseases. However, the therapeutic effect of HSYA on polymicrobial sepsis remains unknown. This study was undertaken to investigate the therapeutic effects and the mechanisms of action of HSYA on immunosuppression in a murine model of sepsis induced by cecal ligation and puncture (CLP). NIH mice were randomly divided into four groups: control group, sham group, CLP group, and CLP+HSYA group. HSYA (120 mg/kg) was intravenously injected into experimental mice at 12 h before CLP, concurrent with CLP and 12 h after CLP. The levels of circulating inflammatory cytokines, the apoptosis of CD4+ and CD8+ T lymphocytes, and protein expression of cytochrome C (Cytc), Bax, Bcl-2, cleaved caspase-9, and cleaved caspase-3 were examined. Plasma levels of IL-6, IL-10 and TNF-alpha as well as the apoptosis of CD4+ T lymphocytes were increased compared with sham group. These changes were accompanied by increases of pro-apoptotic proteins including Cytc, Bax, cleaved caspase-9, and cleaved caspase-3 and decreases of anti-apoptotic protein Bcl-2 in CD4+ T lymphocytes from mice undergoing CLP. In contrast, we fail to observe significant effect of HSYA on the apoptosis of CD8+ T lymphocytes in CLP-treated group. Of note, HSYA treatment reversed all above changes observed in CD4+ T lymphocytes, and significantly increased the ratio of CD4+:CD8+ T lymphocytes in CLP-treated mice. In conclusion, HSYA was an effective therapeutic agent in ameliorating sepsis-induced apoptosis of CD4+ T lymphocytes probably through its anti-inflammatory and anti-apoptotic effects.
The chemopreventive and anticancer effects of resveratrol (RSV) are widely reported in the literature. Specifically, mechanisms involving epigenetic regulation are promising targets to regulate tumor development. Bromodomains act as epigenetic readers by recognizing lysine acetylation on histone tails and boosting gene expression in order to regulate tissue-specific transcription. In this work, we showed that RSV is a pan-BET inhibitor. Using Differential Scanning Fluorimetry (DSF), we showed that RSV at 100 µM increased the melting temperature (∆Tm) of BET bromodomains by around 2.0 °C. The micromolar dissociation constant (Kd) range was characterized using Isothermal Titration Calorimetry (ITC). The RSV Kd value accounted to 6.6 µM in case of BRD4(1). Molecular docking proposed the binding mode of RSV against BRD4(1) mimicking the acetyl-lysine interactions. All these results suggest that RSV can also recognize epigenetic readers domains by interacting with BET bromodomains.
Binding free energy calculations that make use of alchemical pathways are becoming increasingly feasible thanks to advances in hardware and algorithms. Although relative binding free energy (RBFE) calculations are starting to find widespread use, absolute binding free energy (ABFE) calculations are still being explored mainly in academic settings due to the high computational requirements and still uncertain predictive value. However, in some drug design scenarios, RBFE calculations are not applicable and ABFE calculations could provide an alternative. Computationally cheaper end-point calculations in implicit solvent, such as molecular mechanics Poisson–Boltzmann surface area (MMPBSA) calculations, could too be used if one is primarily interested in a relative ranking of affinities. Here, we compare MMPBSA calculations to previously performed absolute alchemical free energy calculations in their ability to correlate with experimental binding free energies for three sets of bromodomain–inhibitor pairs. Different MMPBSA approaches have been considered, including a standard single-trajectory protocol, a protocol that includes a binding entropy estimate, and protocols that take into account the ligand hydration shell. Despite the improvements observed with the latter two MMPBSA approaches, ABFE calculations were found to be overall superior in obtaining correlation with experimental affinities for the test cases considered. A difference in weighted average Pearson () and Spearman () correlations of 0.25 and 0.31 was observed when using a standard single-trajectory MMPBSA setup ( = 0.64 and = 0.66 for ABFE; = 0.39 and = 0.35 for MMPBSA). The best performing MMPBSA protocols returned weighted average Pearson and Spearman correlations that were about 0.1 inferior to ABFE calculations: = 0.55 and = 0.56 when including an entropy estimate, and = 0.53 and = 0.55 when including explicit water molecules. Overall, the study suggests that ABFE calculations are indeed the more accurate approach, yet there is also value in MMPBSA calculations considering the lower compute requirements, and if agreement to experimental affinities in absolute terms is not of interest. Moreover, for the specific protein–ligand systems considered in this study, we find that including an explicit ligand hydration shell or a binding entropy estimate in the MMPBSA calculations resulted in significant performance improvements at a negligible computational cost.
Alzheimer’s disease is a chronic neurodegenerative disease that causes problems with memory, thinking and behavior. The pathophysiological hallmarks of AD are extracellular senile plaques and intracellular neurofibrillary tangles. Amyloid plaques mainly contain the amyloid-β (Aβ) peptide, which appears as a cleavage product of the APP. APP is a type I transmembrane protein with a large extracellular domain and a short cytoplasmic tail. It is expressed in variety of tissues e.g. in neuronal tissue (brain, spinal cord, retina), and non-neuronal tissues (kidney, lung, pancreas, prostate gland, and thyroid gland) (Dawkins and Small, 2014). APP has been studied because of its link to AD, however, its role in normal brain function is poorly understood. APP is processed by two different pathways, amyloidogenic pathway and non-amyloidogenic pathway. In physiological condition, the majority of APP is processed via the non-amyloidogenic, thus leading to the generation of the secreted N-terminal APP processing product sAPPα. sAPPα is formed due to the cleavage of APP by α-secretase. In previous studies, our group has shown that sAPPα produce potent neuroprotective effect by altering gene expression, as well as by antagonizing several different types of neurotoxic stress stimuli (Copanaki et al., 2010; Kögel et al., 2003, 2005; Milosch et al., 2014). Several studies have shown that protein degradation is reduced in AD (Hong et al., 2014; Lipinski et al., 2010) but the role of APP and its cleavage products in protein degradation is still unknown. This thesis discusses about the physiological functions of APP in neuroprotection and protein homeostasis.
In the first part of the thesis (Section 4.1 - 4.4), the neuroprotective properties of yeast derived sAPPα and E1 (N-terminal domain of sAPPα) were investigated under serum and glucose deprivation conditions. In previous work, it was shown that recombinant sAPPα evoked a significant decrease in serum deprivation triggered cell death in human SH-SY5Y neuroblastoma cells and mouse embryonic fibroblast MEF cells. It was also observed that sAPPα induces the phosphorylation of Akt which leads to neuroprotection (Milosch et al., 2014). This study investigated whether this neuroprotection is associated with altered expression of downstream intracellular Akt targets such as FoxO, Bim, Bcl-xL and Mcl-1 under stress conditions. Here it was shown that sAPPα prevents activation and nuclear translocation of FoxO. FoxO act as a transcription factor for different proapoptotic genes such as Bim. It was also observed that Bim protein and mRNA expression was significantly reduced with sAPPα and E1 treatment. The expression of antiapoptotic protiens such as Bcl-xL and Mcl-1 were also examined and it was observed that sAPPα and E1 increases expression of both these proteins. Furthermore, it was previously demonstrated that uncleaved holo-APP functionally cooperates with sAPPα to activate Akt and provide neuroprotection (Milosch et al., 2014). Therefore, to investigate the function of the APP in sAPPα regulated Akt downstream proteins expressions, MEF APP KO cells were used. E1 and sAPPα only showed neuroprotective modulatory effect on these Akt downstream targets in MEF wt cells, but not in APP KO cells. In addition, sAPPα also showed neuroprotection in primary wt hippocampal neurons under trophic factor deprivation. Cellular fractionation experiments were also done to determine the role of sAPPα in cytochrome c release from mitochondria. It was observed that sAPPα treatment can inhibit mitochondrial cytochrome c release in wt MEF cells.
The second part of the thesis (Section 4.5 - 4.9) discusses about the role of sAPPα in protein homeostasis. It was observed that sAPPα prevents proteotoxic stress induced BAG3 protein expression in SH-SY5Y and MEF cells. This was also observed in mRNA levels which indicate a transcriptional regulation. Furthermore, treatment with sAPPα was also shown to decrease aggresomes formation. Aggresomes are perinuclear aggregates which are formed due to accumulation of damaged and misfolded proteins and BAG3 plays important role in their formation and the transport of degradation prone proteins into these structures. The analysis of proteasomal activity showed a reduced accumulation of proteasomal substrate d2 by sAPPα under proteasomal stress. In proteasomal activity assay, sAPPα was shown to increase the degradation of proteasomal substrate SUC-LLVY-AMC and the fluorigenic signal was measured spectrophotometrically. The sAPPβ fragment which is generated via the amyloidogenic pathway was also examined for its role in BAG3 expression and proteasomal degradation. sAPPβ, which has almost similar structure as sAPPα, only 17 amino acids at the C-terminus is missing, was failed to modulate BAG3 expression and proteostasis. This indicates that these biological effects are highly specific for sAPPα.
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Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases.
Die 5-LO ist ein Schlüsselenzym der LT-Biosynthese. Sie katalysiert in einem ersten Schritt zunächst die Umsetzung freigesetzter AA zu 5-HPETE und wandelt diese anschließend in LTA4 um. LT sind starke Entzündungsmediatoren, die an entzündlichen und allergischen Reaktionen des Körpers beteiligt sind. Sie lösen eine Immunantwort aus und können zur Entstehung von Asthma bronchiale, allergischer Rhinitis, Herz-Kreislauf-Erkrankungen und verschiedenen Krebserkrankungen beitragen [28]. NFS gehören zur Klasse der michaelreaktiven Verbindungen und inhibieren die 5-LO durch Interaktion mit katalytisch aktiven Cysteinresten in der Nähe der Substrateintrittspforte. Diese Tatsache macht michaelreaktive Verbindungen innerhalb der Entzündungsforschung zu einer interessanten Substanzklasse. Michaelreaktive Verbindungen besitzen eine durch Elektronenzug aktivierte Doppelbindung. Hierdurch verfügen diese Wirkstoffe über elekrophile Eigenschaften, wodurch sie leicht mit Nukleophilen reagieren können. Cysteine bestehen aus nukleophilen Thiolgruppen, die mit einer positiv polarisierten Doppelbindung, wie sie in michaelreaktiven Verbindungen vorliegt, reagieren können. Diese Tatsache kann sie zu effektiven und nachhaltigen Enzymaktivitätsmodulatoren machen. In dieser Arbeit wurde eine große Bandbreite verschiedenster michaelreaktiver Verbindungen auf ihre Fähigkeit untersucht, die 5-LO über Michael-Addition an ihren Cysteinen zu inhibieren. Zum einen wurden Pflanzeninhaltsstoffe mit antiinflammatorischen Eigenschaften, zugelassenene Wirkstoffe mit Michael-Akzeptorfunktion und zum anderen Verbindungen, die durch gezielte Struktursuche ausgewählt wurden, untersucht. Die Testung verschiedenster Strukturen sollte Aufschluss über strukturelle Voraussetzungen für die 5-LO-Inhibition durch Interaktion mit Cysteinen liefern. Hierfür wurden die Substanzen zunächst im intakten Zellsystem und schließlich am aufgereinigten Enzym (r5LO-wt) auf ihre 5-LO-inhibierenden Eigenschaften untersucht. Nachfolgende Messungen an r5LO-4C, deren vier prominente Cysteine durch Serin mutiert wurden, zeigten an, ob die Inhibition der 5-LO-Produktbildung cysteinabhängig war. Die hierbei erhaltenen Ergebnisse deuten darauf hin, dass ganz bestimmte strukturelle Eigenschaften des Michael-Akzeptors, Voraussetzung für eine Interaktion mit den Cysteinen der 5-LO sind. Vor allem Verbindungen mit chinoidem Grundgerüst stellten sich als thiolreaktive Verbindungen heraus, die die 5-LO hauptsächlich über Interaktion mit ihren Cysteinen inhibierten. Weiterhin zeigten die erhaltenen Ergebnisse, dass die strukturelle Umgebung um die aktivierte Doppelbindung des Michael-Akzeptors enorme Auswirkungen auf die Thiolreaktivität hatte. TQ hemmte die 5-LO hauptsächlich über Interaktion mit Cysteinen, wohingegen die 5-LO-Inhibition durch Embelin unabhängig von Cysteinen zu sein schien. Eine daraufhin durchgeführte MALDI-MS-Analyse bestätigte die Bindung von NAPQI und TQ an die Cysteine 416 und 418. Durch diese Arbeit konnte erstmals gezeigt werden, dass eine Reihe antiinflammatorisch wirksamer, natürlich vorkommender Verbindungen wie TQ, Plumbagin, Primin und auch synthetisch generierte Verbindungen wie AA861, CDDO, Methyl-BQ, Methoxy-BQ, Methoxy-Nitrostyren, NAPQI und OH-BQ die 5-LO über Interaktion mit ihren Cysteinen inhibieren.
Serine/arginine-protein kinase 1 (SRPK1) regulates alternative splicing of VEGF-A to pro-angiogenic isoforms and SRPK1 inhibition can restore the balance of pro/antiangiogenic isoforms to normal physiological levels. The lack of potency and selectivity of available compounds has limited development of SRPK1 inhibitors, with the control of alternative splicing by splicing factor-specific kinases yet to be translated. We present here compounds that occupy a binding pocket created by the unique helical insert of SRPK1, and trigger a backbone flip in the hinge region, that results in potent (<10 nM) and selective inhibition of SRPK1 kinase activity. Treatment with these inhibitors inhibited SRPK1 activity and phosphorylation of serine/arginine splicing factor 1 (SRSF1), resulting in alternative splicing of VEGF-A from pro-angiogenic to antiangiogenic isoforms. This property resulted in potent inhibition of blood vessel growth in models of choroidal angiogenesis in vivo. This work identifies tool compounds for splice isoform selective targeting of pro-angiogenic VEGF, which may lead to new therapeutic strategies for a diversity of diseases where dysfunctional splicing drives disease development.
Drug product performance testing is an important part of quality-by-design approaches, but this process often lacks the underlying mechanistic understanding of the complex interactions between the disintegration and dissolution processes involved. Whereas a recent draft guideline by the US Food and Drug Administration (FDA) has allowed the replacement of dissolution testing with disintegration testing, the mentioned criteria are not globally accepted. This study provides scientific justification for using disintegration testing rather than dissolution testing as a quality control method for certain immediate release (IR) formulations. A mechanistic approach, which is beyond the current FDA criteria, is presented. Dissolution testing via United States Pharmacopeial Convention Apparatus II at various paddle speeds was performed for immediate and extended release formulations of metronidazole. Dissolution profile fitting via DDSolver and dissolution profile predictions via DDDPlus™ were performed. The results showed that Fickian diffusion and drug particle properties (DPP) were responsible for the dissolution of the IR tablets, and that formulation factors (eg, coning) impacted dissolution only at lower rotation speeds. Dissolution was completely formulation controlled if extended release tablets were tested and DPP were not important. To demonstrate that disintegration is the most important dosage form attribute when dissolution is DPP controlled, disintegration, intrinsic dissolution and dissolution testing were performed in conventional and disintegration impacting media (DIM). Tablet disintegration was affected by DIM and model fitting to the Korsmeyer–Peppas equation showed a growing effect of the formulation in DIM. DDDPlus was able to predict tablet dissolution and the intrinsic dissolution profiles in conventional media and DIM. The study showed that disintegration has to occur before DPP-dependent dissolution can happen. The study suggests that disintegration can be used as performance test of rapidly disintegrating tablets beyond the FDA criteria. The scientific criteria and justification is that dissolution has to be DPP dependent, originated from active pharmaceutical ingredient characteristics and formulations factors have to be negligible.