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- ItemOptical, electrical and chemical properties of PEO:I2 complex composite films(Heidelberg [u.a.] : Springer, 2022) Telfah, Ahmad; Al-Bataineh, Qais M.; Tolstik, Elen; Ahmad, Ahmad A.; Alsaad, Ahmad M.; Ababneh, Riad; Tavares, Carlos J.; Hergenröder, RolandSynthesized PEO:I2 complex composite films with different I2 concentrations were deposited onto fused silica substrates using a dip-coating method. Incorporation of PEO films with I2 increases the electrical conductivity of the composite, reaching a maximum of 46 mS/cm for 7 wt% I2. The optical and optoelectronic properties of the complex composite films were studied using the transmittance and reflectance spectra in the UV-Vis region. The transmittance of PEO decreases with increasing I2 content. From this study, the optical bandgap energy decreases from 4.42 to 3.28 eV as I2 content increases from 0 to 7 wt%. In addition, the refractive index for PEO films are in the range of 1.66 and 2.00.1H NMR spectra of pure PEO film shows two major peaks at 3.224 ppm and 1.038 ppm, with different widths assigned to the mobile polymer chains in the amorphous phase, whereas the broad component is assigned to the more rigid molecules in the crystalline phase, respectively. By adding I2 to the PEO, both peaks (amorphous and crystal) are shifted to lower NMR frequencies indicating that I2 is acting as a Lewis acid, and PEO is acting as Lewis base. Hence, molecular iodine reacts favorably with PEO molecules through a charge transfer mechanism, and the formation of triiodide (I3-), the iodite (IO2-) anion, I 2· · · PEO and I2+···PEO complexes. PEO:I2 complex composite films are expected to be suitable for optical, electrical, and optoelectronic applications.
- ItemSynthesis, in Vitro Profiling, and in Vivo Evaluation of Benzohomoadamantane-Based Ureas for Visceral Pain: A New Indication for Soluble Epoxide Hydrolase Inhibitors(Washington, DC : ACS, 2022) Codony, Sandra; Entrena, José M.; Calvó-Tusell, Carla; Jora, Beatrice; González-Cano, Rafael; Osuna, Sílvia; Corpas, Rubén; Morisseau, Christophe; Pérez, Belén; Barniol-Xicota, Marta; Griñán-Ferré, Christian; Pérez, Concepción; Rodríguez-Franco, María Isabel; Martínez, Antón L.; Loza, M. Isabel; Pallàs, Mercè; Verhelst, Steven H. L.; Sanfeliu, Coral; Feixas, Ferran; Hammock, Bruce D.; Brea, José; Cobos, Enrique J.; Vázquez, SantiagoThe soluble epoxide hydrolase (sEH) has been suggested as a pharmacological target for the treatment of several diseases, including pain-related disorders. Herein, we report further medicinal chemistry around new benzohomoadamantane-based sEH inhibitors (sEHI) in order to improve the drug metabolism and pharmacokinetics properties of a previous hit. After an extensive in vitro screening cascade, molecular modeling, and in vivo pharmacokinetics studies, two candidates were evaluated in vivo in a murine model of capsaicin-induced allodynia. The two compounds showed an anti-allodynic effect in a dose-dependent manner. Moreover, the most potent compound presented robust analgesic efficacy in the cyclophosphamide-induced murine model of cystitis, a well-established model of visceral pain. Overall, these results suggest painful bladder syndrome as a new possible indication for sEHI, opening a new range of applications for them in the visceral pain field.
- ItemDeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning(Basel : Molecular Diversity Preservation International, 2023) Sun, Jianfeng; Ru, Jinlong; Ramos-Mucci, Lorenzo; Qi, Fei; Chen, Zihao; Chen, Suyuan; Cribbs, Adam P.; Deng, Li; Wang, XiaAberrant miRNA expression has been associated with a large number of human diseases. Therefore, targeting miRNAs to regulate their expression levels has become an important therapy against diseases that stem from the dysfunction of pathways regulated by miRNAs. In recent years, small molecules have demonstrated enormous potential as drugs to regulate miRNA expression (i.e., SM-miR). A clear understanding of the mechanism of action of small molecules on the upregulation and downregulation of miRNA expression allows precise diagnosis and treatment of oncogenic pathways. However, outside of a slow and costly process of experimental determination, computational strategies to assist this on an ad hoc basis have yet to be formulated. In this work, we developed, to the best of our knowledge, the first cross-platform prediction tool, DeepsmirUD, to infer small-molecule-mediated regulatory effects on miRNA expression (i.e., upregulation or downregulation). This method is powered by 12 cutting-edge deep-learning frameworks and achieved AUC values of 0.843/0.984 and AUCPR values of 0.866/0.992 on two independent test datasets. With a complementarily constructed network inference approach based on similarity, we report a significantly improved accuracy of 0.813 in determining the regulatory effects of nearly 650 associated SM-miR relations, each formed with either novel small molecule or novel miRNA. By further integrating miRNA–cancer relationships, we established a database of potential pharmaceutical drugs from 1343 small molecules for 107 cancer diseases to understand the drug mechanisms of action and offer novel insight into drug repositioning. Furthermore, we have employed DeepsmirUD to predict the regulatory effects of a large number of high-confidence associated SM-miR relations. Taken together, our method shows promise to accelerate the development of potential miRNA targets and small molecule drugs.
- ItemIn vitro effect of Withania somnifera, AYUSH-64, and remdesivir on the activity of CYP-450 enzymes: Implications for possible herb−drug interactions in the management of COVID-19(Lausanne : Frontiers Media, 2022) Kasarla, Siva Swapna; Borse, Swapnil P.; Kumar, Yashwant; Sharma, Neha; Dikshit, MadhuAyurvedic medicines Withania somnifera Dunal (ashwagandha) and AYUSH-64 have been used for the prevention and management of COVID-19 in India. The present study explores the effect of Ashwagandha and AYUSH-64 on important human CYP enzymes (CYP3A4, CYP2C8, and CYP2D6) to assess their interaction with remdesivir, a drug used for COVID-19 management during the second wave. The study also implies possible herb−drug interactions as ashwagandha and AYUSH-64 are being used for managing various pathological conditions. Aqueous extracts of ashwagandha and AYUSH-64 were characterized using LC-MS/MS. A total of 11 and 24 phytoconstituents were identified putatively from ashwagandha and AYUSH-64 extracts, respectively. In addition, in silico studies revealed good ADME properties of most of the phytoconstituents of these herbal drugs and suggested that some of these might possess CYP-450 inhibitory activity. In vitro CYP-450 studies with human liver microsomes showed moderate inhibition of CYP3A4, 2C8, and 2D6 by remdesivir, while ashwagandha had no inhibitory effect alone or in combination with remdesivir. AYUSH-64 also exhibited a similar trend; however, a moderate inhibitory effect on CYP2C8 was noticed. Thus, ashwagandha seems to be safe to co-administer with the substrates of CYP3A4, CYP2C8, and CYP2D6. However, caution is warranted in prescribing AYUSH-64 along with CYP2C8 substrate drugs. Furthermore, preclinical and clinical PK studies would be helpful for their effective and safer use in the management of various ailments along with other drugs.
- ItemThe human TRPA1 intrinsic cold and heat sensitivity involves separate channel structures beyond the N-ARD domain([London] : Nature Publishing Group UK, 2022) Moparthi, Lavanya; Sinica, Viktor; Moparthi, Vamsi K.; Kreir, Mohamed; Vignane, Thibaut; Filipovic, Milos R.; Vlachova, Viktorie; Zygmunt, Peter M.TRP channels sense temperatures ranging from noxious cold to noxious heat. Whether specialized TRP thermosensor modules exist and how they control channel pore gating is unknown. We studied purified human TRPA1 (hTRPA1) truncated proteins to gain insight into the temperature gating of hTRPA1. In patch-clamp bilayer recordings, ∆1–688 hTRPA1, without the N-terminal ankyrin repeat domain (N-ARD), was more sensitive to cold and heat, whereas ∆1–854 hTRPA1, also lacking the S1–S4 voltage sensing-like domain (VSLD), gained sensitivity to cold but lost its heat sensitivity. In hTRPA1 intrinsic tryptophan fluorescence studies, cold and heat evoked rearrangement of VSLD and the C-terminus domain distal to the transmembrane pore domain S5–S6 (CTD). In whole-cell electrophysiology experiments, replacement of the CTD located cysteines 1021 and 1025 with alanine modulated hTRPA1 cold responses. It is proposed that hTRPA1 CTD harbors cold and heat sensitive domains allosterically coupled to the S5–S6 pore region and the VSLD, respectively.
- ItemThe influence of Sb doping on the local structure and disorder in thermoelectric ZnO:Sb thin films(Lausanne : Elsevier, 2023) Ribeiro, Joana M.; Rodrigues, Frederico J.; Correia, Filipe C.; Pudza, Inga; Kuzmin, Alexei; Kalinko, Aleksandr; Welter, Edmund; Barradas, Nuno P.; Alves, Eduardo; LaGrow, Alec P.; Bondarchuk, Oleksandr; Welle, Alexander; Telfah, Ahmad; Tavares, Carlos J.Thermoelectric transparent ZnO:Sb thin films were deposited by magnetron sputtering, with Sb content varying between 2 and 14 at%. As evidenced by X-ray diffraction analysis, the films crystallize in the ZnO wurtzite structure for lower levels of Sb-doping, developing a degree of amorphization for higher levels of Sb-doping. Temperature-dependent (10–300 K) X-ray absorption spectroscopy studies of the produced thin films were performed at the Zn and Sb K-edges to shed light on the influence of Sb doping on the local atomic structure and disorder in the ZnO:Sb thin films. The analysis of the Zn K-edge EXAFS spectra by the reverse Monte Carlo method allowed to extract detailed and accurate structural information in terms of the radial and bond angle distribution functions. The obtained results suggest that the introduction of antimony to the ZnO matrix promotes static disorder, which leads to partial amorphization with very small crystallites (∼3 nm) for large (12–14 at%) Sb content. Rutherford backscattering spectrometry (RBS) experiments enabled the determination of the in-depth atomic composition profiles of the films. The film composition at the surfaces determined by X-ray photoelectron spectroscopy (XPS) matches that of the bulk determined by RBS, except for higher Sb-doping in ZnO films, where the concentration of oxygen determined by XPS is smaller near the surface, possibly due to the formation of oxygen vacancies that lead to an increase in electrical conductivity. Traces of Sb–Sb metal bonds were found by XPS for the sample with the highest level of Sb-doping. Time-of-flight secondary ion mass spectrometry obtained an Sb/Zn ratio that follows that of the film bulk determined by RBS, although Sb is not always homogeneous, with samples with smaller Sb content (2 and 4 at% of Sb) showing a larger Sb content closer to the film/substrate interface. From the optical transmittance and reflectance curves, it was determined that the films with the lower amount of Sb doping have larger optical band-gaps, in the range of 2.9–3.2 eV, while the partially amorphous films with higher Sb content have smaller band-gaps in the range of 1.6–2.1 eV. Albeit the short-range crystalline order (∼3 nm), the film with 12 at% of Sb has the highest absolute Seebeck coefficient (∼56 μV/K) and a corresponding thermoelectric power factor of ∼0.2 μW·K−2·m−1.
- ItemInhibiting the glycerophosphodiesterase EDI3 in ER-HER2+ breast cancer cells resistant to HER2-targeted therapy reduces viability and tumour growth(Berlin, Heidelberg : Springer, 2023) Keller, Magdalena; Rohlf, Katharina; Glotzbach, Annika; Leonhardt, Gregor; Lüke, Simon; Derksen, Katharina; Demirci, Özlem; Göçener, Defne; AlWahsh, Mohammad; Lambert, Jörg; Lindskog, Cecilia; Schmidt, Marcus; Brenner, Walburgis; Baumann, Matthias; Zent, Eldar; Zischinsky, Mia-Lisa; Hellwig, Birte; Madjar, Katrin; Rahnenführer, Jörg; Overbeck, Nina; Reinders, Jörg; Cadenas, Cristina; Hengstler, Jan G.; Edlund, Karolina; Marchan, RosemarieBackground: Intrinsic or acquired resistance to HER2-targeted therapy is often a problem when small molecule tyrosine kinase inhibitors or antibodies are used to treat patients with HER2 positive breast cancer. Therefore, the identification of new targets and therapies for this patient group is warranted. Activated choline metabolism, characterized by elevated levels of choline-containing compounds, has been previously reported in breast cancer. The glycerophosphodiesterase EDI3 (GPCPD1), which hydrolyses glycerophosphocholine to choline and glycerol-3-phosphate, directly influences choline and phospholipid metabolism, and has been linked to cancer-relevant phenotypes in vitro. While the importance of choline metabolism has been addressed in breast cancer, the role of EDI3 in this cancer type has not been explored. Methods: EDI3 mRNA and protein expression in human breast cancer tissue were investigated using publicly-available Affymetrix gene expression microarray datasets (n = 540) and with immunohistochemistry on a tissue microarray (n = 265), respectively. A panel of breast cancer cell lines of different molecular subtypes were used to investigate expression and activity of EDI3 in vitro. To determine whether EDI3 expression is regulated by HER2 signalling, the effect of pharmacological inhibition and siRNA silencing of HER2, as well as the influence of inhibiting key components of signalling cascades downstream of HER2 were studied. Finally, the influence of silencing and pharmacologically inhibiting EDI3 on viability was investigated in vitro and on tumour growth in vivo. Results: In the present study, we show that EDI3 expression is highest in ER-HER2 + human breast tumours, and both expression and activity were also highest in ER-HER2 + breast cancer cell lines. Silencing HER2 using siRNA, as well as inhibiting HER2 signalling with lapatinib decreased EDI3 expression. Pathways downstream of PI3K/Akt/mTOR and GSK3β, and transcription factors, including HIF1α, CREB and STAT3 were identified as relevant in regulating EDI3 expression. Silencing EDI3 preferentially decreased cell viability in the ER-HER2 + cells. Furthermore, silencing or pharmacologically inhibiting EDI3 using dipyridamole in ER-HER2 + cells resistant to HER2-targeted therapy decreased cell viability in vitro and tumour growth in vivo. Conclusions: Our results indicate that EDI3 may be a potential novel therapeutic target in patients with HER2-targeted therapy-resistant ER-HER2 + breast cancer that should be further explored.
- ItemLUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus(Hoboken, NJ [u.a.] : Wiley, 2022) Wu, Zhixiao; Berlemann, Lena A.; Bader, Verian; Sehr, Dominik A.; Dawin, Eva; Covallero, Alberto; Meschede, Jens; Angersbach, Lena; Showkat, Cathrin; Michaelis, Jonas B.; Münch, Christian; Rieger, Bettina; Namgaladze, Dmitry; Herrera, Maria Georgina; Fiesel, Fabienne C.; Springer, Wolfdieter; Mendes, Marta; Stepien, Jennifer; Barkovits, Katalin; Marcus, Katrin; Sickmann, Albert; Dittmar, Gunnar; Busch, Karin B.; Riedel, Dietmar; Brini, Marisa; Tatzelt, Jörg; Cali, Tito; Winklhofer, Konstanze F.Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
- ItemE/Z reversible photoisomerization of methyl orange doped polyacrylic acid-based polyelectrolyte brush films(Hoboken, NJ [u.a.] : Wiley InterScience, 2022) Al‐Bataineh, Qais M.; Telfah, Ahmad D.; Ahmad, Ahmad A.; Bani‐Salameh, Areen A.; Abu‐Zurayk, Rund; Hergenröder, RolandThe photoswitching behavior of the polyacrylic acid (PAA) doped by methyl orange (MO) brush film was investigated using spectral analysis of UV-Vis absorbance, Fourier Transformation Infrared spectroscopy, 2D electrical conductivity mapping and Atomic Force Microscopy. The kinetics and time evolution of the photoisomerization of the PAA-MO PEBs film from E-state to Z-state by UV-light irradiation, and reverse thermal relaxation to E-state was explored. The results confirm that the photoisomerization kinetics of the overall peak is the superposition of the photoisomerization kinetics of (Formula presented.) transition, low- and high-frequency of the (Formula presented.) transition bands. The E–Z transformation led to transforming the azobenzene from flat with no dipole moment to 3.0 D dipole moment. Hence, the electrical conductivity escalated accordingly. The transformation of E-state to Z-state led to the collapse of the formed brushes because of the angular rotational momentum consequent to E–Z isomerization.
- ItemGlycolytic flux control by drugging phosphoglycolate phosphatase([London] : Nature Publishing Group UK, 2022) Jeanclos, Elisabeth; Schlötzer, Jan; Hadamek, Kerstin; Yuan-Chen, Natalia; Alwahsh, Mohammad; Hollmann, Robert; Fratz, Stefanie; Yesilyurt-Gerhards, Dilan; Frankenbach, Tina; Engelmann, Daria; Keller, Angelika; Kaestner, Alexandra; Schmitz, Werner; Neuenschwander, Martin; Hergenröder, Roland; Sotriffer, Christoph; von Kries, Jens Peter; Schindelin, Hermann; Gohla, AntjeTargeting the intrinsic metabolism of immune or tumor cells is a therapeutic strategy in autoimmunity, chronic inflammation or cancer. Metabolite repair enzymes may represent an alternative target class for selective metabolic inhibition, but pharmacological tools to test this concept are needed. Here, we demonstrate that phosphoglycolate phosphatase (PGP), a prototypical metabolite repair enzyme in glycolysis, is a pharmacologically actionable target. Using a combination of small molecule screening, protein crystallography, molecular dynamics simulations and NMR metabolomics, we discover and analyze a compound (CP1) that inhibits PGP with high selectivity and submicromolar potency. CP1 locks the phosphatase in a catalytically inactive conformation, dampens glycolytic flux, and phenocopies effects of cellular PGP-deficiency. This study provides key insights into effective and precise PGP targeting, at the same time validating an allosteric approach to control glycolysis that could advance discoveries of innovative therapeutic candidates.
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