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- ItemQuantification of Dolichyl Phosphates Using Phosphate Methylation and Reverse-Phase Liquid Chromatography-High Resolution Mass Spectrometry(Columbus, Ohio : American Chemical Society, 2023) Kale, Dipali; Kikul, Frauke; Phapale, Prasad; Beedgen, Lars; Thiel, Christian; Brügger, BrittaDolichyl monophosphates (DolPs) are essential lipids in glycosylation pathways that are highly conserved across almost all domains of life. The availability of DolP is critical for all glycosylation processes, as these lipids serve as membrane-anchored building blocks used by various types of glycosyltransferases to generate complex post-translational modifications of proteins and lipids. The analysis of DolP species by reverse-phase liquid chromatography-mass spectrometry (RPLC-MS) remains a challenge due to their very low abundance and wide range of lipophilicities. Until now, a method for the simultaneous qualitative and quantitative assessment of DolP species from biological membranes has been lacking. Here, we describe a novel approach based on simple sample preparation, rapid and efficient trimethylsilyl diazomethane-dependent phosphate methylation, and RPLC-MS analysis for quantification of DolP species with different isoprene chain lengths. We used this workflow to selectively quantify DolP species from lipid extracts derived of Saccharomyces cerevisiae, HeLa, and human skin fibroblasts from steroid 5-α-reductase 3- congenital disorders of glycosylation (SRD5A3-CDG) patients and healthy controls. Integration of this workflow with global lipidomics analyses will be a powerful tool to expand our understanding of the role of DolPs in pathophysiological alterations of metabolic pathways downstream of HMG-CoA reductase, associated with CDGs, hypercholesterolemia, neurodegeneration, and cancer.
- ItemIR-MALDI Mass Spectrometry Imaging with Plasma Post-Ionization of Nonpolar Metabolites(Columbus, Ohio : American Chemical Society, 2022) Schneemann, Julian; Schäfer, Karl-Christian; Spengler, Bernhard; Heiles, SvenAmbient mass spectrometry imaging (MSI) methods come with the advantage of visualizing biomolecules from tissues with no or minimal sample preparation and operation under atmospheric-pressure conditions. Similar to all other MSI methodologies, however, ambient MSI modalities suffer from a pronounced bias toward either polar or nonpolar analytes due to the underlying desorption and ionization mechanisms of the ion source. In this study, we present the design, construction, testing, and application of an in-capillary dielectric barrier discharge (DBD) module for post-ionization of neutrals desorbed by an ambient infrared matrix-assisted laser desorption/ionization (IR-MALDI) MSI source. We demonstrate that the DBD device enhances signal intensities of nonpolar compounds by up to 104 compared to IR-MALDI without affecting transmission of IR-MALDI ions. This allows performing MSI experiments of mouse tissue and Danaus plexippus caterpillar tissue sections, visualizing the distribution of sterols, fatty acids, monoglycerides, and diglycerides that are not detected in IR-MALDI MSI experiments. The pronounced signal enhancement due to IR-MALDI-DBD compared to IR-MALDI MSI enables mapping of nonpolar analytes with pixel resolutions down to 20 μm in mouse brain tissue and to discern the spatial distribution of sterol lipids characteristic for histological regions of D. plexippus.
- ItemAzapeptide activity-based probes for the SARS-CoV-2 main protease enable visualization of inhibition in infected cells(Cambridge : RSC, 2023) Vanhoutte, Roeland; Barniol-Xicota, Marta; Chiu, Winston; Vangeel, Laura; Jochmans, Dirk; De Jonghe, Steven; Zidane, Hadeer; Barr, Haim M.; London, Nir; Neyts, Johan; Verhelst, Steven H. L.The COVID-19 pandemic has revealed the vulnerability of the modern, global society. With expected waves of future infections by SARS-CoV-2, treatment options for infected individuals will be crucial in order to decrease mortality and hospitalizations. The SARS-CoV-2 main protease is a validated drug target, for which the first inhibitor has been approved for use in patients. To facilitate future work on this drug target, we designed a solid-phase synthesis route towards azapeptide activity-based probes that are capped with a cysteine-reactive electrophile for covalent modification of the active site of Mpro. This design led to the most potent ABP for Mpro and one of the most potent inhibitors reported thus far. We demonstrate that this ABP can be used to visualize Mpro activity and target engagement by drugs in infected cells.
- 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.
- 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.
- 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.
- 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.