Protein NMR assignment by isotope pattern recognition.

The current standard method for amino acid signal identification in protein NMR spectra is sequential assignment using triple-resonance experiments. Good software and elaborate heuristics exist, but the process remains laboriously manual. Machine learning does help, but its training databases need millions of samples that cover all relevant physics and every kind of instrumental artifact. In this communication, we offer a solution to this problem. We propose polyadic decompositions to store millions of simulated three-dimensional NMR spectra, on-the-fly generation of artifacts during training, a probabilistic way to incorporate prior and posterior information, and integration with the industry standard CcpNmr software framework. The resulting neural nets take [1H,13C] slices of mixed pyruvate-labeled HNCA spectra (different CA signal shapes for different residue types) and return an amino acid probability table. In combination with primary sequence information, backbones of common proteins (GB1, MBP, and INMT) are rapidly assigned from just the HNCA spectrum.

Metal-Free Synthesis of 2-(per)Fluoroalkyl-3-nitro Indoles via Intramolecular Cyclization of Amides.

A metal-free intramolecular cyclization of N-acyl amides for the synthesis of 3-nitro-2-(per)fluoroalkyl indoles is reported. Good functional group tolerance and a broad range of substrates are the features of this approach. The developed method is easy to operate and is suitable for the preparation of 2-difluoromethyl/trifluoromethyl/perfluoroethyl/perfluoropropyl indoles in yields of 84 to 99%. Also, the application of this protocol in the gram scale is shown.

Organophosphorus S-adenosyl-L-methionine mimetics: synthesis, stability, and substrate properties.

S-Adenosyl-l-methionine (SAM)-mediated methylation of biomolecules controls their function and regulates numerous vital intracellular processes. Analogs of SAM with a reporter group in place of the S-methyl group are widely used to study these processes. However, many of these analogs are chemically unstable that largely limits their practical application. We have developed a new compound, SAM-P H , which contains an H-phosphinic group (-P(O)(H)OH) instead of the SAM carboxylic group. SAM-P H is significantly more stable than SAM, retains functional activity in catechol-O-methyltransferase and methyltransferase WBSCR27 reactions. The last is associated with Williams-Beuren syndrome. Rac-SAM-P H was synthesized chemically, while (R,S)-SAM-P H and its analogs were prepared enzymatically either from H-phosphinic analogs of methionine (Met-PH) or H-phosphinic analog of S-adenosyl-l-homocysteine (SAH-P H ) using methionine adenosyltransferase 2A or halide methyltransferases, respectively. SAH-P H undergoes glycoside bond cleavage in the presence of methylthioadenosine nucleosidase like natural SAH. Thus, SAM-P H and its analogs are promising new tools for investigating methyltransferases and incorporating reporter groups into their substrates.

Single-Ion Magnetism of the [DyIII(hfac)4]- Anions in the Crystalline Semiconductor {TSeT1.5}●+[DyIII(hfac)4]- Containing Weakly Dimerized Stacks of Tetraselenatetracene.

The oxidation of tetraselenatetracene (TSeT) by tetracyanoquinodimethane in the presence of dysprosium(III) tris(hexafluoroacetylacetonate), DyIII(hfac)3, produces black crystals of {TSeT1.5}●+[DyIII(hfac)4]- (1) salt, which combines conducting and magnetic sublattices. It contains one-dimensional stacks composed of partially oxidized TSeT molecules (formal averaged charge is +2/3). Dimers and monomers can be outlined within these stacks with charge and spin density redistribution. The spin triplet state of the dimers is populated above 128 K with an estimated singlet-triplet energy gap of 542 K, whereas spins localized on the monomers show paramagnetic behavior. A semiconducting behavior is observed for 1 with the activation energy of 91 meV (measured by the four-probe technique for an oriented single crystal). The DyIII ions coordinate four hfac- anions in [DyIII(hfac)4]-, providing D2d symmetry. Slow magnetic relaxation is observed for DyIII under an applied static magnetic field of 1000 Oe, and 1 is a single-ion magnet (SIM) with spin reversal barrier Ueff = 40.2 K and magnetic hysteresis at 2 K. Contributions from DyIII and TSeT●+ paramagnetic species are seen in EPR. The DyIII ion rarely manifests EPR signals, but such signal is observed in 1. It appears due to narrowing below 30 K and has g4 = 6.1871 and g5 = 2.1778 at 5.4 K.

Synthesis, X-ray Crystallography, Spectroscopic Characterizations, Density Functional Theory, and Hirshfeld Surface Analyses of a Novel (Carbonato) Picket Fence Iron(III) Complex.

An Fe(III)-carbonato six-coordinate picket fence porphyrin complex with the formula [K(2,2,2-crypt)][FeIII(TpivPP)(CO3)]·C6H5Cl·3H2O (I) has been synthesized and characterized by UV-Vis and FT-IR spectra. The structure of (carbonato)(α,α,α,α-tetrakis(o-pivalamidophenyl)porphinato)ferrate(III) was also established by XRD. The iron atom is hexa-coordinated by the four nitrogen atoms of the pyrrol rings and the two oxygen atoms of the CO32- group. Complex I, characterized as a ferric high-spin complex (S = 5/2), presented higher Fe-Np (2.105(6) Å) and Fe-PC (0.654(2) Å) distances. Both X-ray molecular structure and Hirshfeld surface analysis results show that the crystal packing of I is made by C-H⋯O and C-H⋯Cg weak intermolecular hydrogen interactions involving neighboring [FeIII(TpivPP)(CO3)]- ion complexes. Computational studies were carried out at DFT/B3LYP-D3/LanL2DZ to investigate the HOMO and LUMO molecular frontier orbitals and the reactivity within the studied compound. The stability of compound I was investigated by analyzing both intra- and inter-molecular interactions using the 2D and 3DHirshfeld surface (HS) analyses. Additionally, the frontier molecular orbital (FMO) calculations and the molecular electronic potential (MEP) analyses were conducted to determine the electron localizations, electrophilic, and nucleophilic regions, as well as charge transfer (ECT) within the studied system.

Cage-like microstructures via sequential Ugi reactions in aqueous emulsions.

Cage-like microstructures were obtained in two steps by sequential Ugi reactions. At the first stage, submicron colloidal particles based on carboxymethylcellulose and chitosan with a domain structure were obtained in an aqueous suspension. In the second stage, the Ugi reaction was carried out on the surface of the Pickering emulsions with toluene. Removal of toluene and redissolution in water resulted in colloidosomes with large holes on the surface. Varying the cross-link density during the Ugi reaction made it possible to obtain structures with different hole sizes.

Lignin Structural Characterization and Its Antioxidant Potential: A Comparative Evaluation by EPR, UV-Vis Spectroscopy, and DPPH Assays.

The natural aromatic polymer lignin and its lignin-like oligomeric fragments have attracted attention for their antioxidant capacity and free radical scavenging activities. In this study, a 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay was employed to assess the antioxidant capacity of fractionated and partially depolymerized organosolv lignin by electron paramagnetic resonance (EPR) and UV-Vis spectroscopy. The results show significant antioxidant activity for both the lignin and oligomeric fragments, with the EPR measurements demonstrating their efficiency in quenching the free radicals. The EPR data were analyzed to derive the kinetic rate constants. The radical scavenging activity (RSA) of lignins was then determined by UV-Vis spectroscopy and the results were compared with the EPR method. This two-method approach improves the reliability and understanding of the antioxidant potential of lignin and its derivatives and provides valuable insights for their potential applications in various industries, including pharmaceuticals, food preservation, and cosmetics.

Relationship between thermal stability of collagens and the fraction of hydrophobic residues in their molecules.

In this study, a database of the thermal stability of collagens and their synthetic analogues has been compiled taking into account literature sources. In total, our database includes 1200 records. As a result of a comparative theoretical analysis of the collected experimental data, the relationship between the melting temperature (Tm) or denaturation temperature (Td) of collagens and the fraction of hydrophobic residues (f) in their molecules has been established. It is shown that this relationship is linear: the larger the f value, the higher the denaturation or melting temperature of a given collagen.

Novel convenient 2-step synthesis of pyrido[1,2-a]indoles from pyrylium salts and o-bromoanilines.

A novel convenient 2-step synthesis of substituted pyrido[1,2-a]indoles is developed starting from easily available pyrylium tetrafluoroborates and ortho-bromoanilines. A conversion of the pyrylium tetrafluoroborates to pyridinium ones followed by their palladium catalyzed intramolecular cyclization allows the formation of 24 examples of N-fused heterocycles. A one-pot two-stage cyclization procedure was developed. The utility of the methodology was demonstrated with the synthesis of new pyrido[1,2-a]indoles bearing different alkyl, aryl, chlorine, fluorine and methoxy substituents.

Theoretical modeling of electronic absorption spectra of ionized species of ß-diketones.

CONTEXT: Direct DFT evaluation of negatively charged or highly π-delocalized systems is intrinsically problematic. Single ionized (anionic) forms of ß-diketones combine both these issues. In this article, we have summarized and analyzed the experimental and theoretical spectral dataset for anionic forms of different substituted perfluorinated ß-diketones that were obtained by our team during the past few years. Using previously collected experimental data, spectra of anion of diketones containing phenol, 2-furoyl, 2-thiophen, 2-selenophen, 2-tellorphe, 2-pyridin, 2-naphthyl, and N-methyl-pyrrole substituted rings were considered and chosen for the simulation. The X3LYP density functional demonstrates good results in both ultraviolet and visible parts of the diketones spectra. Minnesota family show predictable ability within the reasonable errors. The linear correlation between the Hartree-Fock exchange and the errors of estimation has been observed. Density functionals with a low contribution of HF weight (0-30%) provide better prediction accuracy. METHODS: Quantum chemistry calculations were performed under eighteen density functionals (Slater, Becke, OPTX, LYP, PW91C, BPE0, B3LYP, CAM-B3LYP, X3LYP, TPSS, revTPSS, TPSSh, M06-L, M06, M06-2X, M06-HF, M11-L, MN15-L), paired with the SMD solvation model implemented in GAMESS US program package. Def2-SVP basis set functions were applied to light atoms, and CRENBL effective core potential was used to Tellurium.

Creation of spin switching in graphene oxide-based hybrid film materials with an anionic Fe(III) 5Cl-salicyaldehyde-thiosemicarbazone complex.

The present article describes the synthesis of hybrid composite film materials formed during the self-assembly process through non-covalent interactions of graphene oxide (GO) nanosheets with salt 1, represented by an anionic spin-crossover complex [FeIII(5Cl-thsa)2]- (5Cl-thsa - 5-chlorosalicylaldehyde thiosemicarbazone) and the organic tetraethylammonium cation [Et4N]+. The insertion of the salt 1 molecules into the interlayer space of GO nanosheets with the subsequent formation of a hybrid material GO-1 was observed. The film of the hybrid material GO-1 was characterized by scanning electron and confocal laser microscopy, EDX and XPS analysis, IR, Raman and 57Fe Mössbauer spectroscopy, dc magnetic measurements, and powder X-ray diffraction. Comparison of the magnetic properties of salt 1 and a film of the hybrid material GO-1 demonstrated a significant influence of the GO nanosheets matrix on the completeness of spin transition and showed a slight shift of the hysteresis loop by 1 K in the temperature range of 200-230 K. DFT calculations showed an important role of the organic cation [Et4N]+ in the process of adsorption of the spin-crossover anion [FeIII(5Cl-thsa)2]- on the GO nanosheet surface.

Mesenchymal stem/stromal cells alleviate early-stage pulmonary fibrosis in a uPAR-dependent manner.

Pulmonary fibrosis, a debilitating lung disorder characterised by excessive fibrous tissue accumulation in lung parenchyma, compromises respiratory function leading to a life-threatening respiratory failure. While its origins are multifaceted and poorly understood, the urokinase system, including urokinase-type plasminogen activator (uPA) and its receptor (uPAR), plays a significant role in regulating fibrotic response, extracellular matrix remodelling, and tissue repair. Mesenchymal stem/stromal cells (MSCs) hold promise in regenerative medicine for treating pulmonary fibrosis. Our study aimed to investigate the potential of MSCs to inhibit pulmonary fibrosis as well as the contribution of uPAR expression to this effect. We found that intravenous MSC administration significantly reduced lung fibrosis in the bleomycin-induced pulmonary fibrosis model in mice as revealed by MRI and histological evaluations. Notably, administering the MSCs isolated from adipose tissue of uPAR knockout mice (Plaur-/- MSCs) attenuated lung fibrosis to a lesser extent as compared to WT MSCs. Collagen deposition, a hallmark of fibrosis, was markedly reduced in lungs treated with WT MSCs versus Plaur-/- MSCs. Along with that, endogenous uPA levels were affected differently; after Plaur-/- MSCs were administered, the uPA content was specifically decreased within the blood vessels. Our findings support the potential of MSC treatment in attenuating pulmonary fibrosis. We provide evidence that the observed anti-fibrotic effect depends on uPAR expression in MSCs, suggesting that uPAR might counteract the uPA accumulation in lungs.

An Improved Migratory Birds Optimization Algorithm for Closed- Loop Supply Chain Network Planning in a Fuzzy Environment.

Recycling of used products can provide substantial economic and environmental benefits for supply chain players. However, many factors associated with the design of closed-loop supply chain networks are uncertain in their nature, including demand, opening cost of facilities, capacity of opened facilities, transportation cost, and procurement cost. Therefore, this study proposes a novel fuzzy programming model for closed-loop supply chain network design, which directly relies on the fuzzy ranking method based on a credibility measure. The objective of the presented optimization model aims at minimizing the total cost of the network when selecting the facility locations and transportation routes between the nodes of the network. Based on the problem characteristics, a Migratory Birds Optimization Algorithm with a new product source encoding scheme is developed as a solution approach. The inspiration for the product source coding method originates from the label information of raw material supplier and manufacturing factories on product packaging, as well as the information of each logistics node on the delivery order. This novel encoding method aims to address the limitations of four traditional encoding methods: Prüfer number based encoding, spanning tree based encoding, forest data structure based encoding, and priority based encoding, thereby increasing the likelihood of heuristic algorithms finding the optimal solution. Thirty-five illustrative examples are developed to evaluate the proposed algorithm against the exact optimization method (LINGO) and a Genetic Algorithm, Ant Colony Optimization, Simulated Annealing, which are recognized as well-known metaheuristic algorithms. The results from extensive experiments show that the proposed algorithm is able to provide optimal and good-quality solutions within acceptable computational time even for large-scale numerical examples. The suitability of the model is confirmed through a meticulous sensitivity analysis. This analysis involves adjusting the confidence level incrementally from 50% to 100%, in 5% intervals, with respect to the model's uncertain parameters. Consequently, it yields valuable managerial insights. The outcomes of this research are expected to provide scientific support for related supply chain enterprises and stakeholders.

Role of TGF-ß1/SMADs signalling pathway in resveratrol-induced reduction of extracellular matrix deposition by dexamethasone-treated human trabecular meshwork cells.

Deposition of extracellular matrix (ECM) in the trabecular meshwork (TM) increases aqueous humour outflow resistance leading to elevation of intraocular pressure (IOP) in primary open-angle glaucoma, which remains the only modifiable risk factor. Resveratrol has been shown to counteract the steroid-induced increase in IOP and increase the TM expression of ECM proteolytic enzymes; however, its effects on the deposition of ECM components by TM and its associated pathways, such as TGF-ß-SMAD signalling remain uncertain. This study, therefore, explored the effects of trans-resveratrol on the expression of ECM components, SMAD signalling molecules, plasminogen activator inhibitor-1 and tissue plasminogen activator in dexamethasone-treated human TM cells (HTMCs). We also studied the nature of molecular interaction of trans -resveratrol with SMAD4 domains using ensemble docking. Treatment of HTMCs with 12.5 µM trans-resveratrol downregulated the dexamethasone-induced increase in collagen, fibronectin and α-smooth muscle actin at gene and protein levels through downregulation of TGF-ß1, SMAD4, and upregulation of SMAD7. Downregulation of TGF-ß1 signalling by trans-resveratrol could be attributed to its effect on the transcriptional activity due to high affinity for the MH2 domain of SMAD4. These effects may contribute to resveratrol's IOP-lowering properties by reducing ECM deposition and enhancing aqueous humour outflow in the TM.

Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues.

Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development; it is also necessary for the choice of targeted therapy. The Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements, such as inversions and translocations. We propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. The developed protocol allows to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for the targeted therapy selection. The practical value of molecular genetic testing is its ability to influence the treatment strategies and to provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of the targeted therapies, which is a critical aspect of personalized medicine in oncology.

Metabolic Adaptations and Functional Activity of Macrophages in Homeostasis and Inflammation.

In recent years, the role of cellular metabolism in immunity has come into the focus of many studies. These processes form a basis for the maintenance of tissue integrity and homeostasis, as well as represent an integral part of the immune response, in particular, inflammation. Metabolic adaptations not only ensure energy supply for immune response, but also affect the functions of immune cells by controlling transcriptional and post-transcriptional programs. Studying the immune cell metabolism facilitates the search for new treatment approaches, especially for metabolic disorders. Macrophages, innate immune cells, are characterized by a high functional plasticity and play a key role in homeostasis and inflammation. Depending on the phenotype and origin, they can either perform various regulatory functions or promote inflammation state, thus exacerbating the pathological condition. Furthermore, their adaptations to the tissue-specific microenvironment influence the intensity and type of immune response. The review examines the effect of metabolic reprogramming in macrophages on the functional activity of these cells and their polarization. The role of immunometabolic adaptations of myeloid cells in tissue homeostasis and in various pathological processes in the context of inflammatory and metabolic diseases is specifically discussed. Finally, modulation of the macrophage metabolism-related mechanisms reviewed as a potential therapeutic approach.

Neuron-Specific Enolase-What Are We Measuring?

Since the discovery of the neuron-specific protein by Moore and McGregor in 1965, tens of thousands of studies have investigated the basic and applied significance of neuron-specific enolase (NSE). This promising biomarker, according to many researchers, has not found widespread use in clinical practice, particularly in acute cerebrovascular accidents. Moreover, the several studies refuting the usefulness of serum NSE measurement in critically ill patients leads us to consider the reasons for such contradictory conclusions. In this article, we have analyzed the main directions in the study of NSE and expressed our perspective on the reasons for the contradictory results and the difficulties in implementing the results of these studies in clinical practice. In our opinion, the method of the enzyme-linked immunosorbent assay (ELISA) used in the majority of the studies is inappropriate for the evaluation of NSE as a marker of central nervous system damage, because it does not allow for the differentiation of heterodimers of enolases and the assessment of the enzymatic activity of this group of enzymatic proteins. Therefore, the methodological approach for the evaluation of NSE (γγ-enolase) as a biomarker needs to be elaborated and improved. Furthermore, the specificity of the applied research methods and the appropriateness of the continued use of the term "neuron-specific enolase" must be addressed.

Mild and efficient synthesis and base-promoted rearrangement of novel isoxazolo[4,5-b]pyridines.

An efficient method for the synthesis of isoxazolo[4,5-b]pyridines has been developed on the basis of readily available 2-chloro-3-nitropyridines via the intramolecular nucleophilic substitution of the nitro group as a key step. The previously unknown base-promoted Boulton-Katritzky rearrangement of isoxazolo[4,5-b]pyridine-3-carbaldehyde arylhydrazones into 3-hydroxy-2-(2-aryl[1,2,3]triazol-4-yl)pyridines was observed.

HLA-DR Expression in Natural Killer Cells Marks Distinct Functional States, Depending on Cell Differentiation Stage.

HLA-DR-positive NK cells, found in both healthy individuals and patients with different inflammatory diseases, are characterized as activated cells. However, data on their capacity for IFNγ production or cytotoxic response vary between studies. Thus, more precise investigation is needed of the mechanisms related to the induction of HLA-DR expression in NK cells, their associations with NK cell differentiation stage, and functional or metabolic state. In this work, HLA-DR-expressing NK cell subsets were investigated using transcriptomic analysis, metabolic activity assays, and analysis of intercellular signaling cascades. We demonstrated that HLA-DR+CD56bright NK cells were characterized by a proliferative phenotype, while HLA-DR+CD56dim NK cells exhibited features of adaptive cells and loss of inhibitory receptors with increased expression of MHC class II trans-activator CIITA. The activated state of HLA-DR-expressing NK cells was confirmed by higher levels of ATP and mitochondrial mass observed in this subset compared to HLA-DR- cells, both ex vivo and after stimulation in culture. We showed that HLA-DR expression in NK cells in vitro can be induced both through stimulation by exogenous IL-2 and IL-21, as well as through auto-stimulation by NK-cell-produced IFNγ. At the intracellular level, HLA-DR expression depended on the activation of STAT3- and ERK1/2-mediated pathways, with subsequent activation of isoform 3 of the transcription factor CIITA. The obtained results broaden the knowledge about HLA-DR-positive NK cell appearance, diversity, and functions, which might be useful in terms of understanding the role of this subset in innate immunity and assessing their possible implications in NK cell-based therapy.

Synthesis of 5-(Aryl)amino-1,2,3-triazole-containing 2,1,3-Benzothiadiazoles via Azide-Nitrile Cycloaddition Followed by Buchwald-Hartwig Reaction.

An efficient access to the novel 5-(aryl)amino-1,2,3-triazole-containing 2,1,3-benzothiadiazole derivatives has been developed. The method is based on 1,3-dipolar azide-nitrile cycloaddition followed by Buchwald-Hartwig cross-coupling to afford the corresponding N-aryl and N,N-diaryl substituted 5-amino-1,2,3-triazolyl 2,1,3-benzothiadiazoles under NHC-Pd catalysis. The one-pot diarylative Pd-catalyzed heterocyclization opens the straightforward route to triazole-linked carbazole-benzothiadiazole D-A systems. The optical and electrochemical properties of the compound obtained were investigated to estimate their potential application as emissive layers in OLED devises. The quantum yield of photoluminescence (PLQY) of the synthesized D-A derivatives depends to a large extent on electron-donating strengths of donor (D) component, reaching in some cases the values closed to 100%. Based on the most photoactive derivative and wide bandgap host material mCP, a light-emitting layer of OLED was made. The device showed a maximum brightness of 8000 cd/m2 at an applied voltage of 18 V. The maximum current efficiency of the device reaches a value of 3.29 cd/A.