Search Results (18)

The interaction of cobalt(II) with first-generation quinolones oxolinic acid (Hoxo), flumequine (Hflmq), pipemidic acid (Hppa) and cinoxacin (Hcx) in the presence of the N,N′-donor heterocyclic ligands 2,2′-bipyridine (bipy) or 1,10-phenanthroline (phen) afforded a series of novel cobalt complexes, namely [Co(bipy)₂(oxo)](PF₆)₂·H₂O (1), [Co(phen)₂(oxo)](PF₆)₂·0.5CH₃OH·0.5H₂O (2), [Co(bipy)₂(flmq)](PF₆)₂·0.5CH₃OH·0.5H₂O (3), [Co(bipy)₂(ppa)](PF₆)₂·CH₃OH·0.5H₂O (4), [Co(phen)₂(cx)](PF₆)₂·CH₃OH·0.5H₂O (5), and [Co(phen)₂(flmq)](PF₆)·0.5CH₃OH·H₂O (6). The characterization of the complexes involved physicochemical techniques, various spectroscopies and single-crystal X-ray crystallography. The affinity of complexes to calf-thymus (CT) DNA was monitored with various techniques, suggesting intercalation in-between the DNA-nucleobases as the most probable interaction mode, which may be combined with electrostatic interactions as a result of the cationic nature of the complexes. The affinity of the complexes for bovine and human serum albumin proteins was monitored, and the determined corresponding albumin-binding constants revealed a tight and reversible interaction. Full article

It is particularly important to develop efficient air–rail intermodal path planning methods for making full use of the advantages of air–rail intermodal networks and providing passengers with richer and more reasonable travel options. A Time-Expanded Graph (TEG) is used to model the timetable information of public transportation providing a theoretical basis for public transportation path planning. However, if the TEG includes a large amount of data such as train stations, airports, train and air schedules, the network scale will become very large, making path planning extremely time-consuming. This study proposes an XGBoost-based heuristic path planning algorithm (XGB-HPPA) for large scale air–rail intermodal networks, which use the XGBoost model to predict transfer stations before path planning, and quickly eliminate unreasonable transfer edges by adding a heuristic factor, reducing the network scale, thus accelerating the computation speed. Comparative results indicate that XGB-HPPA can markedly enhance computational speed within large-scale networks, while obtaining as many valid solutions as possible and approximating the optimal solution. Full article

Inorganic pyrophosphatases, or PPases, are ubiquitous enzymes whose activity is necessary for a large number of biosynthetic reactions. The catalytic function of PPases is dependent on certain conformational changes that have been previously characterized based on the comparison of the crystal structures of various complexes. The current work describes the conformational dynamics of a structural model of human mitochondrial pyrophosphatase hPPA2 using molecular dynamics simulation, all-atom principal component analysis, and coarse-grained normal mode analysis. In addition to the wild-type enzyme, four mutant variants of hPPA2 were characterized that correspond to the natural pathogenic variants causing severe mitochondrial dysfunction and cardio pathologies. As a result, we identified the global type of flexible motion that seems to be shared by other dimeric PPases. This motion is discussed in terms of the allosteric behavior of the protein. Analysis of the observed conformational dynamics revealed the formation of a binding site for anionic ligands in the active site that could be relevant to enzyme catalysis. Based on the comparison of the wild-type and mutant PPases dynamics, we suggest the possible molecular mechanisms of the functional incompetence of hPPA2 caused by mutations. The results of this work allow for deeper insight into the structural basis of PPase function and the possible effects of pathogenic mutations on the protein structure and function. Full article

A simple and efficient method for the synthesis of biodegradable, highly branched polycaprolactone (PCL) is presented. The solvent-free (bulk) reaction was carried out via ring opening polymerization (ROP), catalyzed by tin octanoate Sn(Oct)₂, and it employed hyperbranched polyamide (HPPA) as a macro-initiator. The core–shell structure of the obtained products (PCL-HPPA), with the hyperbranched HPPA core and linear PCL chains as shell, was in the focus of the product characterization. ¹H nuclear magnetic resonance (¹H NMR) and elemental analysis confirmed the covalent incorporation of the HPPA in the products, as well as a high degree of grafting conversion of its amino functional groups. Confocal Raman Micro spectroscopy, and especially Time-of-Flight Secondary Ion Mass Spectrometry, further supported the existence of a core–shell structure in the products. Direct observation of macromolecules by means of cryogenic transmission electron microscopy, as well as gel permeation chromatography (GPC), suggested the existence of a minor ‘aggregated’ product fraction with multiple HPPA cores, which was attributed to transesterification reactions. Differential scanning calorimetry, as well as X-ray diffraction, demonstrated that the PCL-HPPA polymers displayed a similar degree of crystallinity to linear neat PCL, but that the branched products possessed smaller and less regular crystallites. Full article

D-serine plays an essential role in the field of medicine and cosmetics. Diaminopimelate dehydrogenase (DAPDH) is a kind of oxidoreductase that can reduce keto acid into the corresponding D-amino acid. Because of its high stereoselectivity and lack of by-product production, DAPDH has become the preferred enzyme for the efficient one-step synthesis of D-amino acids. However, the types of DAPDH with a reductive amination function reported so far are limited. Although the DAPDH from Symbiobacterium thermophilum (StDAPDH) demonstrates reductive amination activity toward a series of macromolecular keto acids, activity toward hydroxypyruvate (HPPA) for D-serine synthesis has not been reported. In this study, we investigated the activity of the available StDAPDH/H227V toward HPPA by measuring the desired product D-serine. After homologous structure modeling and docking analysis concerning the substrate-binding pocket, four residues, D92, D122, M152, and N253, in the active pocket were predicted for catalyzing HPPA. Through single-point saturation mutation and iterative mutation, a mutant D92E/D122W/M152S was obtained with an 8.64-fold increase in enzyme activity, exhibiting a specific activity of 0.19 U/mg and k_cat value of 3.96 s⁻¹ toward HPPA. Using molecular dynamics simulation, it was speculated that the increase in enzyme activity might be related to the change in substrate pocket size and the enhancement of the interactions between the substrate and key residues. Full article

Inorganic pyrophosphatases (PPases) catalyze an essential reaction, namely, the hydrolysis of PP_i, which is formed in large quantities as a side product of numerous cellular reactions. In the majority of living species, PP_i hydrolysis is carried out by soluble cytoplasmic PPase (S-PPases) with the released energy dissipated in the form of heat. In Rhodospirillum rubrum, part of this energy can be conserved by proton-pumping pyrophosphatase (H⁺-PPase^Rru) in the form of a proton electrochemical gradient for further ATP synthesis. Here, the codon-harmonized gene hppa^Rru encoding H⁺-PPase^Rru was expressed in the Escherichia coli chromosome. We demonstrate, for the first time, that H⁺-PPase^Rru complements the essential native S-PPase in E. coli cells. ¹³C-MFA confirmed that replacing native PPase to H⁺-PPase^Rru leads to the re-distribution of carbon fluxes; a statistically significant 36% decrease in tricarboxylic acid (TCA) cycle fluxes was found compared with wild-type E. coli MG1655. Such a flux re-distribution can indicate the presence of an additional method for energy generation (e.g., ATP), which can be useful for the microbiological production of a number of compounds, the biosynthesis of which requires the consumption of ATP. Full article

Freeze-dried apple peel powder (Fd-APP) was subjected to in vitro digestion and colonic fermentation to evaluate the variations in its phenolic composition, bioactivities (antioxidant activity, α-amylase, and α-glucosidase inhibition), and fecal metabolic outputs. A total of 88 phenolics were tentatively identified, of which 51 phenolic compounds were quantitated in Fd-APP sample extracts before digestion, and 34 were released during subsequent phases of digestion. Among these, phenolic acids showed the highest bio accessibility index (BI) of 68%, followed by flavonoids (63%) and anthocyanins (52%). The inhibitory functions of Fd-APP extract against α-amylase and α-glucosidase pre- and post-digestion were moderate and ranged from 41.88 to 44.08% and 35.23 to 41.13%, respectively. Additionally, the antioxidant activities revealed a significant (p ≤ 0.05) decline during the in vitro digestion. However, the colonic fermentation stage presented different products where the intact parent phenolic compounds present in Fd-APP were utilized by gut microbes and produced various phenolic metabolites such as 3- hydroxyphenyl acetic acid (3-HPAA), ferulic acid (FA), 3-(4-hydroxyphenyl) propionic acid (3,4 HPPA) and 4- hydroxybenzoic acid (4-HBA). Furthermore, colonic fermentation of Fd-APP accelerated the production of short-chain fatty acids (SCFAs), with acetic acid being the most prevalent (97.53 ± 9.09 mM). The decrease in pH of fermentation media to 4.3 significantly (p ≤ 0.05) enhanced counts of Bifidobacterium (10.27 log CFU/mL), which demonstrated the potential prebiotic effects of Fd-APP. These findings indicated that the consumption of apple peel as a constituent of novel functional foods may support and protect the intestinal microbiota and consequently promote human health. Full article

Changes in the phenylalanine (PHE)/tyrosine (TYR) pathway metabolites before and during homogentisic acid (HGA)-lowering by nitisinone in the Suitability of Nitisinone in Alkaptonuria (AKU) 2 (SONIA 2) study enabled the magnitude of the flux in the pathway to be examined. SONIA 2 was a 48-month randomised, open-label, evaluator-blinded, parallel-group study performed in the UK, France and Slovakia recruiting patients with confirmed AKU to receive either 10 mg nitisinone or no treatment. Site visits were performed at 3 months and yearly thereafter. Results from history, photographs of eyes/ears, whole body scintigraphy, echocardiography and abdomen/pelvis ultrasonography were combined to produce the Alkaptonuria Severity Score Index (cAKUSSI). PHE, TYR, hydroxyphenylpyruvate (HPPA), hydroxyphenyllactate (HPLA) and HGA metabolites were analysed by liquid chromatography/tandem mass spectrometry in 24 h urine and serum samples collected before and during nitisinone. Serum metabolites were corrected for total body water (TBW), and the sum of 24 h urine plus total body water metabolites of PHE, TYR, HPPA, HPLA and HGA were determined. The sum of urine metabolites (PHE, TYR, HPPA, HPLA and HGA) were similar pre- and peri-nitisinone. The sum of TBW metabolites and sum TBW + URINE metabolites were significantly higher peri-nitisinone (p < 0.001 for both) compared with pre-nitisinone baseline. Significantly higher concentrations of metabolites from the tyrosine metabolic pathway were observed during treatment with nitisinone. Arguments for unmasking of the ochronotic pathway and biliary elimination of HGA are put forward. Full article

Nitisinone (NIT) causes tyrosinaemia and corneal keratopathy (KP), especially in men. However, the adaptation within the phenylalanine (PHE)/tyrosine (TYR) catabolic pathway during KP is not understood. The objective of this study is to assess potential differences in the PHE/TYR pathway during KP and the influence of gender in NIT-induced tyrosinaemia in alkaptonuria (AKU). Samples of serum and 24 h urine collected from patients treated with NIT during a 4-year randomized study in NIT vs. no-treatment controls (SONIA 2; Suitability Of Nitisinone In Alkaptonuria 2; EudraCT no. 2013-001633-41) at months 3 (V2), 12 (V3), 24 (V4), 36 (V5) and 48 (V6) were included in these analyses. Homogentisic acid (HGA), TYR, PHE, hydroxyphenylpyruvate (HPPA), hydroxyphenyllactate (HPLA) and sNIT were analysed at all time-points in serum and urine in the NIT-group. All statistical analyses were post hoc. Keratopathy occurred in 10 out of 69 AKU patients, eight of them male. Thirty-five sampling points (serum and 24 h urine) were analysed in patients experiencing KP and 272 in those with no-KP (NKP) during NIT therapy. The KP group had a lower HPLA/TYR ratio and a higher TYR/PHE ratio compared with the NKP group (p < 0.05 for both). There were 24, 45, 100 and 207 sampling points (serum and 24 h urine) in the NIT group which were pre-NIT female, pre-NIT male, NIT female and NIT male, respectively. The PHE/TYR ratio and the HPLA/TYR ratio were lower in males (p < 0.001 and p < 0.01, respectively). In the KP group and in the male group during NIT therapy, adaptive responses to minimise TYR formation were impaired compared to NKP group and females, respectively. Full article

Hepatitis E Virus (HEV) is a quasi-enveloped virus having a single-stranded, positive-sense RNA genome (~7.2 kb), flanked with a 5′ methylated cap and a 3′ polyadenylated tail. The HEV open reading frame 1 (ORF1) encodes a 186-kDa polyprotein speculated to get processed and produce Methyltransferase (MTase), one of the four essential replication enzymes. In this study, we report the identification of the MTase inhibitor, which may potentially deplete its enzymatic activity, thus causing the cessation of viral replication. Using in silico screening through docking, we identified ten putative compounds, which were tested for their anti-MTase activity. This resulted in the identification of 3-(4-Hydroxyphenyl)propionic acid (HPPA), with an IC₅₀ value of 0.932 ± 0.15 μM, which could be perceived as an effective HEV inhibitor. Furthermore, the compound was tested for inhibition of HEV replication in the HEV culture system. The viral RNA copies were markedly decreased from ~3.2 × 10⁶ in untreated cells to ~4.3 × 10^2.8 copies in 800 μM HPPA treated cells. Therefore, we propose HPPA as a potential drug-like inhibitor against HEV-MTase, which would need further validation through in vivo analysis using animal models and the administration of Pharmacokinetic and Pharmacodynamic (PK/PD) studies. Full article

Ensuring the security of modern cyberphysical devices is the most important task of the modern world. The reason for this is that such devices can cause not only informational, but also physical damage. One of the approaches to solving the problem is the static analysis of the machine code of the firmware of such devices. The situation becomes more complicated in the case of a Smart Home, since its devices can have different processor architectures (means instruction sets). In the case of cyberphysical devices of the Smart Home, the destruction of machine code due to physical influences is also possible. Therefore, the first step is to correctly identify the processor architecture. In the interests of this, a machine code model is proposed that has a formal notation and takes into account the possibility of code destruction. The article describes the full cycle of research (including experiment) in order to obtain this model. The model is based on byte-frequency machine code signatures. The experiment resulted in obtaining template signatures for the Top-16 processor architectures: Alpha, X32, Amd64, Arm64, Hppa64, I486, I686, Ia64, Mips, Mips64, Ppc, Ppc64, RiscV64, S390, S390x and Sparc64. Full article

Obesity is one of the most incident and concerning disease worldwide. Definite strategies to prevent obesity and related complications remain elusive. Among the risk factors of the onset of obesity, gut microbiota might play an important role in the pathogenesis of the disease, and it has received extensive attention because it affects the host metabolism. In this study, we aimed to define a metabolic profile of the segregated obesity-associated gut dysbiosis risk factor. The study of the metabolome, in an obesity-associated gut dysbiosis model, provides a relevant way for the discrimination on the different biomarkers in the obesity onset. Thus, we developed a model of this obesity risk factors through the transference of gut microbiota from obese to non-obese male Wistar rats and performed a subsequent metabolic analysis in the receptor rats. Our results showed alterations in the lipid metabolism in plasma and in the phenylalanine metabolism in urine. In consequence, we have identified metabolic changes characterized by: (1) an increase in DG:34:2 in plasma, a decrease in hippurate, (2) an increase in 3-HPPA, and (3) an increase in o-coumaric acid. Hereby, we propose these metabolites as a metabolic profile associated to a segregated dysbiosis state related to obesity disease. Full article

An efficient and convenient chemoenzymatic route for the synthesis of novel phenolic mono-, di- and oligosaccharide esters is described. Acetal derivatives of glucose, sucrose, lactose and inulin were obtained by chemical synthesis. The fully characterized pure sugar acetals were subjected to enzymatic esterification with 3-(4-hydroxyphenyl) propionic acid (HPPA) in the presence of Novozyme 435 lipase as a biocatalyst. The aromatic esters of alkyl glycosides and glucose acetal were obtained with good esterification yields, characterized by mass spectrometry (MALDI-TOF MS), infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy (¹H NMR, ¹³C NMR). The synthesis of aromatic esters of disaccharide acetals was successful only for the enzymatic esterification of sucrose acetal. The new chemoenzymatic route allowed the synthesis of novel aromatic esters of inulin as the inulin monoacetal monoester and diester and the inulin diacetal monoester with a polymerization degree of two, as well as the inulin monoacetal monoester with a degree of polymerization of three, were obtained by enzymatic acylation of inulin acetals with HPPA. These compounds could represent a new class of sugar ester surfactants with enhanced bioactivity, antioxidative and antimicrobial properties and with potential application in drug delivery systems. Full article

The aggregation and deposition of α-synuclein (αS) are major pathologic features of Parkinson’s disease, dementia with Lewy bodies, and other α-synucleinopathies. The propagation of αS pathology in the brain plays a key role in the onset and progression of clinical phenotypes. Thus, there is increasing interest in developing strategies that attenuate αS aggregation and propagation. Based on cumulative evidence that αS oligomers are neurotoxic and critical species in the pathogenesis of α-synucleinopathies, we and other groups reported that phenolic compounds inhibit αS aggregation including oligomerization, thereby ameliorating αS oligomer-induced cellular and synaptic toxicities. Heterogeneity in gut microbiota may influence the efficacy of dietary polyphenol metabolism. Our recent studies on the brain-penetrating polyphenolic acids 3-hydroxybenzoic acid (3-HBA), 3,4-dihydroxybenzoic acid (3,4-diHBA), and 3-hydroxyphenylacetic acid (3-HPPA), which are derived from gut microbiota-based metabolism of dietary polyphenols, demonstrated an in vitro ability to inhibit αS oligomerization and mediate aggregated αS-induced neurotoxicity. Additionally, 3-HPPA, 3,4-diHBA, 3-HBA, and 4-hydroxybenzoic acid significantly attenuated intracellular αS seeding aggregation in a cell-based system. This review focuses on recent research developments regarding neuroprotective properties, especially anti-αS aggregation effects, of phenolic compounds and their metabolites by the gut microbiome, including our findings in the pathogenesis of α-synucleinopathies. Full article

Quercetin is proven to decrease arterial blood pressure when given orally. Its bioavailability is, however, low and, therefore, its metabolites could rather be responsible for this effect. In particular, the colonic metabolites of quercetin, 3,4-dihydroxyphenylacetic acid (DHPA), 4-methylcatechol (4MC), and 3-(3-hydroxyphenyl)propionic acid (3HPPA), have been previously shown to decrease the blood pressure in spontaneously hypertensive rats (SHR). Interestingly, the mechanisms of action of these three metabolites are different. The aim of this study is hence to investigate if these metabolites can potentiate each other and thus decrease blood pressure in reduced doses. Three double-combinations of previously mentioned metabolites were administered to SHR as infusions to mimic a real biological situation. All combinations significantly decreased the blood pressure in SHR but there were important differences. The effect of DHPA and 4MC was mild and very short. A combination of DHPA with 3HPPA caused more pronounced effects, which were also rather short-lived. The last combination of 3HPPA and 4MC caused a long-lasting effect. In conclusion, certain combinations of quercetin metabolites have a more pronounced antihypertensive effect than single metabolites. Full article