D-ribose

BACKGROUND: To identify key and shared insulin resistance (IR) molecular signatures across all insulin-sensitive tissues (ISTs), and their potential targeted drugs. METHODS: Three datasets from Gene Expression Omnibus (GEO) were acquired, in which the ISTs (fat, muscle, and liver) were from the same individual with obese mice. Integrated bioinformatics analysis was performed to obtain the differentially expressed genes (DEGs). Weighted gene co-expression network analysis (WGCNA) was carried out to determine the "most significant trait-related genes" (MSTRGs)...

Furpenthiazinate is a yellow pigment formed by the Maillard reaction between cysteine and furfural under strongly acidic conditions. Here, we describe the conditions and mechanism of pigment formation in a model system and in an acid hydrolyzate of food and analyze its biological properties. A reaction solution containing 32 mM cysteine and 128 mM furfural or 64 mM cysteine and 256 mM furfural in the presence of 2-6 M hydrochloric acid that was heated to 110 °C for 1-2 h yielded approximately 3 mM furpenthiazinate...

In this study, we present a novel series of (E)-4-((2-(pyrazine-2-carbonyl) hydrazineylidene)methyl)phenyl benzenesulfonate (T1-T8) and 4-((E)-(((Z)-amino(pyrazin-2-yl)methylene)hydrazineylidene)methyl)phenyl benzenesulfonate (T9-T16) derivatives which exert their inhibitory effects on decaprenylphosphoryl-β-D-ribose 2'-epimerase (DprE1) through the formation of hydrogen bonds with the pivotal active site Cys387 residue. Their effectiveness against the M. tuberculosis H37Rv strain was examined and notably, three compounds (namely T4, T7, and T12) exhibited promising antitubercular activity, with a minimum inhibitory concentration (MIC) of 1...

UNLABELLED: All organisms utilize S -adenosyl-l-methionine (SAM) as a key co-substrate for the methylation of biological molecules, the synthesis of polyamines, and radical SAM reactions. When these processes occur, 5'-deoxy-nucleosides are formed as byproducts such as S -adenosyl-l-homocysteine, 5'-methylthioadenosine (MTA), and 5'-deoxyadenosine (5dAdo). A prevalent pathway found in bacteria for the metabolism of MTA and 5dAdo is the dihydroxyacetone phosphate (DHAP) shunt, which converts these compounds into dihydroxyacetone phosphate and 2-methylthioacetaldehyde or acetaldehyde, respectively...

Three Gram-stain-positive bacterial strains (designated 231-9T , 142-6 and 463-4) were isolated from traditional Chinese pickle, and were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strains 231-9T , 142-6 and 463-4 were phylogenetically related to the type strains of Lactiplantibacillus xiangfangensis , Lactiplantibacillus garii , Lactiplantibacillus carotarum , Lactiplantibacillus plajomi and Lactiplantibacillus modestisalitolerans , having 98...

The world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D-configured and the encoded amino acids that comprise the proteins of all living species feature an all-L-configuration at the α-carbon atoms. The homochirality of α-amino acids is essential for folding of the peptides into well-defined and functional 3D structures and the homochirality of D-ribose is crucial for helix formation and base-pairing. The question of why nature uses only encoded L-α-amino acids is not understood...

Enzymatic synthesis of β-nicotinamide mononucleotide (NMN) from D-ribose has garnered widespread attention due to its cheap material, the use of mild reaction conditions, and the ability to produce highly pure products with the desired optical properties. However, the overall NMN yield of this method is impeded by the low activity of rate-limiting enzymes. The ribose-phosphate diphosphokinase (PRS) and nicotinamide phosphoribosyltransferase (NAMPT), that control the rate of the reaction, were engineered to improve the reaction efficacy...

Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z...

Commercially available 2-deoxy-D-ribose was used to synthesize the appropriate oxolane derivative-(2 R ,3 S )-2-(hydroxymethyl)oxolan-3-ol-by reduction and dehydration/cyclization in an acidic aqueous solution. Its monotosyl derivative, as a result of the quaternization reaction, allowed us to obtain eight new muscarine-type derivatives containing a quaternary nitrogen atom and a hydroxyl group linked to the oxolane ring. Their structure was fully confirmed by the results of NMR, MS and IR analyses. The crystal structure of the pyridinium derivative showed a high similarity of the conformation of the oxolane ring to previously published crystal structures of muscarine...

The operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways...

BACKGROUND: Human health is seriously threatened by antibiotic-induced intestinal disorders. Herein, we aimed to determine the effects of Autoinducer-2 (AI-2) combined with Lactobacillus rhamnosus GG (LGG) on the intestinal barrier function of antibiotic-induced intestinal dysbiosis neonatal mice. METHODS: An antibiotic-induced intestinal dysbiosis neonatal mouse model was created using antibiotic cocktails, and the model mice were randomized into the control, AI-2, LGG, and LGG + AI-2 groups...

In this paper, a mild strategy for the oxidative cleavage of carbon-carbon bonds catalyzed by Lewis acid was developed in air condition at room temperature. Under such conditions, the bis-carbonyl compounds 3 were directly afforded from the reaction of D-ribose tosylate 1 and aniline in excellent yields through the oxidative cleavage of the key intermediate iminium-ion A and its tautomer enamine B . A series of N -arylated lactam-type iminosugars 5 were then successfully obtained by removing the isopropylidene group from 3 with the aid of the condensation agent DCC...

Advanced glycation end products (AGEs) stochastically accrue in skeletal muscle and on collagen over an individual's lifespan, stiffening the muscle and modifying the stem cell (MuSC) microenvironment while promoting proinflammatory, anti-regenerative signaling via the receptor for advanced glycation end products (RAGE). In the present study, a novel in vitro model was developed of this phenomenon by cross-linking a 3D collagen scaffold with AGEs and investigating how myoblasts responded to such an environment...

D-ribose, an ubiquitous pentose compound found in all living cells, serves as a vital constituent of numerous essential biomolecules, including RNA, nucleotides, and riboflavin. It plays a crucial role in various fundamental life processes. Within the cellular milieu, exogenously supplied D-ribose can undergo phosphorylation to yield ribose-5-phosphate (R-5-P). This R-5-P compound serves a dual purpose: it not only contributes to adenosine triphosphate (ATP) production through the nonoxidative phase of the pentose phosphate pathway (PPP) but also participates in nucleotide synthesis...

Natural chiral amino acids typically adopt an L structural configuration. While a preference for specific molecular chiralities is observed throughout biology and cellular chemistry, the origins of this preference are unclear. In a previous report the origin of enantiomeric selectivity was analyzed in terms of an "RNA World" model, and a pathway to a chiral preference for d-ribose was proposed based on the autocatalytic transformation of glyceraldehyde as a precursor to the formation of sugars. Metal-ion-promoted catalysis allows the parity non-conserving (PNC) weak nuclear interaction to influence the chirality of a nascent chiral carbon center...

BACKGROUND: Delamanid and bedaquiline are two of the most recently developed antituberculosis (TB) drugs that have been extensively studied in patients with multidrug-resistant TB. There is currently a need for more potent, less-toxic drugs with novel mechanisms of action that can be used in combination with these newer agents to shorten the duration of treatment as well as prevent the development of drug resistance. Quabodepistat (QBS) is a newly discovered inhibitor of decaprenylphosphoryl-β-D-ribose-2'-oxidase, an essential enzyme for Mycobacterium tuberculosis to synthesize key components of its cell wall...

Decaprenylphosphoryl-β-d-ribose oxidase (DprE1) is a promising target for treating tuberculosis (TB). Currently, most novel DprE1 inhibitors are discovered through high-throughput screening, while computer-aided drug design (CADD) strategies are expected to promote the discovery process. In this study, with the aid of structure-based virtual screening and computationally guided design, a series of novel scaffold N -(1-(6-oxo-1,6-dihydropyrimidine)-pyrazole) acetamide derivatives with significant antimycobacterial activities were identified...

Our previous work has shown that D-ribose (RIB)-induced depressive-like behaviors in mice. However, the relationship between variations in RIB levels and depression as well as potential RIB participation in depressive disorder is yet unknown. Here, a reanalysis of metabonomics data from depressed patients and depression model rats is performed to clarify whether the increased RIB level is positively correlated with the severity of depression. Moreover, we characterize intestinal epithelial barrier damage, gut microbial composition and function, and microbiota-gut-brain metabolic signatures in RIB-fed mice using colonic histomorphology, 16 S rRNA gene sequencing, and untargeted metabolomics analysis...

Modern artificial intelligence-based protein structure prediction methods, such as Alphafold2, can predict structures of folded proteins with reasonable accuracy. However, Alphafold2 provides a static view of a protein, which does not show the conformational variability of the protein, domain movement in a multi-domain protein, or ligand-induced conformational changes it might undergo in solution. Small-angle X-ay scattering (SAXS) and wide-angle X-ray scattering (WAXS) are solution techniques that can aid in integrative modeling of conformationally flexible proteins, or in validating their predicted ensemble structures...

In the last 50 years, nucleoside analogs have been introduced to drug therapy as antivirals for different types of cancer due to their interference in cellular proliferation. Among the first line of nucleoside treatment drugs, ribavirin (RBV) is a synthetic N-nucleoside with a 1,2,4-triazole moiety that acts as a broad-spectrum antiviral. It is on the World Health Organization (WHO) list of essential medicines. However, this important drug therapy causes several side effects due to its nonspecific mechanism of action...