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Morgan N Price, Jayashree Ray, Anthony T Iavarone, Hans K Carlson, Elizabeth M Ryan, Rex R Malmstrom, Adam P Arkin, Adam M Deutschbauer
Using genome-wide mutant fitness assays in diverse bacteria, we identified novel oxidative pathways for the catabolism of 2-deoxy-d-ribose and 2-deoxy-d-ribonate. We propose that deoxyribose is oxidized to deoxyribonate, oxidized to ketodeoxyribonate, and cleaved to acetyl coenzyme A (acetyl-CoA) and glyceryl-CoA. We have genetic evidence for this pathway in three genera of bacteria, and we confirmed the oxidation of deoxyribose to ketodeoxyribonate in vitro . In Pseudomonas simiae, the expression of enzymes in the pathway is induced by deoxyribose or deoxyribonate, while in Paraburkholderia bryophila and in Burkholderia phytofirmans, the pathway proceeds in parallel with the known deoxyribose 5-phosphate aldolase pathway...
January 2019: MSystems
Klaus Brilisauer, Johanna Rapp, Pascal Rath, Anna Schöllhorn, Lisa Bleul, Elisabeth Weiß, Mark Stahl, Stephanie Grond, Karl Forchhammer
Antimetabolites are small molecules that inhibit enzymes by mimicking physiological substrates. We report the discovery and structural elucidation of the antimetabolite 7-deoxy-sedoheptulose (7dSh). This unusual sugar inhibits the growth of various prototrophic organisms, including species of cyanobacteria, Saccharomyces, and Arabidopsis. We isolate bioactive 7dSh from culture supernatants of the cyanobacterium Synechococcus elongatus. A chemoenzymatic synthesis of 7dSh using S. elongatus transketolase as catalyst and 5-deoxy-D-ribose as substrate allows antimicrobial and herbicidal bioprofiling...
February 1, 2019: Nature Communications
Gaspar Banfalvi
D-ribose and D-arabinose differ only by the steric orientation of their C2-OH groups. The initial reactions and emergence of RNA depended on the position, reactivity, and flexibility of the C2-OH moiety in the ribose molecule. The steric relationship of the C2- and C3-OH groups favored the selection of ribose, ribonucleotide, and RNA synthesis and excluded the possibility of xenonucleic acid-based life on Earth. This brief review provides a hypothesis based on the absence of nucleotides and enzymes under prebiotic conditions and on the polymerization of ribose 5-phosphate units leading to the polarized formation of the ribose-phosphate backbone...
January 14, 2019: DNA and Cell Biology
Ya Gao, Jinshan Xie, Ruotian Tang, Kaiyin Yang, Yahan Zhang, Lixia Chen, Hua Li
Despite the increasing need of new antituberculosis drugs, the number of agents approved for the market has fallen to an all-time low. In response to the emerging drug resistance followed, structurally unique chemical entities will be highlighted. decaprenylphosphoryl-β-d-ribose oxidase (DprE1) participating in the biosynthesis of mycobacterium cell wall is a highly vulnerable and validated antituberculosis target. On the basis of it, a systematic strategy was applied to identify a high-quality lead compound (compound 50) that inhibits the essential enzyme DprE1, thus blocking the synthesis of the mycobacterial cell wall to kill M...
December 13, 2018: Bioorganic Chemistry
Weijun Shou, Fuxing Kang, Shuhan Huang, Chunyao Yan, Jiaxin Zhou, Yijin Wang
Mobile antibiotic resistance genes (ARGs) in environmental systems may pose a threat to public health. The coexisting substituted aromatic pollutants may help the ARGs cross the extracellular polymeric substance permeable barrier into the interior of cells, facilitating ARG dissemination, but the mechanism is still unknown. Here, we demonstrated that a specific anti-hydrolysis mechanism of mobile plasmid in the extracellular matrix makes a greater contribution to this facilitated dissemination. Specifically, fluorescence microtitration with a Tb3+-labeled pUC19 plasmid was used to study the formation of substituted aromatic-plasmid complexes associated with ARG dissemination...
December 18, 2018: Environmental Science & Technology
Wei-Syun Song, Si-Xian Liu, Che-Chien Chang
The preparation of 2-deoxy-l-ribose derivatives or mirror image deoxyribonucleosides (l-deoxyribonucleosides) from d-ribose is reported. Starting from inexpensive d-ribose, an acyclic d-form carbohydrate precursor was synthesized to study a unique carbonyl translocation process. In this novel radical reaction, not only was the configuration of the sugar transformed from the d-form to the l-form, but also deoxygenation at the C(2) position of the sugar was successfully achieved. This is one of the most practical methods for converting a d-sugar to a 2-deoxy-l-sugar in a one-step reaction...
November 29, 2018: Journal of Organic Chemistry
Ya-Nan Wang, Yan-Hua Mou, Yu Dong, Yan Wu, Bing-Yu Liu, Jian Bai, Dao-Jiang Yan, Le Zhang, Dan-Qing Feng, Yue-Hu Pei, You-Cai Hu
Six new diphenyl ethers ( 1 ⁻ 6 ) along with eleven known analogs were isolated from the ethyl acetate extract of a marine-derived Aspergillus sydowii guided by LC-UV-MS. Their structures were unambiguously characterized by HRESIMS, NMR, as well as chemical derivatization. Compounds 1 and 2 are rare diphenyl ether glycosides containing d-ribose. The absolute configuration of the sugar moieties in compounds 1 ⁻ 3 was determined by a LC-MS method. All the compounds were evaluated for their cytotoxicities against eight cancer cell lines, including 4T1, U937, PC3, HL-60, HT-29, A549, NCI-H460, and K562, and compounds 1 , 5 , 6 , and 8 ⁻ 11 were found to exhibit selective cytotoxicity against different cancer cell lines...
November 16, 2018: Marine Drugs
Zeba Siddiqui, Mohammad Faisal, Abdulrahman A Alatar, Saheem Ahmad
Non-enzymatic glycation occurs rapidly which ultimately leads to the formation of advanced glycation endproducts (AGEs). These AGEs have shown to associated with the development of many diseases such as diabetes-mellitus. This study is focused on immunological characterization of glycated-Hb induced by d-ribose. Here, we analysed the immunogenicity of glycated-Hb by direct binding and competitive inhibition ELISA. Direct binding ELISA confirmed that glycated-Hb was highly immunogenic and induced high titre antibodies as compared to native-Hb...
November 13, 2018: International Journal of Biological Macromolecules
Chong Liu, Qi Chen, Steven Cardinale, Terry L Bowlin, Stewart W Schneller
A convenient stereospecific synthesis of 6'-fluoro-3-deazaneplanocin (6) has been accomplished from d-ribose in 15 steps. It is reported to possess significant activity towards Ebola (Zaire, Vero, μM: EC50  < 0.36; CC50 125; SI > 347) with moderate inhibition of the target enzyme (S-adenosylhomocysteine hydrolase), which did not correlate directly with its anti-Ebola effects. Compound 6, with limited cytotoxicity, also displayed activity against measles, H1N1 and Pichinde.
October 22, 2018: Bioorganic & Medicinal Chemistry Letters
Keisuke Hirata, Takashi Uchida, Yoshikata Nakajima, Toru Maekawa, Toru Mizuki
Rare sugars are defined as monosaccharides and their derivatives, which rarely exist in nature and have various beneficial effects on organisms, biomaterials and foods. Glycolipids are composed of sugars and lipids and have been intensively studied in various fields such as environmental engineering, nanotechnology and molecular biology. Here, we synthesise new types of glycolipids composed of rare sugars, glycerol and lipids (RSGLs), using 6 different types of rare sugars by combining the modified Fischer and lipase reverse reactions...
October 2018: Heliyon
Sangmi Oh, Yumi Park, Curtis A Engelhart, Joshua B Wallach, Dirk Schnappinger, Kriti Arora, Michelle Manikkam, Brian Gac, Hongwu Wang, Nicholas Murgolo, David B Olsen, Michael Goodwin, Michelle Sutphin, Danielle M Weiner, Laura E Via, Helena I M Boshoff, Clifton E Barry
Magnesium plays an important role in infection with Mycobacterium tuberculosis ( Mtb) as a signal of the extracellular environment, as a cofactor for many enzymes, and as a structural element in important macromolecules. Raltegravir, an antiretroviral drug that inhibits HIV-1 integrase is known to derive its potency from selective sequestration of active-site magnesium ions in addition to binding to a hydrophobic pocket. In order to determine if essential Mtb-related phosphoryl transfers could be disrupted in a similar manner, a directed screen of known molecules with integrase inhibitor-like pharmacophores ( N-alkyl-5-hydroxypyrimidinone carboxamides) was performed...
November 21, 2018: Journal of Medicinal Chemistry
João Paulo Bizarro Lopes, Luana Silva, Gabriela da Costa Franarin, Marco Antonio Ceschi, Diogo Seibert Lüdtke, Rafael Ferreira Dantas, Cristiane Martins Cardoso de Salles, Floriano Paes Silva-Jr, Mario Roberto Senger, Isabella Alvim Guedes, Laurent Emmanuel Dardenne
A series of hybrids containing tacrine linked to carbohydrate-based moieties, such as d-xylose, d-ribose, and d-galactose derivatives, were synthesized by the nucleophilic substitution between 9-aminoalkylamino-1,2,3,4-tetrahydroacridines and the corresponding sugar-based tosylates. All compounds were found to be potent inhibitors of both acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) in the nanomolar IC50 scale. Most of the d-xylose derivatives (6a-e) were selective for AChE and the compound 6e (IC50  = 2...
October 9, 2018: Bioorganic & Medicinal Chemistry
Joanna M Watt, Mark P Thomas, Barry V L Potter
Cyclic adenosine 5'-diphosphate ribose (cADPR) is an emerging Ca2+ -mobilising second messenger. cADPR analogues have been generated as chemical biology tools via both chemo-enzymatic and total synthetic routes. Both routes rely on the cyclisation of a linear precursor to close an 18-membered macrocyclic ring. We show here that, after cyclisation, there are two possible macrocyclic product conformers that may be formed, depending on whether cyclisation occurs to the "right" or the "left" of the adenine base (as viewed along the H-8 → C-8 base axis)...
October 15, 2018: Scientific Reports
Yi Li, Mohd Shahnawaz Khan, Firoz Akhter, Fohad Mabood Husain, Saheem Ahmad, Lihui Chen
Advanced glycation end-products (AGEs) can aggregate amid incessant inflammation, as may be available in patients with rheumatoid arthritis. d-Ribose reacts more promptly than glucose monosaccharide to the proteins and forms heterogeneous group of products known as AGEs. Obesity includes persons with provocative joint inflammation with increased lipid profile. Immunogenic evidences recommend a cross-sectional relationship between glycated LDL-Apo B100 and inflammation. The point of this examination was to look at the connection between d-ribose glycated ApoB100 (ApoB100-AGE) with obesity and rheumatoid arthritis...
October 9, 2018: International Journal of Biological Macromolecules
Vladimir E Oslovsky, Mikhail S Drenichev, Cyril S Alexeev, Pavel N Solyev, Roman S Esipov, Sergey N Mikhailov
This unit describes an effective method for the preparation of natural cytokinins and their synthetic derivatives based on enzymatic cleavage of the N-glycosidic bond of N6 -substituted adenosine or O6 -substituted inosine derivatives in the presence of purine nucleoside phosphorylase (PNP) and Na2 HAsO4 . The arsenolysis reaction is irreversible due to the hydrolysis of the resulting α-D-ribose-1-arsenate. As a result, the desired products are formed in near-quantitative yields, as indicated by high-performance liquid chromatography (HPLC) analysis, and can easily be isolated...
October 9, 2018: Current Protocols in Nucleic Acid Chemistry
Meera Haridas, Eman M M Abdelraheem, Ulf Hanefeld
2-Deoxy-D-ribose-5-phosphate aldolase (DERA) is a class I aldolase that offers access to several building blocks for organic synthesis. It catalyzes the stereoselective C-C bond formation between acetaldehyde and numerous other aldehydes. However, the practical application of DERA as a biocatalyst is limited by its poor tolerance towards industrially relevant concentrations of aldehydes, in particular acetaldehyde. Therefore, the development of proper experimental conditions, including protein engineering and/or immobilization on appropriate supports, is required...
October 3, 2018: Applied Microbiology and Biotechnology
Dan Zeng, Can Hu, Ru-Liu Li, Chuan-Quan Lin, Jia-Zhong Cai, Ting-Ting Wu, Jing-Jing Sui, Wen-Biao Lu, Wei-Wen Chen
Astragalus membranaceus (Radix Astragali, RA) and Atractylodes macrocephala (Rhizoma Atractylodis Macrocephalae, RAM) are often used to treat gastrointestinal diseases. In the present study, we determined the effects of polysaccharides extracts from these two herbs on IEC-6 cell migration and explored the potential underlying mechanisms. A migration model with IEC-6 cells was induced using a single-edged razor blade along the diameter of cell layers in six-well polystyrene plates. The cells were grown in control media or media containing spermidine (5 μmol·L-1 , SPD), alpha-difluoromethylornithine (2...
September 2018: Chinese Journal of Natural Medicines
Heithem Ben Amara, Hyun Y Song, Eunju Ryu, Ji S Park, Frank Schwarz, Byeong M Kim, Bong-Kyu Choi, Ki-Tae Koo
This study aimed to verify, in in vivo settings, whether quorum-sensing inhibition molecules could attenuate alveolar bone loss induced by Porphyromonas gingivalis/Fusobacterium nucleatum co-infection and reduce the bacterial colonization of periodontal tissues. In BALB/c mice, periodontitis was induced through oral inoculation with P. gingivalis and F. nucleatum six times during a 42-d period. Quorum sensing inhibitors (a furanone compound and D-ribose) were administered simultaneously with bacterial infection...
September 19, 2018: European Journal of Oral Sciences
Adrian Richter, Ines Rudolph, Ute Möllmann, Kerstin Voigt, Chun-Wa Chung, Onkar M P Singh, Michael Rees, Alfonso Mendoza-Losana, Robert Bates, Lluís Ballell, Sarah Batt, Natacha Veerapen, Klaus Fütterer, Gurdyal Besra, Peter Imming, Argyrides Argyrou
Nitro-substituted 1,3-benzothiazinones (nitro-BTZs) are mechanism-based covalent inhibitors of Mycobacterium tuberculosis decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1) with strong antimycobacterial properties. We prepared a number of oxidized and reduced forms of nitro-BTZs to probe the mechanism of inactivation of the enzyme and to identify opportunities for further chemistry. The kinetics of inactivation of DprE1 was examined using an enzymatic assay that monitored reaction progress up to 100 min, permitting compound ranking according to kinact /Ki values...
September 7, 2018: Scientific Reports
Sang Eun Jeong, Byung Hee Chun, Kyung Hyun Kim, Dongbin Park, Seong Woon Roh, Se Hee Lee, Che Ok Jeon
The genomic and metabolic features of Weissella koreensis, one of the major lactic acid bacteria in kimchi, were investigated through genomic, metabolic, and transcriptomic analyses for the genomes of strains KCTC 3621T , KACC 15510, and WiKim0080. W. koreensis strains were intrinsically vancomycin-resistant and harbored potential hemolysin genes that were actively transcribed although no hemolysin activity was detected. KEGG and reconstructed fermentative metabolic pathways displayed that W. koreensis strains commonly employ the heterolactic pathway to produce d-lactate, ethanol, acetate, CO2 , d-sorbitol, thiamine, and folate from various carbohydrates including d-glucose, d-mannose, d-lactose, l-malate, d-xylose, l-arabinose, d-ribose, N-acetyl-glucosamine, and gluconate, and strains KCTC 3621T and WiKim0080 additionally have metabolic pathways of d-galacturonate and d-glucoronate...
December 2018: Food Microbiology
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