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Dikici S, Yar M, Bullock AJ, Shepherd J, Roman S, MacNeil S. Developing Wound Dressings Using 2-deoxy- D-Ribose to Induce Angiogenesis as a Backdoor Route for Stimulating the Production of Vascular Endothelial Growth Factor. Int J Mol Sci 2021; 22:ijms222111437. [PMID: 34768868 PMCID: PMC8583821 DOI: 10.3390/ijms222111437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022] Open
Abstract
2-deoxy-D-Ribose (2dDR) was first identified in 1930 in the structure of DNA and discovered as a degradation product of it later when the enzyme thymidine phosphorylase breaks down thymidine into thymine. In 2017, our research group explored the development of wound dressings based on the delivery of this sugar to induce angiogenesis in chronic wounds. In this review, we will survey the small volume of conflicting literature on this and related sugars, some of which are reported to be anti-angiogenic. We review the evidence of 2dDR having the ability to stimulate a range of pro-angiogenic activities in vitro and in a chick pro-angiogenic bioassay and to stimulate new blood vessel formation and wound healing in normal and diabetic rat models. The biological actions of 2dDR were found to be 80 to 100% as effective as VEGF in addition to upregulating the production of VEGF. We then demonstrated the uptake and delivery of the sugar from a range of experimental and commercial dressings. In conclusion, its pro-angiogenic properties combined with its improved stability on storage compared to VEGF, its low cost, and ease of incorporation into a range of established wound dressings make 2dDR an attractive alternative to VEGF for wound dressing development.
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Affiliation(s)
- Serkan Dikici
- Department of Bioengineering, Izmir Institute of Technology, 35430 Izmir, Turkey
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
- Correspondence: (S.D.); (S.M.)
| | - Muhammad Yar
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan;
| | - Anthony J. Bullock
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
| | - Joanna Shepherd
- School of Clinical Dentistry, University of Sheffield, Sheffield S10 2TA, UK;
| | - Sabiniano Roman
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
| | - Sheila MacNeil
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
- Correspondence: (S.D.); (S.M.)
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Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. mSystems 2019; 4:mSystems00297-18. [PMID: 30746495 PMCID: PMC6365646 DOI: 10.1128/msystems.00297-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/12/2019] [Indexed: 12/13/2022] Open
Abstract
Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways. 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. We identified another oxidative pathway for the catabolism of deoxyribonate, with acyl-CoA intermediates, in Klebsiella michiganensis. Of these four bacteria, only P. simiae relies entirely on an oxidative pathway to consume deoxyribose. The deoxyribose dehydrogenase of P. simiae is either nonspecific or evolved recently, as this enzyme is very similar to a novel vanillin dehydrogenase from Pseudomonas putida that we identified. So, we propose that these oxidative pathways evolved primarily to consume deoxyribonate, which is a waste product of metabolism. IMPORTANCE Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.
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Azofra LM, Quesada-Moreno MM, Alkorta I, Avilés-Moreno JR, López-González JJ, Elguero J. Carbohydrates in the gas phase: conformational preference ofd-ribose and 2-deoxy-d-ribose. NEW J CHEM 2014. [DOI: 10.1039/c3nj01076g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Conformational studies of gas-phase ribose and 2-deoxyribose by density functional, second order PT and multi-level method calculations: the pyranoses, furanoses, and open-chain structures. Carbohydr Res 2014; 384:20-36. [DOI: 10.1016/j.carres.2013.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 09/09/2013] [Accepted: 10/18/2013] [Indexed: 11/21/2022]
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Quesada-Moreno MM, Azofra LM, Avilés-Moreno JR, Alkorta I, Elguero J, López-González JJ. Conformational preference and chiroptical response of carbohydrates D-ribose and 2-deoxy-D-ribose in aqueous and solid phases. J Phys Chem B 2013; 117:14599-614. [PMID: 24134404 DOI: 10.1021/jp405121s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work targets the structural preferences of D-ribose and 2-deoxy-D-ribose in water solution and solid phase. A theoretical DFT (B3LYP and M06-2X) and MP2 study has been undertaken considering the five possible configurations (open-chain, α-furanose, β-furanose, α-pyranose, and β-pyranose) of these two carbohydrates with a comparison of the solvent treatment using only a continuum solvation model (PCM) and the PCM plus one explicit water molecule. In addition, experimental vibrational studies using both nonchiroptical (IR-Raman) and chiroptical (VCD) techniques have been carried out. The theoretical and experimental results show that α- and β-pyranose forms are the dominant configurations for both compounds. Moreover, it has been found that 2-deoxy-D-ribose presents a non-negligible percentage of open-chain forms in aqueous solution, while in solid phase this configuration is absent.
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Affiliation(s)
- María Mar Quesada-Moreno
- Department of Physical and Analytical Chemistry, University of Jaén , Campus Las Lagunillas, E-23071 Jaén, Spain
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Hess D, Klüfers P. Phenylboronic acid esters of the common 2-deoxy-aldoses. Carbohydr Res 2011; 346:1752-9. [PMID: 21816393 DOI: 10.1016/j.carres.2011.05.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/24/2011] [Accepted: 05/27/2011] [Indexed: 11/18/2022]
Abstract
Phenylboronic acid esters are formed by the three common 2-deoxy aldoses: 2-deoxy-d-erythro-pentose ('2-deoxy-d-ribose'), 2-deoxy-d-lyxo-hexose ('2-deoxy-d-galactose'), and 2-deoxy-d-arabino-hexose ('2-deoxy-d-glucose'). The major species that was formed from equimolar quantities of boronic acid and the aldose, was the 3,4-monoester of the pentopyranose in a skew-boat conformation, and the 4,6-monoester in the case of the two hexopyranoses. A double molar quantity of boronic acid led, for both 2-deoxy-hexoses, to the diester of the open-chain aldehydo isomer as the major product: the 3,5:4,6-diester for the lyxo-configured deoxy-hexose, and the 3,4:5,6-diester of the arabino-configured isomer. Minor products of all reactions were identified by a combined NMR/DFT methodology.
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Affiliation(s)
- David Hess
- Ludwig-Maximilians-Universität, Department Chemie, Butenandtstraße 5-13, München, Germany
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Coxon B. Two-Dimensional Proton Chemical Shift Correlated NMR Spectroscopy of Digitoxose1. J Carbohydr Chem 2006. [DOI: 10.1080/07328308408057916] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Assairi L, Bertrand T, Ferdinand J, Slavova-Azmanova N, Christensen M, Briozzo P, Schaeffer F, Craescu CT, Neuhard J, Bârzu O, Gilles AM. Deciphering the function of an ORF: Salmonella enterica DeoM protein is a new mutarotase specific for deoxyribose. Protein Sci 2004; 13:1295-303. [PMID: 15075407 PMCID: PMC2286760 DOI: 10.1110/ps.03566004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We identified in Salmonella enterica serovar Typhi a cluster of four genes encoding a deoxyribokinase (DeoK), a putative permease (DeoP), a repressor (DeoQ), and an open reading frame encoding a 337 amino acid residues protein of unknown function. We show that the latter protein, called DeoM, is a hexamer whose synthesis is increased by a factor over 5 after induction with deoxyribose. The CD spectrum of the purified recombinant protein indicated a dominant contribution of betatype secondary structure and a small content of alpha-helix. Temperature and guanidinium hydrochloride induced denaturation of DeoM indicated that the hexamer dissociation and monomer unfolding are coupled processes. DeoM exhibits 12.5% and 15% sequence identity with galactose mutarotase from Lactococcus lactis and respectively Escherichia coli, which suggested that these three proteins share similar functions. Polarimetric experiments demonstrated that DeoM is a mutarotase with high specificity for deoxyribose. Site-directed mutagenesis of His183 in DeoM, corresponding to a catalytically active residue in GalM, yielded an almost inactive deoxyribose mutarotase. DeoM was crystallized and diffraction data collected for two crystal systems, confirmed its hexameric state. The possible role of the protein and of the entire gene cluster is discussed in connection with the energy metabolism of S. enterica under particular growth conditions.
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Affiliation(s)
- Liliane Assairi
- Laboratoire de Chimie Structurale des Macromolécules, Unité de Recherche Associeé 2185 du Cantre National de la Recherche Scientifique, Institut Pasteur, 75724 Paris 15, France
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Nowacki A, Smiataczowa K, Kasprzykowska R, Dmochowska B, Wiśniewski A. Acid-catalyzed isomerization of methyl 2-deoxy-D-arabino-hexosides: equilibria, kinetics and mechanism. Carbohydr Res 2002; 337:265-72. [PMID: 11844496 DOI: 10.1016/s0008-6215(01)00305-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Four isomers of methyl 2-deoxy-D-arabino-hexosides were isolated by HPLC as chromatographically homogeneous compounds. The rates of pyranoside isomerization (alpha(p) and beta(p)) at 40 degrees C and of furanoside isomerization (alpha(f) and beta(f)) at 26 degrees C were determined. A mechanism has been suggested for transformations taking place during isomerization of methyl 2-deoxy-D-arabino-hexosides in methanolic solution catalyzed with hydrogen chloride.
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Affiliation(s)
- Andrzej Nowacki
- Department of Chemistry, Sugar Chemistry Group, University of Gdañsk, 18 Sobieskiego, PL-80-952, Gdañsk, Poland
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Mega TL, Van Etten RL. Oxygen exchange and bond cleavage reactions of carbohydrates studied using the 18O isotope shift in 13C NMR spectroscopy. BASIC LIFE SCIENCES 1990; 56:85-93. [PMID: 2078181 DOI: 10.1007/978-1-4684-5868-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- T L Mega
- Purdue University, Chemistry Department, W. Lafayette, IN 47907
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Van Eijck B, Kroon J. Molecular-dynamics simulations of β-d-ribose and β-d-deoxyribose solutions. J Mol Struct 1989. [DOI: 10.1016/0022-2860(89)80164-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Bauer H, Brinkmeier A, Buddrus J, Jablonowski M. Ring-Ketten- Tautomerie von 2-Desoxy-D-ribose: Vollständige Analyse der Dynamik durch NMR-Linienformsimulation und Spinsättigungsübertragung. ACTA ACUST UNITED AC 1986. [DOI: 10.1002/jlac.198619861014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Fesik SW, Kohlbrenner WE, Gampe RT, Olejniczak ET. Interconversion rates of tautomers of 3-deoxy-d-manno-octulosonic acid (KDO) from a quantitative analysis of two-dimensional n.m.r. exchange data. Carbohydr Res 1986. [DOI: 10.1016/s0008-6215(00)90203-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Angyal SJ. The Composition of Reducing Sugars in Solution. Adv Carbohydr Chem Biochem 1984. [DOI: 10.1016/s0065-2318(08)60122-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Barbat J, Gelas J, Horton D. Acetonation of l-fucose, l-rhamnose, and 2-deoxy-d-erythro-pentose under kinetically controlled conditions. Carbohydr Res 1983. [DOI: 10.1016/0008-6215(83)88122-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nicole D, Gillet B, Eppiger E, Delpuech JJ. La mutarotation du β-D-fructose en milieu acide dans le dimethylsulfoxyde. Tetrahedron Lett 1982. [DOI: 10.1016/s0040-4039(00)87186-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zeeck A. Lipomycine, III. Isolierung und Zuordnung der Methyl-2,6-didesoxy-D-ribo-hexoside. ACTA ACUST UNITED AC 1975. [DOI: 10.1002/jlac.197519751117] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Stankovič L, Linek K, Fedoron̆ko M. Ketoses and their derivatives. Part II1. The synthesis of methyl glycosides of 2-pentuloses by the fischer method, but with catalysis by acetic acid. Carbohydr Res 1974. [DOI: 10.1016/s0008-6215(00)84850-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cadet J. Chimie des acides nucleiques. Anomerisation et isomerisation furanno-pyrannique des derives dihydro-5,6 sulfonate-6 de la desoxy-2′-uridine et de la thymidine en milieu acide. Tetrahedron Lett 1974. [DOI: 10.1016/s0040-4039(01)82354-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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The tautomerization and mutarotation of β-L-arabinopyranose. Participation of both furanose anomers. Carbohydr Res 1972. [DOI: 10.1016/s0008-6215(00)82751-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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