1
|
Sun Q, Ni J, Li S, Ding H, Wang P, Song N, Wang X, Li M. Access to Reverse Glycosyl Azides and Rare Sugar-Based Glycosyl Azides via Radical Decarboxylative Azidation: Divergent Synthesis of 4'- C-Azidonucleosides as Potential Antiviral Agents. Org Lett 2024; 26:3997-4001. [PMID: 38687048 DOI: 10.1021/acs.orglett.4c01084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The radical decarboxylative azidation of structurally diverse uronic acids has been established as an efficient approach to reverse glycosyl azides and rare sugar-derived glycosyl azides under the action of Ag2CO3, 3-pyridinesulfonyl azide, and K2S2O8. The power of this method has been highlighted by the divergent synthesis of 4'-C-azidonucleosides using Vorbrüggen glycosylation of nucleobases with 4-C-azidofuranosyl acetates. The antiviral assessment of the resulting nucleosides revealed one compound as a potential inhibitor of covalently closed circular DNA.
Collapse
Affiliation(s)
- Qikai Sun
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Jingxuan Ni
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Shanshan Li
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Han Ding
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Peng Wang
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Ni Song
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xin Wang
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education and One Health Institute, School of Pharmaceutical Sciences, Hainan University, Haikou 570228, China
- Song Li' Academician Workstation, School of Pharmaceutical Sciences, Hainan University, Sanya 572000, China
| | - Ming Li
- Key Laboratory of Marine Medicine, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
2
|
Binding pattern of intermediate UDP-4-keto-xylose to human UDP-xylose synthase: Synthesis and STD NMR of model keto-saccharides. Carbohydr Res 2017; 437:50-58. [DOI: 10.1016/j.carres.2016.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 11/30/2022]
|
3
|
Sagar R, Rudić S, Gamblin DP, Scanlan EM, Vaden TD, Odell B, Claridge TDW, Simons JP, Davis BG. Conformational effects in sugar ions: spectroscopic investigations in the gas phase and in solution. Chem Sci 2012. [DOI: 10.1039/c2sc20341c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
|
4
|
Jones RA, Davidson R, Tran AT, Smith N, Carmen Galan M. Iodine-catalyzed one-pot acetalation–esterification reaction for the preparation of orthogonally protected glycosides. Carbohydr Res 2010; 345:1842-5. [DOI: 10.1016/j.carres.2010.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 06/17/2010] [Accepted: 07/04/2010] [Indexed: 10/19/2022]
|
5
|
Yu Q, Schwidom D, Exner A, Carlsen P. Synthesis of novel homo-N-nucleoside analogs composed of a homo-1,4-dioxane sugar analog and substituted 1,3,5-triazine base equivalents. Molecules 2008; 13:3092-106. [PMID: 19078851 PMCID: PMC6245424 DOI: 10.3390/molecules13123092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 11/21/2008] [Accepted: 12/03/2008] [Indexed: 11/23/2022] Open
Abstract
Enantioselective syntheses from dimethyl tartrate of 1,3,5-triazine homo-N-nucleoside analogs, containing a 1,4-dioxane moiety replacing the sugar unit in natural nucleosides, were accomplished. The triazine heterocycle in the nucleoside analogs was further substituted with combinations of NH2, OH and Cl in the 2,4-triazine positions.
Collapse
Affiliation(s)
- Qiang Yu
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway; E-mail: (Q. Y.)
| | - Dirk Schwidom
- Socrates exchange student: Department of Chemistry, University of Hamburg, D-20146 Hamburg, Germany
| | - Alexander Exner
- Socrates exchange student: Department of Chemistry, University of Hamburg, D-20146 Hamburg, Germany
| | - Per Carlsen
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway; E-mail: (Q. Y.)
- Author to whom correspondence should be addressed; E-mail: ; Fax: +47-73594256
| |
Collapse
|
6
|
Rye CS, Matte A, Cygler M, Withers SG. An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase. Chembiochem 2006; 7:631-7. [PMID: 16521140 DOI: 10.1002/cbic.200500428] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chondroitin AC lyase from Flavobacterium heparinum catalyses the degradation of chondroitin by an anionic E1cb elimination mechanism that involves proton abstraction from C5 of glucuronic acid. The lyase also carries out efficient proton transfer to a sugar nitronate anion, which was designed originally as an inhibitor of the enzyme, with a second-order rate constant of kcat/Km=2.7x10(6) M(-1) s(-); this is very similar to that of the natural chondroitin substrate (kcat/Km=1.3x10(6) M(-1) s(-1)). Studies with this nitronate should therefore provide insight into the proton-transfer step (general base catalysis) within this mechanism. Indeed, the Tyr234Phe mutant of the enzyme was essentially inactive with the natural substrate and correspondingly did not catalyse proton transfer to the nitronate, thereby implicating this residue as the general base catalyst. Parallel studies designed to identify the acid catalyst were carried out by using a substrate with a 2,4-dinitrophenol leaving group that needs no acid assistance for departure. These results are consistent with Tyr234 also playing the role of acid catalyst. Not only do these studies confirm the suspected role of Tyr234, but also they validate a new methodology for identification of acid/base catalysts in lyases and epimerases of this type. In addition a structural and mechanistic rationale is provided for different active-site acid/base configurations in syn and anti lyases.
Collapse
Affiliation(s)
- Carl S Rye
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1, Canada
| | | | | | | |
Collapse
|
7
|
Becher J, Seidel I, Plass W, Klemm D. Synthesis pathway to carbohydrate-derived salicylidene hydrazides as ligands for oxovanadium complexes. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.03.094] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
8
|
Prabhakar V, Sasisekharan R. The biosynthesis and catabolism of galactosaminoglycans. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2006; 53:69-115. [PMID: 17239763 DOI: 10.1016/s1054-3589(05)53005-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Vikas Prabhakar
- Division of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | |
Collapse
|
9
|
|
10
|
Michel G, Pojasek K, Li Y, Sulea T, Linhardt RJ, Raman R, Prabhakar V, Sasisekharan R, Cygler M. The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery. J Biol Chem 2004; 279:32882-96. [PMID: 15155751 PMCID: PMC4135467 DOI: 10.1074/jbc.m403421200] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chondroitinase B from Pedobacter heparinus is the only known enzyme strictly specific for dermatan sulfate and is a widely used enzymatic tool for the structural characterization of glycosaminoglycans. This beta-helical polysaccharide lyase belongs to family PL-6 and cleaves the beta(1,4) linkage of dermatan sulfate in a random manner, yielding 4,5-unsaturated dermatan sulfate disaccharides as the product. The previously reported structure of its complex with a dermatan sulfate disaccharide product identified the -1 and -2 subsites of the catalytic groove. We present here the structure of chondroitinase B complexed with several dermatan sulfate and chondroitin sulfate oligosaccharides. In particular, the soaking of chondroitinase B crystals with a dermatan sulfate hexasaccharide results in a complex with two dermatan sulfate disaccharide reaction products, enabling the identification of the +2 and +1 subsites. Unexpectedly, this structure revealed the presence of a calcium ion coordinated by sequence-conserved acidic residues and by the carboxyl group of the l-iduronic acid at the +1 subsite. Kinetic and site-directed mutagenesis experiments have subsequently demonstrated that chondroitinase B absolutely requires calcium for its activity, indicating that the protein-Ca(2+)-oligosaccharide complex is functionally relevant. Modeling of an intact tetrasaccharide in the active site of chondroitinase B provided a better understanding of substrate specificity and the role of Ca(2+) in enzymatic activity. Given these results, we propose that the Ca(2+) ion neutralizes the carboxyl moiety of the l-iduronic acid at the cleavage site, whereas the conserved residues Lys-250 and Arg-271 act as Brønsted base and acid, respectively, in the lytic degradation of dermatan sulfate by chondroitinase B.
Collapse
Affiliation(s)
- Gurvan Michel
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
- Montreal Joint Centre for Structural Biology, Montreal, Quebec H4P 2R2, Canada
| | - Kevin Pojasek
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Yunge Li
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
- Montreal Joint Centre for Structural Biology, Montreal, Quebec H4P 2R2, Canada
| | - Traian Sulea
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
| | - Robert J. Linhardt
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Rahul Raman
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Vikas Prabhakar
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Ram Sasisekharan
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Miroslaw Cygler
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
- Montreal Joint Centre for Structural Biology, Montreal, Quebec H4P 2R2, Canada
- To whom correspondence should be addressed: Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada. Tel.: 514-496-6321; Fax: 514-496-5143;
| |
Collapse
|
11
|
Rye CS, Withers SG. Development of an assay and determination of kinetic parameters for chondroitin AC lyase using defined synthetic substrates. Anal Biochem 2002; 308:77-82. [PMID: 12234466 DOI: 10.1016/s0003-2697(02)00223-3] [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: 11/22/2022]
Abstract
Many techniques have been developed for the assay of polysaccharide lyases; however, none have allowed the measurement of defined and reproducible k(cat) and K(m) values due to the inhomogeneous nature of the polymeric substrates. We have designed three different substrates for chondroitin AC lyase from Flavobacterium heparinum that can be monitored by three different techniques: UV/Vis spectroscopy, fluorescence spectroscopy, and use of a fluoride ion-selective electrode. Each is a continuous assay, free from interferences caused by other components present in crude enzyme preparations, and allows meaningful and reproducible kinetic parameters to be determined. The development of these defined synthetic substrates has opened up a wide variety of mechanistic studies that can be performed to elucidate the detailed catalytic mechanism of this, and other, polysaccharide lyases. The application of these techniques, which include kinetic isotope effects and linear free energy analyses, was not possible with the previous polymeric substrates and will allow this relatively poorly understood class of polysaccharide-degrading enzymes to be studied mechanistically.
Collapse
Affiliation(s)
- Carl S Rye
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
| | | |
Collapse
|