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Shen K, Bai B, Liu YH, Lowary TL. Synthesis of a Tridecasaccharide Lipooligosaccharide Antigen from the Opportunistic Pathogen Mycobacterium kansasii. Angew Chem Int Ed Engl 2021; 60:24859-24863. [PMID: 34553821 DOI: 10.1002/anie.202111549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 11/06/2022]
Abstract
The outer surfaces of mycobacteria, including the organism that causes tuberculosis, are decorated with an array of immunomodulatory glycans. Among these are lipooligosaccharides (LOSs), a class of molecules for which the function remains poorly understood. We describe the chemical synthesis of the glycan portion of a tridecasaccharide LOS from the opportunistic pathogen Mycobacterium kansasii. The target contains a number of unusual structural motifs that complicate its assembly and is the most complex mycobacterial LOS glycan to be synthesized to date when considering size and number of unique monosaccharides and glycosidic linkages. These studies not only provide a roadmap for the preparation of additional members of this family of glycans, but also provides a valuable probe for use in structure-activity relationship investigations.
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Affiliation(s)
- Ke Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Bing Bai
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Yu-Hsuan Liu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.,Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National (Taiwan) University, Roosevelt Road, Section 4, #1, Taipei, 10617, Taiwan
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2
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Shen K, Bai B, Liu Y, Lowary TL. Synthesis of a Tridecasaccharide Lipooligosaccharide Antigen from the Opportunistic Pathogen
Mycobacterium kansasii. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ke Shen
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Bing Bai
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Yu‐Hsuan Liu
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
| | - Todd L. Lowary
- Department of Chemistry University of Alberta Edmonton Alberta T6G 2G2 Canada
- Institute of Biological Chemistry Academia Sinica Academia Road, Section 2, #128 Nangang Taipei 11529 Taiwan
- Institute of Biochemical Sciences National (Taiwan) University Roosevelt Road, Section 4, #1 Taipei 10617 Taiwan
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Iglesias-Fernández J, Raich L, Ardèvol A, Rovira C. The complete conformational free energy landscape of β-xylose reveals a two-fold catalytic itinerary for β-xylanases. Chem Sci 2015; 6:1167-1177. [PMID: 29560204 PMCID: PMC5811086 DOI: 10.1039/c4sc02240h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/27/2014] [Indexed: 01/28/2023] Open
Abstract
Unraveling the conformational catalytic itinerary of glycoside hydrolases (GHs) is a growing topic of interest in glycobiology, with major impact in the design of GH inhibitors. β-xylanases are responsible for the hydrolysis of glycosidic bonds in β-xylans, a group of hemicelluloses of high biotechnological interest that are found in plant cell walls. The precise conformations followed by the substrate during catalysis in β-xylanases have not been unambiguously resolved, with three different pathways being proposed from structural analyses. In this work, we compute the conformational free energy landscape (FEL) of β-xylose to predict the most likely catalytic itineraries followed by β-xylanases. The calculations are performed by means of ab initio metadynamics, using the Cremer-Pople puckering coordinates as collective variables. The computed FEL supports only two of the previously proposed itineraries, 2SO → [2,5B]ǂ → 5S1 and 1S3 → [4H3]ǂ → 4C1, which clearly appear in low energy regions of the FEL. Consistently, 2SO and 1S3 are conformations preactivated for catalysis in terms of free energy/anomeric charge and bond distances. The results however exclude the OE → [OS2]ǂ → B2,5 itinerary that has been recently proposed for a family 11 xylanase. Classical and ab initio QM/MM molecular dynamics simulations reveal that, in this case, the observed OE conformation has been enforced by enzyme mutation. These results add a word of caution on using modified enzymes to inform on catalytic conformational itineraries of glycoside hydrolases.
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Affiliation(s)
- Javier Iglesias-Fernández
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB) , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain .
| | - Lluís Raich
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB) , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain .
| | - Albert Ardèvol
- Department of Chemistry and Applied Biosciences , ETH Zürich , USI Campus , 6900 Lugano , Switzerland
| | - Carme Rovira
- Departament de Química Orgànica and Institut de Química Teòrica i Computacional (IQTCUB) , Universitat de Barcelona , Martí i Franquès 1 , 08028 Barcelona , Spain .
- Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluís Companys , 23 , 08018 Barcelona , Spain
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Computerized Models of Carbohydrates. POLYSACCHARIDES 2015. [DOI: 10.1007/978-3-319-16298-0_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Morris MJ, Striegel AM. Determining the solution conformational entropy of oligosaccharides by SEC with on-line viscometry detection. Carbohydr Polym 2014; 106:230-7. [DOI: 10.1016/j.carbpol.2014.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 11/30/2022]
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7
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Does the “C3effect” offset the Δ2 effect, as regards the solution flexibility of aldoses? Biopolymers 2014; 101:703-11. [DOI: 10.1002/bip.22446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 10/23/2013] [Accepted: 11/15/2013] [Indexed: 02/06/2023]
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8
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Siegbahn A, Aili U, Ochocinska A, Olofsson M, Rönnols J, Mani K, Widmalm G, Ellervik U. Synthesis, conformation and biology of naphthoxylosides. Bioorg Med Chem 2011; 19:4114-26. [DOI: 10.1016/j.bmc.2011.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 04/29/2011] [Accepted: 05/04/2011] [Indexed: 10/18/2022]
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Allscher T, Arendt Y, Klüfers P. Conformational fluctuation in palladium(II)–methyl aldopentopyranoside complexes. Carbohydr Res 2010; 345:2381-9. [DOI: 10.1016/j.carres.2010.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 08/09/2010] [Accepted: 08/12/2010] [Indexed: 10/19/2022]
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Kräutler V, Müller M, Hünenberger PH. Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field. Carbohydr Res 2007; 342:2097-124. [PMID: 17573054 DOI: 10.1016/j.carres.2007.05.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 04/06/2007] [Accepted: 05/01/2007] [Indexed: 11/23/2022]
Abstract
The present article reports long timescale (200 ns) simulations of four beta-D-hexopyranoses (beta-D-glucose, beta-D-mannose, beta-D-galactose and beta-D-talose) using explicit-solvent (water) molecular dynamics and vacuum stochastic dynamics simulations together with the GROMOS 45A4 force field. Free-energy and solvation free-energy differences between the four compounds are also calculated using thermodynamic integration. Along with previous experimental findings, the present results suggest that the formation of intramolecular hydrogen-bonds in water is an 'opportunistic' consequence of the close proximity of hydrogen-bonding groups, rather than a major conformational driving force promoting this proximity. In particular, the conformational preferences of the hydroxymethyl group in aqueous environment appear to be dominated by 1,3-syn-diaxial repulsion, with gauche and solvation effects being secondary, and intramolecular hydrogen-bonding essentially negligible. The rotational dynamics of the exocyclic hydroxyl groups, which cannot be probed experimentally, is found to be rapid (10-100 ps timescale) and correlated (flip-flop hydrogen-bonds interconverting preferentially through an asynchronous disrotatory pathway). Structured solvent environments are observed between the ring and lactol oxygen atoms, as well as between the 4-OH and hydroxymethyl groups. The calculated stability differences between the four compounds are dominated by intramolecular effects, while the corresponding differences in solvation free energies are small. An inversion of the stereochemistry at either C(2) or C(4) from equatorial to axial is associated with a raise in free energy. Finally, the particularly low hydrophilicity of beta-D-talose appears to be caused by the formation of a high-occurrence hydrogen-bonded bridge between the 1,3-syn-diaxial 2-OH and 4-OH groups. Overall, good agreement is found with available experimental and theoretical data on the structural, dynamical, solvation and energetic properties of these compounds. However, this detailed comparison also reveals some discrepancies, suggesting the need (and providing a solid basis) for further refinement.
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Affiliation(s)
- Vincent Kräutler
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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Fabian WMF. Metal Binding Induced Conformational Interconversions in Methyl ß-D-xylopyranoside. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0130-4] [Citation(s) in RCA: 4] [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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Navarro DA, Stortz CA. Modeling ring puckering in strained systems: application to 3,6-anhydroglycosides. Carbohydr Res 2005; 340:2030-8. [PMID: 16023621 DOI: 10.1016/j.carres.2005.05.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Accepted: 05/28/2005] [Indexed: 11/26/2022]
Abstract
Different conformations of methyl 3,6-anhydroglycosides with the beta-D-galacto, alpha-D-galacto, and beta-D-gluco configurations were studied by molecular mechanics (using the program mm3) and by quantum mechanical (QM) methods at the HF/- and B3LYP/6-31+G** levels, with and without solvent emulation. Using molecular mechanics, the energies were plotted against the phi, theta puckering coordinates of Cremer and Pople. In such strained systems, only two extreme conformations of the six-membered ring are likely: (1)C(4) and B(1,4), or any one close to either of them. Results show the preponderance of a distorted chair conformation over that of the distorted boat, though the energy difference is lower and the distortions are larger for the compound with the beta-D-galacto configuration. For derivatives of this compound, experimental data in solution indicate both chair and boat forms, depending on the compound and the solvent, whereas for the remaining compounds, experimental data always show the preponderance of the chair conformation. The more accurate DFT calculations lead to the lower energy differences, suggesting that HF and MM3 underestimate the stability of the boat-like conformations. Similar studies on model compounds depict the importance of the anomeric effect in the conformational preferences.
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Affiliation(s)
- Diego A Navarro
- Departamento de Química Orgánica-CIHIDECAR, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina
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Pham TN, Hinchley SL, Rankin DWH, Liptaj T, Uhrín D. Determination of sugar structures in solution from residual dipolar coupling constants: methodology and application to methyl beta-D-xylopyranoside. J Am Chem Soc 2005; 126:13100-10. [PMID: 15469309 DOI: 10.1021/ja047242+] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed methodology for the determination of solution structures of small molecules from residual dipolar coupling constants measured in dilute liquid crystals. The power of the new technique is demonstrated by the determination of the structure of methyl beta-d-xylopyranoside (I) in solution. An oriented sample of I was prepared using a mixture of C(12)E(5) and hexanol in D(2)O. Thirty residual dipolar coupling constants, ranging from -6.44 to 4.99 Hz, were measured using intensity-based J-modulated NMR techniques. These include 15 D(HH), 4 (1)D(CH), and 11 (n)D(CH) coupling constants. The accuracy of the dipolar coupling constants is estimated to be < +/- 0.02 Hz. New constant-time HMBC NMR experiments were developed for the measurement of (n)D(CH) coupling constants, the use of which was crucial for the successful structure determination of I, as they allowed us to increase the number of fitted parameters. The structure of I was refined using a model in which the directly bonded interatom distances were fixed at their ab initio values, while 16 geometrical and 5 order parameters were optimized. These included 2 CCC and 6 CCH angles, and 2 CCCC and 6 CCCH dihedral angles. Vibrationally averaged dipolar coupling constants were used during the refinement. The refined solution structure of I is very similar to that obtained by ab initio calculations, with 11 bond and dihedral angles differing by 0.8 degrees or less and the remaining 5 parameters differing by up to 3.3 degrees . Comparison with the neutron diffraction structure showed larger differences attributable to crystal packing effects. Reducing the degree of order by using dilute liquid crystalline media in combination with precise measurement of small residual dipolar coupling constants, as shown here, is a way of overcoming the limitation of strongly orienting liquid crystals associated with the complexity of (1)H NMR spectra for molecules with more than 12 protons.
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Affiliation(s)
- Tran N Pham
- Contribution from the School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland, U.K
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Mohal N, Vasella A. Synthesis of Fusion-Isomeric Imidazopyridines and Their Evaluation as Inhibitors ofsyn- andanti-Protonating Glycosidases. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200490287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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