1
|
Erichsen A, Peters GHJ, Beeren SR. Templated Enzymatic Synthesis of δ-Cyclodextrin. J Am Chem Soc 2023; 145:4882-4891. [PMID: 36802551 DOI: 10.1021/jacs.3c00341] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine Ka1, Ka2, and Ka3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T12. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.
Collapse
Affiliation(s)
- Andreas Erichsen
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
2
|
Takagi H, Suzuki S, Kitamura S. Selective Adsorption of Essential Oil Compounds by Waxy/Amylose Extender
( wx/ae
) Double-Mutant Rice Starch Revealed by Gas Chromatography. STARCH-STARKE 2019. [DOI: 10.1002/star.201700301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroki Takagi
- Graduate School of Life and Environmental Sciences; Osaka Prefecture University; Sakai 599-8531 Japan
- Nihon Shokuhin Kako Co., Ltd.; Fuji 417-8530 Japan
| | - Shiho Suzuki
- Graduate School of Life and Environmental Sciences; Osaka Prefecture University; Sakai 599-8531 Japan
| | - Shinichi Kitamura
- Graduate School of Life and Environmental Sciences; Osaka Prefecture University; Sakai 599-8531 Japan
| |
Collapse
|
3
|
Assaf KI, Gabel D, Zimmermann W, Nau WM. High-affinity host-guest chemistry of large-ring cyclodextrins. Org Biomol Chem 2018; 14:7702-6. [PMID: 27456317 DOI: 10.1039/c6ob01161f] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The host-guest chemistry of large-ring cyclodextrins (LRCDs) has been largely unexplored due to the lack of suitable guest molecules that bind with significant affinities to enable potential applications. Herein, we report their complexation with dodecaborate anions (B12X12(2-)), a novel class of guest molecules. The binding constants of the inorganic guests (10(4)-10(6) M(-1)) allow their classification as the first tight binders for LRCDs.
Collapse
Affiliation(s)
- Khaleel I Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
| | - Detlef Gabel
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
| | - Wolfgang Zimmermann
- Department of Microbiology and Bioprocess Technology, Institute of Biochemistry, Leipzig University, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Werner M Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany.
| |
Collapse
|
4
|
Ivanov PM, Atanassov EJ, Jaime C. Computational study on the intramolecular self-organization of the macrorings of some ‘giant’ cyclodextrins (CDn, n = 40, 70, 85, 100). Org Biomol Chem 2015; 13:1680-9. [DOI: 10.1039/c4ob02218a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A limited number of modes determine the overall deformations of the macrorings, which may have more than one cavity. Accordingly, they have the potential to accommodate more than one substrate molecule.
Collapse
Affiliation(s)
- Petko M. Ivanov
- Institute of Organic Chemistry with Centre of Phytochemistry
- Bulgarian Academy of Sciences
- 1113 Sofia
- Bulgaria
| | - Emanouil J. Atanassov
- Institute of Information and Communication Technologies
- Bulgarian Academy of Sciences
- 1113 Sofia
- Bulgaria
| | - Carlos Jaime
- Universitat Autònoma de Barcelona
- Departament de Química
- Facultat de Ciències
- Spain
| |
Collapse
|
6
|
Gallois-Montbrun D, Le Bas G, Mason SA, Prangé T, Lesieur S. A highly hydrated α-cyclodextrin/1-undecanol inclusion complex: crystal structure and hydrogen-bond network from high-resolution neutron diffraction at 20 K. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2013. [DOI: 10.1107/s0108768113001778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
9
|
Bernatowicz P, Ruszczyńska-Bartnik K, Ejchart A, Dodziuk H, Kaczorowska E, Ueda H. Carbon-13 NMR Relaxation Study of the Internal Dynamics in Cyclodextrins in Isotropic Solution. J Phys Chem B 2009; 114:59-65. [DOI: 10.1021/jp9084734] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Bernatowicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Katarzyna Ruszczyńska-Bartnik
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Andrzej Ejchart
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Helena Dodziuk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Ewa Kaczorowska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Haruhisa Ueda
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| |
Collapse
|
11
|
French AD, Johnson GP. Linkage and pyranosyl ring twisting in cyclodextrins. Carbohydr Res 2007; 342:1223-37. [PMID: 17382309 DOI: 10.1016/j.carres.2007.02.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 02/22/2007] [Accepted: 02/23/2007] [Indexed: 10/23/2022]
Abstract
Acylated beta-cyclodextrins (beta-CDs) were studied to gain perspective on maltose octapropanoate, the crystal structure of which was reported in the preceding paper in this issue. Acylated beta-CDs are distorted so we looked at other CDs and gained increased understanding of distortion in CDs and possibly, shapes in starch. Classic CDs have six to eight glucose residues in a doughnut shape that is stabilized by a ring of inter-residue O3,,,O2' hydrogen bonds. On a phi,psi energy map for a maltose analog that does not form hydrogen bonds, classic CD linkages have higher energies than structures that are stabilized by the exo-anomeric effect. In distorted beta-CDs, which lack hydrogen bonding, some linkages attain low-energies from the exo-anomeric effect and acyl stacking. Those linkages result in left-handed helical geometry so other linkages are forced by the CD macrocycle to have counter-balancing right-handed character. Permethylated gamma-CDs have two 'flipping' linkages as do some larger native CDs. Flipping linkages allow two left-handed segments to join into a macrocycle, thus avoiding the higher-energy, right-handed forms. Some glucose rings in derivatized beta-CDs have substantial positive twists of the pseudo torsion angle O1-C1...C4-O4, adding right-handed character to balance the left-handed linkages. In substituted gamma-CD, all residues have negative twists, giving extra left-handed character to the short, pseudo-helical segments. In non-macrocyclic molecules the twists ranged from -14 degrees to +2 degrees , averaging -6.1 degrees. In these beta- and gamma-CDs, the twists ranged from -22 degrees to +16 degrees for (4)C(1) rings, and the (O)S(2) ring in acetylated beta-CD has a twist of +34 degrees . Glucose residues in other CDs were less twisted.
Collapse
Affiliation(s)
- Alfred D French
- Southern Regional Research Center, US Department of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, United States.
| | | |
Collapse
|
12
|
Brynda J, Rezacova P, Fabry M, Horejsi M, Stouracova R, Sedlacek J, Soucek M, Hradilek M, Lepsik M, Konvalinka J. A phenylnorstatine inhibitor binding to HIV-1 protease: geometry, protonation, and subsite-pocket interactions analyzed at atomic resolution. J Med Chem 2004; 47:2030-6. [PMID: 15056001 DOI: 10.1021/jm031105q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The X-ray structure of a complex of HIV-1 protease (PR) with a phenylnorstatine inhibitor Z-Pns-Phe-Glu-Glu-NH(2) has been determined at 1.03 A, the highest resolution so far reported for any HIV PR complex. The inhibitor shows subnanomolar K(i) values for both the wild-type PR and the variant representing one of the most common mutations linked to resistance development. The structure comprising the phenylnorstatine moiety of (2R,3S)-chirality displays a unique pattern of hydrogen bonding to the two catalytic aspartate residues. This high resolution makes it possible to assess the donor and acceptor relations of this hydrogen bonding and to indicate a proton shared by the two catalytic residues. A structural mechanism for the unimpaired inhibition of the protease Val82Ala mutant is also suggested, based on energy calculations and analyses.
Collapse
Affiliation(s)
- Jiri Brynda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16637 Prague 6, Czech Republic.
| | | | | | | | | | | | | | | | | | | |
Collapse
|