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Fittolani G, Tyrikos-Ergas T, Poveda A, Yu Y, Yadav N, Seeberger PH, Jiménez-Barbero J, Delbianco M. Synthesis of a glycan hairpin. Nat Chem 2023; 15:1461-1469. [PMID: 37400598 PMCID: PMC10533408 DOI: 10.1038/s41557-023-01255-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
The primary sequence of a biopolymer encodes the essential information for folding, permitting to carry out sophisticated functions. Inspired by natural biopolymers, peptide and nucleic acid sequences have been designed to adopt particular three-dimensional (3D) shapes and programmed to exert specific functions. In contrast, synthetic glycans capable of autonomously folding into defined 3D conformations have so far not been explored owing to their structural complexity and lack of design rules. Here we generate a glycan that adopts a stable secondary structure not present in nature, a glycan hairpin, by combining natural glycan motifs, stabilized by a non-conventional hydrogen bond and hydrophobic interactions. Automated glycan assembly enabled rapid access to synthetic analogues, including site-specific 13C-labelled ones, for nuclear magnetic resonance conformational analysis. Long-range inter-residue nuclear Overhauser effects unequivocally confirmed the folded conformation of the synthetic glycan hairpin. The capacity to control the 3D shape across the pool of available monosaccharides has the potential to afford more foldamer scaffolds with programmable properties and functions.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Ana Poveda
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
| | - Yang Yu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Simpson Querrey Institute, Northwestern University, Evanston, IL, USA
| | - Nishu Yadav
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research and Technology Alliance, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Department of Organic Chemistry II, Faculty of Science and Technology, University of the Basque Country, Leioa, Spain
- Centro de Investigación Biomedica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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Tyrikos-Ergas T, Gim S, Huang JY, Pinzón Martín S, Varón Silva D, Seeberger PH, Delbianco M. Synthetic phosphoethanolamine-modified oligosaccharides reveal the importance of glycan length and substitution in biofilm-inspired assemblies. Nat Commun 2022; 13:3954. [PMID: 35804023 PMCID: PMC9270332 DOI: 10.1038/s41467-022-31633-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/28/2022] [Indexed: 12/18/2022] Open
Abstract
Bacterial biofilm matrices are nanocomposites of proteins and polysaccharides with remarkable mechanical properties. Efforts understanding and tuning the protein component have been extensive, whereas the polysaccharide part remained mostly overlooked. The discovery of phosphoethanolamine (pEtN) modified cellulose in E. coli biofilms revealed that polysaccharide functionalization alters the biofilm properties. To date, the pattern of pEtN cellulose and its mode of interactions with proteins remains elusive. Herein, we report a model system based on synthetic epitomes to explore the role of pEtN in biofilm-inspired assemblies. Nine pEtN-modified oligosaccharides were synthesized with full control over the length, degree and pattern of pEtN substitution. The oligomers were co-assembled with a representative peptide, triggering the formation of fibers in a length dependent manner. We discovered that the pEtN pattern modulates the adhesion of biofilm-inspired matrices, while the peptide component controls its stiffness. Unnatural oligosaccharides tune or disrupt the assembly morphology, revealing interesting targets for polysaccharide engineering to develop tunable bio-inspired materials.
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Affiliation(s)
- Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Soeun Gim
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Jhih-Yi Huang
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Sandra Pinzón Martín
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniel Varón Silva
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.,Institute of Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.
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Tyrikos-Ergas T, Sletten ET, Huang JY, Seeberger PH, Delbianco M. On resin synthesis of sulfated oligosaccharides. Chem Sci 2022; 13:2115-2120. [PMID: 35308866 PMCID: PMC8848854 DOI: 10.1039/d1sc06063e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/29/2022] [Indexed: 01/19/2023] Open
Abstract
Sulfated glycans are involved in many biological processes, making well-defined sulfated oligosaccharides highly sought molecular probes. These compounds are a considerable synthetic challenge, with each oligosaccharide target requiring specific synthetic protocols and extensive purifications steps. Here, we describe a general on resin approach that simplifies the synthesis of sulfated glycans. The oligosaccharide backbone, obtained by Automated Glycan Assembly (AGA), is subjected to regioselective sulfation and hydrolysis of protecting groups. The protocol is compatible with several monosaccharides and allows for multi-sulfation of linear and branched glycans. Seven diverse, biologically relevant sulfated glycans were prepared in good to excellent overall yield.
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Affiliation(s)
- Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany .,Department of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Eric T Sletten
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Jhih-Yi Huang
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany .,Department of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany .,Department of Chemistry and Biochemistry, Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
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Fittolani G, Djalali S, Chaube MA, Tyrikos-Ergas T, Dal Colle MCS, Grafmüller A, Seeberger PH, Delbianco M. Deoxyfluorination tunes the aggregation of cellulose and chitin oligosaccharides and highlights the role of specific hydroxyl groups in the crystallization process. Org Biomol Chem 2022; 20:8228-8235. [DOI: 10.1039/d2ob01601j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Using synthetic oligosaccharides, we examined how deoxyfluorination (site and pattern) impact the solubility and aggregation of cellulose and chitin oligomers.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Surusch Djalali
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Manishkumar A. Chaube
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Marlene C. S. Dal Colle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Andrea Grafmüller
- Department of Theory and Biosystems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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Fittolani G, Tyrikos-Ergas T, Vargová D, Chaube MA, Delbianco M. Progress and challenges in the synthesis of sequence controlled polysaccharides. Beilstein J Org Chem 2021; 17:1981-2025. [PMID: 34386106 PMCID: PMC8353590 DOI: 10.3762/bjoc.17.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/22/2021] [Indexed: 01/15/2023] Open
Abstract
The sequence, length and substitution of a polysaccharide influence its physical and biological properties. Thus, sequence controlled polysaccharides are important targets to establish structure-properties correlations. Polymerization techniques and enzymatic methods have been optimized to obtain samples with well-defined substitution patterns and narrow molecular weight distribution. Chemical synthesis has granted access to polysaccharides with full control over the length. Here, we review the progress towards the synthesis of well-defined polysaccharides. For each class of polysaccharides, we discuss the available synthetic approaches and their current limitations.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Denisa Vargová
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Manishkumar A Chaube
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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Zhu Y, Tyrikos-Ergas T, Schiefelbein K, Grafmüller A, Seeberger PH, Delbianco M. Automated access to well-defined ionic oligosaccharides. Org Biomol Chem 2020; 18:1349-1353. [PMID: 32037424 DOI: 10.1039/d0ob00137f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ionic polysaccharides are part of many biological events, but lack structural characterisation due to challenging purifications and complex synthesis. Four monosaccharides bearing modifications not found in nature are used for the automated synthesis of a collection of ionic oligosaccharides. Structural analysis reveals how the charge pattern affects glycan conformation.
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Affiliation(s)
- Yuntao Zhu
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany. and Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Kevin Schiefelbein
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Andrea Grafmüller
- Department of Theory, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany. and Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
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Tyrikos-Ergas T, Fittolani G, Seeberger PH, Delbianco M. Structural Studies Using Unnatural Oligosaccharides: Toward Sugar Foldamers. Biomacromolecules 2019; 21:18-29. [DOI: 10.1021/acs.biomac.9b01090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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Kelefiotis-Stratidakis P, Tyrikos-Ergas T, Pavlidis IV. The challenge of using isopropylamine as an amine donor in transaminase catalysed reactions. Org Biomol Chem 2019; 17:1634-1642. [PMID: 30394478 DOI: 10.1039/c8ob02342e] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Amine transaminases (ATAs) propose an appealing alternative to transition metal catalysts as they can provide chiral amines of high purity from pro-chiral compounds by asymmetric synthesis. Industrial interest on ATAs arises from the fact that chiral amines are present in a wide spectrum of pharmaceutical and other high value-added chiral compounds and building blocks. Despite their potential as useful synthetic tools, several drawbacks such as challenges associated with the thermodynamic equilibrium can still impede their utilization. Several methods have been developed to displace the equilibrium, such as the use of alanine as an amine donor and the subsequent removal of pyruvate with a two-enzyme system, or the use of o-xylylene diamine. To date, the preferred amine donor remains isopropylamine (IPA), as the produced acetone can be removed easily under low pressure or slight heating, without complicating the process with other enzymes. Despite its small size, IPA is not widely accepted from wild-type ATAs, and this fact compromises its wide applicability. Herein, we index the reported biocatalytic aminations with IPA, comparing the sequences, while we discuss significant parameters of the process, such as the effect of temperature and pH, as well as the protein engineering and process development advances in the field. This information is expected to provide an insight for potential designs of tailor-made ATAs and IPA processes.
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Affiliation(s)
- An Su
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Theodore Tyrikos-Ergas
- Department of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Greece
| | - Abhijit N. Shirke
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yi Zou
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Abigail L. Dooley
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Ioannis V. Pavlidis
- Department of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Greece
| | - Richard A. Gross
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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Tyrikos-Ergas T, Giannopoulos V, Smonou I. An Efficient Chemoenzymatic Approach towards the Synthesis of Rugulactone. Molecules 2018; 23:E640. [PMID: 29534553 PMCID: PMC6017073 DOI: 10.3390/molecules23030640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/05/2022] Open
Abstract
Rugulactone is a natural product isolated from the plant Cryptocarya rugulosa. It has shown very important biological activity as an inhibitor of the nuclear factor κB (NF-κB) activation pathway. A new chemoenzymatic approach towards the synthesis of rugulactone is presented here. The chirality, induced to the key intermediate by a stereoselective enzymatic reduction utilizing NADPH-dependent ketoreductase, is described in detail.
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Affiliation(s)
- Theodore Tyrikos-Ergas
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003 Heraklion, Crete, Greece.
| | - Vasileios Giannopoulos
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003 Heraklion, Crete, Greece.
| | - Ioulia Smonou
- Department of Chemistry, University of Crete, Vasilika Vouton, 71003 Heraklion, Crete, Greece.
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