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Shepard SM, Jessen HJ, Cummins CC. Beyond Triphosphates: Reagents and Methods for Chemical Oligophosphorylation. J Am Chem Soc 2022; 144:7517-7530. [PMID: 35471019 DOI: 10.1021/jacs.1c07990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligophosphates play essential roles in biochemistry, and considerable research has been directed toward the synthesis of both naturally occurring oligophosphates and their synthetic analogues. Greater attention has been given to mono-, di-, and triphosphates, as these are present in higher concentrations biologically and easier to synthesize. However, extended oligophosphates have potent biochemical roles, ranging from blood coagulation to HIV drug resistance. Sporadic reports have slowly built a niche body of literature related to the synthesis and study of extended oligophosphates, but newfound interests and developments have the potential to rapidly expand this field. Here we report on current methods to synthesize oligophosphates longer than triphosphates and comment on the most important future directions for this area of research. The state of the art has provided fairly robust methods for synthesizing nucleoside 5'-tetra- and pentaphosphates as well as dinucleoside 5',5'-oligophosphates. Future research should endeavor to push such syntheses to longer oligophosphates while developing synthetic methodologies for rarer morphologies such as 3'-nucleoside oligophosphates, polyphosphates, and phosphonate/thiophosphate analogues of these species.
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Affiliation(s)
- Scott M Shepard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg & Cluster of Excellence livMatS, FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
| | - Christopher C Cummins
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
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2
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Liu Q, Knobloch G, Voorneveld J, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Ladurner AG, Filippov DV. Chemical synthesis of linear ADP-ribose oligomers up to pentamer and their binding to the oncogenic helicase ALC1. Chem Sci 2021; 12:12468-12475. [PMID: 34603678 PMCID: PMC8480336 DOI: 10.1039/d1sc02340c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/12/2021] [Indexed: 11/21/2022] Open
Abstract
ADP-ribosylation is a pivotal post-translational modification that mediates various important cellular processes producing negatively charged biopolymer, poly (ADP-ribose), the functions of which need further elucidation. Toward this end, the availability of well-defined ADP-ribose (ADPr) oligomers in sufficient quantities is a necessity. In this work, we demonstrate the chemical synthesis of linear ADPr oligomers of defined, increasing length using a modified solid phase synthesis method. An advanced phosphoramidite building block temporarily protected with the base sensitive Fm-group was designed and implemented in the repeating pyrophosphate formation via a P(v)-P(iii) coupling procedure on Tentagel solid support. Linear ADPr oligomers up to a pentamer were successfully synthesized and their affinity for the poly-(ADP-ribose)-binding macrodomain of the human oncogenic helicase and chromatin remodeling enzyme ALC1 was determined. Our data reveal a length-dependent binding manner of the nucleic acid, with larger ADPr oligomers exhibiting higher binding enthalpies for ALC1, illustrating how the activity of this molecular machine is gated by PAR.
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Affiliation(s)
- Qiang Liu
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Gunnar Knobloch
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine LMU Munich 82152 Planegg-Martinsried Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Nico J Meeuwenoord
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
| | | | - Andreas G Ladurner
- Biomedical Center (BMC), Physiological Chemistry, Faculty of Medicine LMU Munich 82152 Planegg-Martinsried Germany
- Eisbach Bio GmbH Am Klopferspitz 19, Planegg-Martinsried 82152 Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University P.O. Box 9502 2300 RA Leiden The Netherlands
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3
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eddy I. Jiménez
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Clémentine Gibard
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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4
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021; 60:10775-10783. [PMID: 33325148 DOI: 10.1002/anie.202015910] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Indexed: 12/14/2022]
Abstract
Recent demonstrations of RNA-DNA chimeras (RDNA) enabling RNA and DNA replication, coupled with prebiotic co-synthesis of deoxyribo- and ribo-nucleotides, have resurrected the hypothesis of co-emergence of RNA and DNA. As further support, we show that diamidophosphate (DAP) with 2-aminoimidazole (amido)phosphorylates and oligomerizes deoxynucleosides to form DNA-under conditions similar to those of ribonucleosides. The pyrimidine deoxynucleoside 5'-O-amidophosphates are formed in good (≈60 %) yields. Intriguingly, the presence of pyrimidine deoxynucleos(t)ides increased the yields of purine deoxynucleotides (≈20 %). Concomitantly, oligomerization (≈18-31 %) is observed with predominantly 3',5'-phosphodiester DNA linkages, and some (<5 %) pyrophosphates. Combined with previous observations of DAP-mediated chemistries and the constructive role of RDNA chimeras, the results reported here help set the stage for systematic investigation of a systems chemistry approach of RNA-DNA coevolution.
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Affiliation(s)
- Eddy I Jiménez
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Clémentine Gibard
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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5
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Appy L, Chardet C, Peyrottes S, Roy B. Synthetic Strategies for Dinucleotides Synthesis. Molecules 2019; 24:molecules24234334. [PMID: 31783537 PMCID: PMC6930578 DOI: 10.3390/molecules24234334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Dinucleoside 5′,5′-polyphosphates (DNPs) are endogenous substances that play important intra- and extracellular roles in various biological processes, such as cell proliferation, regulation of enzymes, neurotransmission, platelet disaggregation and modulation of vascular tone. Various methodologies have been developed over the past fifty years to access these compounds, involving enzymatic processes or chemical procedures based either on P(III) or P(V) chemistry. Both solution-phase and solid-support strategies have been developed and are reported here. Recently, green chemistry approaches have emerged, offering attracting alternatives. This review outlines the main synthetic pathways for the preparation of dinucleoside 5′,5′-polyphosphates, focusing on pharmacologically relevant compounds, and highlighting recent advances.
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6
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Foy HC, Schwan AL, Dudding T. A mechanistic study of oxygen atom transfer from N-sulfonyloxaziridine to enolates. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.02.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Anderson BA, Krishnamurthy R. Heterogeneous Pyrophosphate-Linked DNA-Oligonucleotides: Aversion to DNA but Affinity for RNA. Chemistry 2018. [PMID: 29532524 DOI: 10.1002/chem.201800538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pyrophosphate linkages are important in extant biology and are hypothesized to have played a role in prebiotic chemistry and in the origination of oligonucleotides. Inspired by pyrophosphate as backbones of primordial oligomers, DNA oligomers with varying amounts of pyrophosphate inserts (ppDNA) were synthesized and investigated for their base-pairing properties. As expected, pyrophosphate inserts into the backbone compromised the thermal stability of ppDNA-DNA duplexes. In contrast, the ppDNA-RNA duplex exhibited, remarkably, duplex stability, even with accumulation of pyrophosphate linkages. This seems to be a consequence of an increase in the diameter of the double-helix with eight-bond-repeat units, and higher inclination of the base-pair axis with respect to the backbone in RNA (A-form), compared with that in DNA (B-form). These results suggest that pyrophosphate-linked oligonucleotides could harbor functional capabilities with implications for their roles in the origins of life and chemical biology.
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Affiliation(s)
- Brooke A Anderson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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Abstract
Synthetic mono-ADPr-peptides are useful for structural, biochemical, and proteomics studies. We describe here a protocol for the preparation of mono-ADPr-peptides based on a fairly standard Fmoc-based solid-phase synthesis. Phosphoribosylated precursor building blocks are introduced into the peptide chain on solid-phase and subsequently converted to ADPr-sites by chemical phosphorylation with adenosine phosphoramidite. Suitably protected phosphoribosylated glutamine, asparagine, and citrulline building blocks described in this protocol allow introduction of ADP-Gln, ADPr-Asn, and ADPr-Cit into peptide chains as demonstrated for three peptides. Trifunctional amino acids, for which base-sensitive side-chain protection is available, can be accommodated in the sequences flanking the ADPr-cites.
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Affiliation(s)
- Hans A V Kistemaker
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Jim Voorneveld
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands
| | - Dmitri V Filippov
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Universiteit Leiden, Leiden, The Netherlands.
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9
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Zhang Q, Howell PL, Overkleeft HS, Filippov DV, van der Marel GA, Codée JDC. Chemical synthesis of guanosine diphosphate mannuronic acid (GDP-ManA) and its C-4-O-methyl and C-4-deoxy congeners. Carbohydr Res 2017; 450:12-18. [PMID: 28822279 DOI: 10.1016/j.carres.2017.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 11/29/2022]
Abstract
Described is the first synthesis of guanosine diphosphate mannuronic acid (GDP-ManA), the sugar donor used by algae and bacteria for the production of alginate, an anionic polysaccharide composed of β-d-mannuronic acid (ManA) and α-l-guluronic acid (GulA). Understanding the biosynthesis of these polyanionic polysaccharides on the molecular level, opens up avenues to use and modulate the biosynthesis machinery for biotechnological and therapeutic applications. The synthesis reported here delivers multi-milligram amounts of the GDP-ManA donor that can be used to study the polymerase (Alg8 in Pseudomonas aeruginosa) that generates the poly-ManA chain. Also reported is the assembly of two close analogues of GDP-ManA: the first bears a C-4-O-methyl group, while the second has been deoxygenated at this position. Both molecules may be used as "chain stoppers" in future enzymatic ManA polymerisation reactions. The crucial pyrophosphate linkage of the GDP-mannuronic acids has been constructed by the phosphorylation of the appropriate ManA-1-phosphates with a guanosine phosphoramidite.
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Affiliation(s)
- Qingju Zhang
- Bio-organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Herman S Overkleeft
- Bio-organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Dmitri V Filippov
- Bio-organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Bio-organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Jeroen D C Codée
- Bio-organic Synthesis Group, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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10
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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11
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Engelsma SB, Meeuwenoord NJ, Overkleeft HS, van der Marel GA, Filippov DV. Combined Phosphoramidite-Phosphodiester Reagents for the Synthesis of Methylene Bisphosphonates. Angew Chem Int Ed Engl 2017; 56:2955-2959. [DOI: 10.1002/anie.201611878] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Sander B. Engelsma
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Gijsbert A. van der Marel
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Department of Bioorganic Synthesis; Leiden University; Einsteinweg 55 2333 CC Leiden The Netherlands
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12
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van der Es D, Groenia NA, Laverde D, Overkleeft HS, Huebner J, van der Marel GA, Codée JDC. Synthesis of E. faecium wall teichoic acid fragments. Bioorg Med Chem 2016; 24:3893-3907. [PMID: 26993744 DOI: 10.1016/j.bmc.2016.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 10/22/2022]
Abstract
The first synthesis of different Enterococcus faecium wall teichoic acid (WTA) fragments is presented. The structure of these major cell wall components was elucidated recently and it was shown that these glycerolphosphate (GroP) based polymers are built up from -6-(GalNAc-α(1-3)-GalNAc-β(1-2)-GroP)- repeating units. We assembled WTA fragments up to three repeating units in length, in two series that differ in the stereochemistry of the glycerolphosphate moiety. The key GalNAc-GalNAc-GroP synthons, required for the synthesis, were generated from galactosazide building blocks that were employed in highly stereoselective glycosylation reactions to furnish both the α- and β-configured linkages. By comparing the NMR spectra of the synthesized fragments with the isolated material it appears that the hereto undefined stereochemistry of the glycerol phosphate moiety is sn-glycerol-3-phosphate. The generated fragments will be valuable tools to study their immunological activity at the molecular level.
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Affiliation(s)
- Daan van der Es
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Nadia A Groenia
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Diana Laverde
- Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Herman S Overkleeft
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes Huebner
- Division of Pediatric Infectious Diseases, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | | | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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13
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Kistemaker HA, Meeuwenoord NJ, Overkleeft HS, Marel GA, Filippov DV. Solid‐Phase Synthesis of Oligo‐ADP‐Ribose. ACTA ACUST UNITED AC 2016; 64:4.68.1-4.68.27. [DOI: 10.1002/0471142700.nc0468s64] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hans A.V. Kistemaker
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Nico J. Meeuwenoord
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Gijsbert A. Marel
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
| | - Dmitri V. Filippov
- Department of Bio‐organic Synthesis, Leiden Institute of Chemistry, Leiden University Leiden The Netherlands
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