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Mondal D, Koehn EM, Yao J, Wiemer DF, Kohen A. Chemo-enzymatic synthesis of the exocyclic olefin isomer of thymidine monophosphate. Bioorg Med Chem 2018; 26:2365-2371. [PMID: 29606487 DOI: 10.1016/j.bmc.2018.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/15/2018] [Accepted: 03/21/2018] [Indexed: 12/19/2022]
Abstract
Exocyclic olefin variants of thymidylate (dTMP) recently have been proposed as reaction intermediates for the thymidyl biosynthesis enzymes found in many pathogenic organisms, yet synthetic reports on these materials are lacking. Here we report two strategies to prepare the exocyclic olefin isomer of dTMP, which is a putative reaction intermediate in pathogenic thymidylate biosynthesis and a novel nucleotide analog. Our most effective strategy involves preserving the existing glyosidic bond of thymidine and manipulating the base to generate the exocyclic methylene moiety. We also report a successful enzymatic deoxyribosylation of a non-aromatic nucleobase isomer of thymine, which provides an additional strategy to access nucleotide analogs with disrupted ring conjugation or with reduced heterocyclic bases. The strategies reported here are straightforward and extendable towards the synthesis of various pyrimidine nucleotide analogs, which could lead to compounds of value in studies of enzyme reaction mechanisms or serve as templates for rational drug design.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Eric M Koehn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - Jiajun Yao
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
| | - David F Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States.
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, United States
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2
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Pradere U, Garnier-Amblard E, Coats SJ, Amblard F, Schinazi RF. Synthesis of nucleoside phosphate and phosphonate prodrugs. Chem Rev 2014; 114:9154-218. [PMID: 25144792 PMCID: PMC4173794 DOI: 10.1021/cr5002035] [Citation(s) in RCA: 391] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 01/29/2023]
Affiliation(s)
- Ugo Pradere
- Center
for AIDS Research, Laboratory of Biochemical Pharmacology, Department
of Pediatrics, Emory University School of
Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | | | | | - Franck Amblard
- Center
for AIDS Research, Laboratory of Biochemical Pharmacology, Department
of Pediatrics, Emory University School of
Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
| | - Raymond F. Schinazi
- Center
for AIDS Research, Laboratory of Biochemical Pharmacology, Department
of Pediatrics, Emory University School of
Medicine, and Veterans Affairs Medical Center, Atlanta, Georgia 30322, United States
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3
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Gardelli C, Attenni B, Donghi M, Meppen M, Pacini B, Harper S, Di Marco A, Fiore F, Giuliano C, Pucci V, Laufer R, Gennari N, Marcucci I, Leone JF, Olsen DB, MacCoss M, Rowley M, Narjes F. Phosphoramidate Prodrugs of 2′-C-Methylcytidine for Therapy of Hepatitis C Virus Infection. J Med Chem 2009; 52:5394-407. [DOI: 10.1021/jm900447q] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cristina Gardelli
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Barbara Attenni
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Monica Donghi
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Malte Meppen
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Barbara Pacini
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Steven Harper
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Annalise Di Marco
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Fabrizio Fiore
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Claudio Giuliano
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Vincenzo Pucci
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Ralph Laufer
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Nadia Gennari
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Isabella Marcucci
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Joseph F. Leone
- Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065
| | - David B. Olsen
- Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania 19486
| | - Malcolm MacCoss
- Department of Medicinal Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065
| | - Michael Rowley
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
| | - Frank Narjes
- Departments of Medicinal Chemistry and Pharmacology, Istituto di Ricerche di Biologia Molecolare, P. Angeletti S.p.A. (IRBM-MRL Rome), Via Pontina Km 30,600, 00040 Pomezia, Italy
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4
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Choy CJ, Drontle DP, Wagner CR. Synthesis of amino acid phosphoramidate monoesters via H-phosphonate intermediates. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2006; Chapter 15:Unit 15.1. [PMID: 18428952 DOI: 10.1002/0471142700.nc1501s25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Diphenyl phosphite and bis(N,N-diisopropylamino)chlorophosphine are used as phosphitylating reagents to generate H-phosphonate monoesters. These H-phosphonate intermediates are subsequently oxidized with iodine to generate the 5'-nucleoside amino acid phosphoramidates.
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Affiliation(s)
- Cindy J Choy
- University of Minnesota, Minneapolis, Minnesota, USA
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Chou TF, Bieganowski P, Shilinski K, Cheng J, Brenner C, Wagner CR. 31P NMR and genetic analysis establish hinT as the only Escherchia coli purine nucleoside phosphoramidase and as essential for growth under high salt conditions. J Biol Chem 2005; 280:15356-61. [PMID: 15703176 PMCID: PMC2556068 DOI: 10.1074/jbc.m500434200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic cells encode AMP-lysine (AMP-N-epsilon-(N-alpha-acetyl lysine methyl ester) 5'-phosphoramidate) hydrolases related to the rabbit histidine triad nucleotide-binding protein 1 (Hint1) sequence. Bacterial and archaeal cells have Hint homologs annotated in a variety of ways, but the enzymes have not been characterized, nor have phenotypes been described due to loss of enzymatic activity. We developed a quantitative (31)P NMR assay to determine whether Escherichia coli possesses an adenosine phosphoramidase activity. Indeed, soluble lysates prepared from wild-type laboratory E. coli exhibited activity on the model substrate adenosine 5'-monophosphoramidate (AMP-NH(2)). The E. coli Hint homolog, which had been comprehensively designated ycfF and is here named hinT, was cloned, overexpressed, purified, and characterized with respect to purine nucleoside phosphoramidate substrates. Bacterial hinT was several times more active than human or rabbit Hint1 on five model substrates. In addition, bacterial and mammalian enzymes preferred guanosine versus adenosine phosphoramidates as substrates. Analysis of the lysates from a constructed hinT knock-out strain of E. coli demonstrated that all of the cellular purine nucleoside phosphoramidase activity is due to hinT. Physiological analysis of this mutant revealed that the loss of hinT results in failure to grow in media containing 0.75 m KCl, 0.9 m NaCl, 0.5 m NaOAc, or 10 mm MnCl(2). Thus, cation-resistant bacterial cell growth may be dependent on the hydrolysis of adenylylated and/or guanylylated phosphoramidate substrates by hinT.
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Affiliation(s)
- Tsui-Fen Chou
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, USA
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6
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Abstract
Bioactivatable protecting groups represent an enormously powerful tool to increase bioavailability or to generally help deliver drugs to cells. This approach is particularly valuable in the case of biologically active phosphates because of the high intrinsic hydrophilicity and the multitude of biological functions phosphate esters exhibit inside cells. Here, the most prominent masking groups used so far are introduced. The stability and toxicology of the resulting prodrugs is discussed. Finally, this review tries to cover briefly some of the work that describes the usefulness and efficiency of the approach in various application areas.
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Affiliation(s)
- Carsten Schultz
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany.
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7
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Chang SL, Griesgraber G, Wagner CR. Comparison of the antiviral activity of hydrophobic amino acid phosphoramidate monoesters of 2'3'-dideoxyadenosine (DDA) and 3'-azido-3'-deoxythymidine (AZT). NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:1571-82. [PMID: 11554546 DOI: 10.1081/ncn-100105248] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A series of hydrophobic, water soluble and non-toxic amino acid phosphoramidate monoesters of dideoxyadenosine (ddA) and 3'-azido-3'-deoxythymidine were shown to inhibit the replication of HIV-1 in human peripheral blood mononuclear cells (PBMC) from two donors. The tryptophan methyl ester phosphoramidates of AZT and ddA were equally potent (EC50S = 0.3-0.4 microM), while the phenyl methyl ester of ddA was 40- to 100- fold more potent than the AZT derivatives. The alaninyl methyl ester of AZT was found to be 70- fold more potent than the ddA derivative. The methyl amide derivatives were found to be 5-20 fold less active than the methyl esters for the ddA series, while for AZT the derivatives were found to be of similar potency or 60- to 166- fold more potent than the methylesters.
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Affiliation(s)
- S L Chang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis 55455, USA
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8
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Chang S, Griesgraber GW, Southern PJ, Wagner CR. Amino acid phosphoramidate monoesters of 3'-azido-3'-deoxythymidine: relationship between antiviral potency and intracellular metabolism. J Med Chem 2001; 44:223-31. [PMID: 11170632 DOI: 10.1021/jm000260r] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of phosphoramidate monoesters of 3'-azido-3'-deoxythymidine (AZT) bearing aliphatic amino acid methyl esters (3a, 3c, 4a, 4c, 5-7) and methyl amides (3b, 3d, 4b, 4d) was prepared and evaluated for anti-HIV-1 activity in peripheral blood mononuclear cells (PBMCs). These compounds, which showed no cytotoxicity at concentrations of 100 microM, were effective at inhibiting HIV-1 replication at concentrations of 0.08-30 microM. Since the D-phenylalanine and D-tryptophan derivatives exhibited equivalent or enhanced antiviral activity compared to their L-counterparts, there appears to be no specific stereochemical requirement for the amino acid side chain. In addition, except for the D-phenylalanine derivatives, the methyl amides had greater antiviral activity than the corresponding methyl esters. On the basis of the observed antiviral activity of AZT phosphoramidate monoesters 3a and 4a in PBMCs and CEM cells, the mechanism of action of these two compounds was investigated. AZT-MP and substantial amounts of either phosphoramidate were detected in PBMCs and CEM cells treated with either 3a or 4a. Biological mechanistic studies demonstrated that 3a and 4a affect viral replication at a stage after virus entry and preceding viral DNA integration. Quantitation of the intracellular levels of AZT-TP in PBMCs and CEM cells treated with 3a and 4a in the presence and absence of exogenous thymidine correlated the intracellular levels of AZT-TP to the antiviral activity and suggested that AZT-TP was responsible for the activity observed. In addition, the reduced toxicity of 3a and 4a toward CEM cells relative to AZT correlated with reduced levels of total phosphorylated AZT and not AZT-TP. Stable carbamate analogues of 3a and 4a were prepared and shown to inhibit the production of AZT-MP from cell-free extracts of CEM cells, further suggesting that a phosphoramidate hydrolase may be responsible for intracellular P-N bond cleavage. Taken together, these results suggest that the biological activity and intracellular metabolism of nucleoside phosphoramidate monoesters are distinct from that of phosphoramidate diesters.
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Affiliation(s)
- S Chang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Abstract
To overcome the many hurdles preventing the use of antiviral and anticancer nucleosides as therapeutics, the development of a prodrug methodology (i.e., pronucleotide) for the in vivo delivery of nucleotides has been proposed as a solution. The ideal pronucleotide should be non-toxic, stable in plasma and blood, capable of being i. v. and/or orally dosed, and intracellularly convertible to the corresponding nucleotide. Although this goal has yet to be achieved, many clever and imaginative pronucleotide approaches have been developed, which are likely to be important pharmacological tools. This review will discuss the major advances and future directions of the emerging field of antiviral and anticancer pronucleotide design and development.
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Affiliation(s)
- C R Wagner
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA
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10
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Iyer VV, Griesgraber GW, Radmer MR, McIntee EJ, Wagner CR. Synthesis, in vitro anti-breast cancer activity, and intracellular decomposition of amino acid methyl ester and alkyl amide phosphoramidate monoesters of 3'-azido-3'-deoxythymidine (AZT). J Med Chem 2000; 43:2266-74. [PMID: 10841805 DOI: 10.1021/jm000110g] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the synthesis and anticancer activity of a series of AZT phosphoramidate monoesters containing amino acid methyl ester (3a-11a) and N-alkyl amide (3b-11b, 9c-9f) moieties. The aromatic amino acid methyl esters were found to be more cytotoxic than the aliphatic analogues toward MCF-7 cells (human pleural effusion breast adenocarcinoma cell line). A marked stereochemical preference for the L-amino acid stereochemistry was also observed in MCF-7 cells. There was no consistent enhancement of cytotoxicity of the methyl amides over the corresponding methyl esters. AZT and the two AZT aromatic amino acid methyl ester phosphoramidates 8a and 9a were found to be more cytotoxic toward MCF-7 cells than to CEM cells (human T-cell lymphoblastic leukemia). The selective cytotoxicity toward MCF-7 cells may be associated with greater intracellular levels of phosphoramidate monoester and/or phosphorylated AZT.
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Affiliation(s)
- V V Iyer
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota, Minneapolis 55455, USA
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11
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Abstract
Nucleic acid-derived drugs exhibit both chemical and physical instability. This mini-review focuses on the prevalent hydrolytic and oxidative pathways of chemical degradation as they are affected by various endogenous (primary structure, chemical modifications in bases, sugars and phosphate residues) and exogenous (pH, buffer concentration, metal cation presence, oxygen presence) factors.
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Affiliation(s)
- D Pogocki
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
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12
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Meier C, Habel L, Haller-Meier F, Lomp A, Herderich M, Klöcking R, Meerbach A, Wutzler P. Chemistry and anti-herpes simplex virus type 1 evaluation of cycloSal-nucleotides of acyclic nucleoside analogues. Antivir Chem Chemother 1998; 9:389-402. [PMID: 9875392 DOI: 10.1177/095632029800900503] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The synthesis of different cycloSal-phosphotriesters of the acyclic nucleoside analogues acyclovir (ACV), penciclovir (PCV) and T-penciclovir (T-PCV) as potential new lipophilic, membrane-soluble pronucleotides is described. The introduction of the cycloSal moiety was achieved by using reactive cyclic chlorophosphane reagents. In addition to the cycloSal-PCV monophosphate (MP) phosphotriesters, a second derivative bearing an acetyl group at the second primary alcohol function was prepared. In hydrolysis studies the cycloSal-ACVMPs showed the expected range of hydrolytic stability dependent on the substituent in the masking group (8-17 h). In contrast, the cycloSal-PCVMP derivatives exhibited a 11- to 15-fold increase in hydrolytic lability as compared to the corresponding cycloSal-ACVMP derivatives. We demonstrated that the free primary alcohol group is responsible for this rate acceleration because cycloSal-OAc-PCVMP, in which the hydroxyl group was blocked by acetylation, did not show the aforementioned acceleration. Unexpectedly, the hydrolysis product was not PCVMP but according to NMR and mass spectrometry it was cycloPCVMP (cPCVMP). The title compounds were evaluated in vitro for their ability to inhibit herpes simplex virus type 1 (HSV-1) and thymidine kinase-negative (TK-) HSV-1 replication in Vero cells. The cycloSal-ACVMP compounds exhibited high antiviral activity in HSV-1-infected cells. More importantly, one derivative retained all activity from the wild-type virus strain in HSV-1/TK(-)-infected Vero cells. The PCV derivatives were markedly less active. The reason for the failure of the cycloSal-PCVMPs seems to be due to the formation of cPCVMP instead of the desired PCVMP.
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Affiliation(s)
- C Meier
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Germany.
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