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Ziemniak M, Pawlędzio S, Zawadzka-Kaźmierczuk A, Dominiak PM, Trzybiński D, Koźmiński W, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B. X-ray wavefunction refinement and comprehensive structural studies on bromo-substituted analogues of 2-deoxy-d-glucose in solid state and solution. RSC Adv 2022; 12:8345-8360. [PMID: 35424802 PMCID: PMC8985090 DOI: 10.1039/d1ra08312k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/01/2022] [Accepted: 03/05/2022] [Indexed: 11/21/2022] Open
Abstract
The structural studies on two bromo-substituted derivatives of 2-deoxy-d-glucose (2-DG), namely 2-deoxy-2-bromo-d-glucose (2-BG) and 2-deoxy-2-bromo-d-mannose (2-BM) are described. 2-DG itself is an inhibitor of hexokinase, the first enzyme in the glycolysis process, playing a vital role in both cancer cell metabolism and viral replication in host cells. Because of that, 2-DG derivatives are considered as potential anti-cancer and anti-viral drugs. An X-ray quantum crystallography approach allowed us to obtain more accurate positions of hydrogen atoms by applying Hirshfeld atom refinement, providing a better description of hydrogen bonding even in the case of data from routine X-ray experiments. Obtained structures showed that the introduction of bromine at the C2 position in the pyranose ring has a minor influence on its conformation but still, it has a noticeable effect on the crystal structure. Bromine imposes the formation of a layered supramolecular landscape containing hydrogen bonds, which involves the bromine atom. Periodic DFT calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings and highlighted energetic changes upon bromine substitution. Based on molecular wavefunction from the refinement, we calculated the electrostatic potential, Laplacian, and ELI-D, and applied them to charge-density studies, which confirmed the geometry of hydrogen bonding and involvement of the bromine atom with these intermolecular interactions. NMR studies in the solution show that both compounds do not display significant differences in their anomeric equilibria compared to 2-DG, and the pyranose ring puckering is similar in both aqueous and solid state.
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Affiliation(s)
- Marcin Ziemniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Anna Zawadzka-Kaźmierczuk
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Paulina M Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Rafał Zieliński
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Izabela Fokt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Waldemar Priebe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center 1901 East Rd. Houston TX 77054 USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw Zwirki i Wigury 101 02-089 Warszawa Poland
| | - Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology Kozielska 4 01-163 Warsaw Poland
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2
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Ziemniak M, Zawadzka-Kazimierczuk A, Pawlędzio S, Malinska M, Sołtyka M, Trzybiński D, Koźmiński W, Skora S, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B. Experimental and Computational Studies on Structure and Energetic Properties of Halogen Derivatives of 2-Deoxy-D-Glucose. Int J Mol Sci 2021; 22:3720. [PMID: 33918425 PMCID: PMC8038202 DOI: 10.3390/ijms22073720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/01/2023] Open
Abstract
The results of structural studies on a series of halogen-substituted derivatives of 2-deoxy-D-glucose (2-DG) are reported. 2-DG is an inhibitor of glycolysis, a metabolic pathway crucial for cancer cell proliferation and viral replication in host cells, and interferes with D-glucose and D-mannose metabolism. Thus, 2-DG and its derivatives are considered as potential anticancer and antiviral drugs. X-ray crystallography shows that a halogen atom present at the C2 position in the pyranose ring does not significantly affect its conformation. However, it has a noticeable effect on the crystal structure. Fluorine derivatives exist as a dense 3D framework isostructural with the parent compound, while Cl- and I-derivatives form layered structures. Analysis of the Hirshfeld surface shows formation of hydrogen bonds involving the halogen, yet no indication for the existence of halogen bonds. Density functional theory (DFT) periodic calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings. NMR studies in the solution show that most of the compounds do not display significant differences in their anomeric equilibria, and that pyranose ring puckering is similar to the crystalline state. For 2-deoxy-2-fluoro-D-glucose (2-FG), electrostatic interaction energies between the ligand and protein for several existing structures of pyranose 2-oxidase were also computed. These interactions mostly involve acidic residues of the protein; single amino-acid substitutions have only a minor impact on binding. These studies provide a better understanding of the structural chemistry of halogen-substituted carbohydrates as well as their intermolecular interactions with proteins determining their distinct biological activity.
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Affiliation(s)
- Marcin Ziemniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Anna Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Maja Sołtyka
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland;
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Stanisław Skora
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Rafał Zieliński
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Izabela Fokt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Waldemar Priebe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland;
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Mestre J, Collado D, Benito-Alifonso D, Rodríguez MA, Matheu MI, Díaz Y, Castillón S, Boutureira O. Highly reactive 2-deoxy-2-iodo-d- allo and d- gulo pyranosyl sulfoxide donors ensure β-stereoselective glycosylations with steroidal aglycones. RSC Adv 2018; 8:30076-30079. [PMID: 35546863 PMCID: PMC9085402 DOI: 10.1039/c8ra06619a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/11/2018] [Indexed: 12/31/2022] Open
Abstract
The preparation of well-defined d-xylo and d-ribo glycosides represents a synthetic challenge due to the limited configurational availability of starting materials and the laborious synthesis of homogeneous 2-deoxy-β-glycosidic linkages, in particular that of the sugar-steroid motif, which represents the “stereoselective determining step” of the overall synthesis. Herein we describe the use of 2-deoxy-2-iodo-glycopyranosyl sulfoxides accessible from widely available d-xylose and d-ribose monosaccharides as privileged glycosyl donors that permit activation at very low temperature. This ensures a precise kinetic control for a complete 1,2-trans stereoselective glycosylation of particularly challenging steroidal aglycones. Highly stereoselective synthesis of challenging steroidal 2-deoxy-β-glycosides with d-xylo and d-ribo configurations enabled by low temperature activation of 2-deoxy-2-iodoglycopyranosyl sulfoxides.![]()
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Affiliation(s)
- Jordi Mestre
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
| | - David Collado
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
| | - David Benito-Alifonso
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
| | - Miguel A Rodríguez
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
| | - M Isabel Matheu
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
| | - Yolanda Díaz
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
| | - Sergio Castillón
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
| | - Omar Boutureira
- Departament de Química Analítica i Química Orgànica, Universitat Rovira i Virgili C/Marcel·lí Domingo 1 43007 Tarragona Spain
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Rasool F, Bhat AH, Hussain N, Mukherjee D. Reaction of Glycals with Organic Peroxides: Synthesis of 2-iodo, 2-Deoxy and 2,3-Unsaturated Glycosides. ChemistrySelect 2016. [DOI: 10.1002/slct.201601849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Faheem Rasool
- Natural Product Chemistry- Miocrobes; Indian Institute of Integrative Medicine (CSIR); Jammu- 180001
- Academy of Scientific and Innovative Research; New Delhi India
| | - Aabid H. Bhat
- Natural Product Chemistry- Miocrobes; Indian Institute of Integrative Medicine (CSIR); Jammu- 180001
| | - Nazar Hussain
- Natural Product Chemistry- Miocrobes; Indian Institute of Integrative Medicine (CSIR); Jammu- 180001
- Academy of Scientific and Innovative Research; New Delhi India
| | - Debaraj Mukherjee
- Natural Product Chemistry- Miocrobes; Indian Institute of Integrative Medicine (CSIR); Jammu- 180001
- Academy of Scientific and Innovative Research; New Delhi India
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5
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Kimura T, Takahashi D, Toshima K. Glycosylations of Glycals using N-Iodosuccinimide (NIS) and Phosphorus Compounds for Syntheses of 2-Iodo- and 2-Deoxyglycosides. J Org Chem 2015; 80:9552-62. [PMID: 26375399 DOI: 10.1021/acs.joc.5b01542] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The glycosylations of glycals and alcohols using N-iodosuccinimide (NIS) and a catalytic amount of PPh3 effectively proceeded under mild conditions to provide the corresponding 2-deoxy-2-iodoglycosides in high yields. The reactivity of the iodoglycosylations with PPh3 significantly increased in comparison to that using NIS alone as an activator. In addition, the glycosylations of glycals and alcohols using catalytic amounts of NIS and P(OPh)3 were effectively realized to give the corresponding 2-deoxyglycosides in high yields.
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Affiliation(s)
- Tomoya Kimura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University , 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Daisuke Takahashi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University , 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kazunobu Toshima
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University , 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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6
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Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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Liu H, Li X. A Stereoselective Ring-Closing Glycosylation via Nonglycosylating Pathway. J Org Chem 2014; 79:5834-41. [DOI: 10.1021/jo5006763] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Han Liu
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, PR China
| | - Xuechen Li
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, PR China
- State
Key Laboratory of Synthetic Chemistry, University of Hong Kong, Hong Kong, PR China
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8
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Kövér A, Boutureira O, Matheu MI, Díaz Y, Castillón S. Tuning the Stereoelectronic Properties of 1-Sulfanylhex-1-enitols for the Sequential Stereoselective Synthesis of 2-Deoxy-2-iodo-β-d-allopyranosides. J Org Chem 2014; 79:3060-8. [DOI: 10.1021/jo5001912] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Andrea Kövér
- Departament
de Química
Analítica i Química Orgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Omar Boutureira
- Departament
de Química
Analítica i Química Orgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - M. Isabel Matheu
- Departament
de Química
Analítica i Química Orgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Yolanda Díaz
- Departament
de Química
Analítica i Química Orgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
| | - Sergio Castillón
- Departament
de Química
Analítica i Química Orgànica, Universitat Rovira i Virgili, C/Marcel·lí Domingo s/n, 43007 Tarragona, Spain
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9
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2013. [DOI: 10.1016/s0040-4020(13)01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Stereoselective total synthesis of Jaspine B (Pachastrissamine) utilizing iodocyclization and an investigation of its cytotoxic activity. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.tetasy.2013.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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The synthesis of 2-deoxy-α-d-glycosides from d-glycals catalyzed by TMSI and PPh3. Carbohydr Res 2012; 358:19-22. [DOI: 10.1016/j.carres.2012.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 05/05/2012] [Accepted: 06/04/2012] [Indexed: 11/18/2022]
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12
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Feng XE, Zhao WY, Ban SR, Zhao CX, Li QS, Lin WH. Structure-activity relationship of halophenols as a new class of protein tyrosine kinase inhibitors. Int J Mol Sci 2011; 12:6104-15. [PMID: 22016647 PMCID: PMC3189771 DOI: 10.3390/ijms12096104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 01/15/2023] Open
Abstract
A series of new benzophenone and diphenylmethane halophenol derivatives were prepared. Their structures were established based on (1)H NMR, (13)C NMR and HRMS data. All prepared compounds were screened for their in vitro protein tyrosine kinase (PTK) inhibitory activities. The effects of modification of the linker, functional groups and substituted positions at the phenyl ring on PTK inhibitory activity were investigated. Twelve halophenols showed significant PTK inhibitory activity. Among them, compounds 6c, 6d, 7d, 9d, 10d, 11d and 13d exhibited stronger activities than that of genistein, the positive reference compound. The results gave a relatively full and definite description of the structure-activity relationship and provided a foundation for further design and structure optimization of the halophenols.
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Affiliation(s)
- Xiu E. Feng
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Wan Yi Zhao
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
| | - Shu Rong Ban
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
| | - Cheng Xiao Zhao
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
| | - Qing Shan Li
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan 030001, Shanxi, China; E-Mails: (X.E.F.); (W.Y.Z.); (S.R.B.); (C.X.Z.)
- School of Public Health, Shanxi Medical University, Taiyuan 030001, Shanxi, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China; E-Mail:
| | - Wen Han Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100083, China; E-Mail:
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13
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2011. [DOI: 10.1016/s0040-4020(11)00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2010. [DOI: 10.1016/s0040-4020(10)01735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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