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Scior T, Cuanalo-Contreras K, Islas AA, Martinez-Laguna Y. Targeting the Human Influenza a Virus: The Methods, Limitations, and Pitfalls of Virtual Screening for Drug-like Candidates Including Scaffold Hopping and Compound Profiling. Viruses 2023; 15:v15051056. [PMID: 37243142 DOI: 10.3390/v15051056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
In this study, we describe the input data and processing steps to find antiviral lead compounds by a virtual screen. Two-dimensional and three-dimensional filters were designed based on the X-ray crystallographic structures of viral neuraminidase co-crystallized with substrate sialic acid, substrate-like DANA, and four inhibitors (oseltamivir, zanamivir, laninamivir, and peramivir). As a result, ligand-receptor interactions were modeled, and those necessary for binding were utilized as screen filters. Prospective virtual screening (VS) was carried out in a virtual chemical library of over half a million small organic substances. Orderly filtered moieties were investigated based on 2D- and 3D-predicted binding fingerprints disregarding the "rule-of-five" for drug likeness, and followed by docking and ADMET profiling. Two-dimensional and three-dimensional screening were supervised after enriching the dataset with known reference drugs and decoys. All 2D, 3D, and 4D procedures were calibrated before execution, and were then validated. Presently, two top-ranked substances underwent successful patent filing. In addition, the study demonstrates how to work around reported VS pitfalls in detail.
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Affiliation(s)
- Thomas Scior
- Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Colonia San Manuel, Puebla 72570, Mexico
| | - Karina Cuanalo-Contreras
- Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Colonia San Manuel, Puebla 72570, Mexico
| | - Angel A Islas
- Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Colonia San Manuel, Puebla 72570, Mexico
- Vicerrectoría de Investigación y Estudios de Posgrado, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico
| | - Ygnacio Martinez-Laguna
- Vicerrectoría de Investigación y Estudios de Posgrado, Benemérita Universidad Autónoma de Puebla, Puebla 72592, Mexico
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2
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Yadav Y, Tyagi R, Kumar R, Sagar R. Conformationally locked sugar derivatives and analogues as potential neuraminidase inhibitors. Eur J Med Chem 2023; 255:115410. [PMID: 37120995 DOI: 10.1016/j.ejmech.2023.115410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/13/2023] [Accepted: 04/21/2023] [Indexed: 05/02/2023]
Abstract
The influenza virus remains a major health concern for mankind because it tends to mutate frequently and cause high morbidity. Influenza prevention and treatment are greatly aided by the use of antivirals. One such class of antivirals is neuraminidase inhibitors (NAIs), effective against influenza viruses. A neuraminidase on the virus's surface serves a vital function in viral propogation by assisting in the release of viruses from infected host cells. Neuraminidase inhibitors are the backbone in stoping such virus propagation thus helps in the treatment of influenza viruses infections. Two NAI medicines are licensed globally: Oseltamivir (Tamiflu™) and Zanamivir (Relanza™). There are two molecules that have acquired Japanese approval recently: Peramivir and Laninamivir, whereas Laninamivir octanoate is in Phase III clinical trials. The need for novel NAIs is due to frequent mutations in viruses and the rise in resistance against existing medication. The NA inhibitors (NAIs) are designed to have (oxa)cyclohexene scaffolds (a sugar scaffold) to mimic the oxonium transition state in the enzymatic cleavage of sialic acid. This review discusses in details and comprises all such conformationally locked (oxa)cyclohexene scaffolds and their analogues which have been recently designed and synthesized as potential neuraminidase inhibitors, thus as antiviral molecules. The structure-activity relationship of such diverese molecules has also been discussed in this review.
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Affiliation(s)
- Yogesh Yadav
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rajdeep Tyagi
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ramesh Kumar
- Department of Chemistry, Kurukshetra University Kurukshetra, Haryana, 136119, India
| | - Ram Sagar
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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3
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Li SJ, Jiao FW, Li W, Zhang X, Yan W, Jiao RH. Cytotoxic Xanthone Derivatives from the Mangrove-Derived Endophytic Fungus Peniophora incarnata Z4. JOURNAL OF NATURAL PRODUCTS 2020; 83:2976-2982. [PMID: 32975117 DOI: 10.1021/acs.jnatprod.0c00523] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The mangrove-derived endophytic fungus Peniophora incarnata Z4 produced seven new xanthone derivatives, including four new tetrahydroxanthones (1-4), one new chromone (5), one new xanthone (6), and one new xanthone dimer (7), together with one known compound, globosuxanthone B (8). Their structures were determined by an extensive analysis of 1D and 2D NMR, HRESIMS, ECD, and single-crystal X-ray diffraction data. In cytotoxic activity assays, compound 2 showed cytotoxicity against three carcinoma cell lines with IC50 values less than 10 μM.
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Affiliation(s)
- Sui Jun Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Fang Wen Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wei Li
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xuan Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wei Yan
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing 210023, China
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4
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Water plays a crucial role: Small molecule catalyzed C–C/C–X bond forming reactions using organosilicon reagents under “wet” conditions. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131254] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Limbani B, Bera S, Mondal D. Synthetic Advancement of Neuraminidase Inhibitor “Tamiflu”. ChemistrySelect 2020. [DOI: 10.1002/slct.202000675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Bhagirath Limbani
- School of Chemical Sciences Central University of Gujarat Gandhinagar, Gujarat 382030 India
| | - Smritilekha Bera
- School of Chemical Sciences Central University of Gujarat Gandhinagar, Gujarat 382030 India
| | - Dhananjoy Mondal
- School of Chemical Sciences Central University of Gujarat Gandhinagar, Gujarat 382030 India
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6
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Curti C, Battistini L, Sartori A, Zanardi F. New Developments of the Principle of Vinylogy as Applied to π-Extended Enolate-Type Donor Systems. Chem Rev 2020; 120:2448-2612. [PMID: 32040305 PMCID: PMC7993750 DOI: 10.1021/acs.chemrev.9b00481] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 12/19/2022]
Abstract
The principle of vinylogy states that the electronic effects of a functional group in a molecule are possibly transmitted to a distal position through interposed conjugated multiple bonds. As an emblematic case, the nucleophilic character of a π-extended enolate-type chain system may be relayed from the legitimate α-site to the vinylogous γ, ε, ..., ω remote carbon sites along the chain, provided that suitable HOMO-raising strategies are adopted to transform the unsaturated pronucleophilic precursors into the reactive polyenolate species. On the other hand, when "unnatural" carbonyl ipso-sites are activated as nucleophiles (umpolung), vinylogation extends the nucleophilic character to "unnatural" β, δ, ... remote sites. Merging the principle of vinylogy with activation modalities and concepts such as iminium ion/enamine organocatalysis, NHC-organocatalysis, cooperative organo/metal catalysis, bifunctional organocatalysis, dicyanoalkylidene activation, and organocascade reactions represents an impressive step forward for all vinylogous transformations. This review article celebrates this evolutionary progress, by collecting, comparing, and critically describing the achievements made over the nine year period 2010-2018, in the generation of vinylogous enolate-type donor substrates and their use in chemical synthesis.
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Affiliation(s)
| | | | | | - Franca Zanardi
- Dipartimento di Scienze degli
Alimenti e del Farmaco, Università
di Parma, Parco Area delle Scienze 27A, 43124 Parma, Italy
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7
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Poláčková V, Šándrik R, Šebesta R. Synthesis of sulfone analog of oseltamivir precursor. CHEMICAL PAPERS 2018. [DOI: 10.1007/s11696-017-0274-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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9
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Lin X, Qin-Hua C, Peng L, Chun-Lei L, Guang-De Y. The hydrophobic side chain of oseltamivir influences type A subtype selectivity of neuraminidase inhibitors. Chem Biol Drug Des 2017. [PMID: 28646621 DOI: 10.1111/cbdd.13060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neuraminidase, which plays a critical role in the influenza virus life cycle, is a target for new therapeutic agents. The study of structure-activity relationships revealed that the C-5 position amino group of oseltamivir was pointed to 150-cavity of the neuraminidase in group 1. This cavity is important for selectivity of inhibitors against N1 versus N2 NA. A serial of influenza neuraminidase inhibitors with the oseltamivir scaffold containing lipophilic side chains at the C-5 position have been synthesized and evaluated for their influenza neuraminidase inhibitory activity and selectivity. The results indicated that compound 13o (H5N1 IC50 = 0.1 ± 0.04 μm, H3N2 IC50 = 0.26 ± 0.18 μm) showed better inhibitory activity and selectivity against the group 1 neuraminidase. This study may provide a clue to design of better group 1 neuraminidase inhibitors.
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Affiliation(s)
- Xiong Lin
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Affiliated Dongfeng Hospital, Hubei University of Medicine, Hubei, China
| | - Chen Qin-Hua
- Affiliated Dongfeng Hospital, Hubei University of Medicine, Hubei, China
| | - Li Peng
- Affiliated Dongfeng Hospital, Hubei University of Medicine, Hubei, China
| | - Li Chun-Lei
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China.,Affiliated Dongfeng Hospital, Hubei University of Medicine, Hubei, China
| | - Yang Guang-De
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, China
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10
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Hajzer V, Fišera R, Latika A, Durmis J, Kollár J, Frecer V, Tučeková Z, Miertuš S, Kostolanský F, Varečková E, Šebesta R. Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation. Org Biomol Chem 2017; 15:1828-1841. [DOI: 10.1039/c6ob02673g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Three diastereoisomers of oseltamivir were synthesized, their properties predicted by quantum-chemical calculations and their antiviral activities evaluated.
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Affiliation(s)
| | | | | | | | - Jakub Kollár
- Comenius University in Bratislava
- Faculty of Pharmacy
- Department of Pharmaceutical Analysis and Nuclear Pharmacy
- SK-83232 Bratislava
- Slovakia
| | - Vladimír Frecer
- Comenius University in Bratislava
- Faculty of Pharmacy
- Department of Physical Chemistry of Drugs
- SK-83232 Bratislava
- Slovakia
| | - Zuzana Tučeková
- University of SS. Cyril and Methodius
- Faculty of Natural Sciences
- Department of Biotechnologies
- SK-91701 Trnava
- Slovakia
| | - Stanislav Miertuš
- ICARST n.o
- SK-84104 Bratislava
- Slovakia
- University of SS. Cyril and Methodius
- Faculty of Natural Sciences
| | - František Kostolanský
- Biomedical Research Center
- Institute of Virology
- Slovak Academy of Sciences
- Department of Orthomyxovirus Research
- SK-84505 Bratislava
| | - Eva Varečková
- Biomedical Research Center
- Institute of Virology
- Slovak Academy of Sciences
- Department of Orthomyxovirus Research
- SK-84505 Bratislava
| | - Radovan Šebesta
- Comenius University in Bratislava
- Faculty of Natural Sciences
- Department of Organic Chemistry
- SK-84215 Bratislava
- Slovakia
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11
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Laborda P, Wang SY, Voglmeir J. Influenza Neuraminidase Inhibitors: Synthetic Approaches, Derivatives and Biological Activity. Molecules 2016; 21:E1513. [PMID: 27845731 PMCID: PMC6274581 DOI: 10.3390/molecules21111513] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 11/16/2022] Open
Abstract
Despite being a common viral disease, influenza has very negative consequences, causing the death of around half a million people each year. A neuraminidase located on the surface of the virus plays an important role in viral reproduction by contributing to the release of viruses from infected host cells. The treatment of influenza is mainly based on the administration of neuraminidase inhibitors. The neuraminidase inhibitors zanamivir, laninamivir, oseltamivir and peramivir have been commercialized and have been demonstrated to be potent influenza viral neuraminidase inhibitors against most influenza strains. In order to create more potent neuraminidase inhibitors and fight against the surge in resistance resulting from naturally-occurring mutations, these anti-influenza drugs have been used as templates for the development of new neuraminidase inhibitors through structure-activity relationship studies. Here, we review the synthetic routes to these commercial drugs, the modifications which have been performed on these structures and the effects of these modifications on their inhibitory activity.
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Affiliation(s)
- Pedro Laborda
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.
| | - Su-Yan Wang
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center, College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China.
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12
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13
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Ye JL, Chen H, Zhang YF, Huang PQ. A versatile access to vicinal diamine motifs by highly anti-selective asymmetric vinylogous Mannich reactions: an efficient total synthesis of (+)-absouline. Org Chem Front 2016. [DOI: 10.1039/c6qo00022c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An anti-stereoselective vinylogous Mannich reaction between 2-TBSO-pyrrole and N-tert-butanesulfinyl imines and its application to the efficient synthesis of (+)-absouline were reported.
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Affiliation(s)
- Jian-Liang Ye
- Department of Chemistry and Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
| | - Hang Chen
- Department of Chemistry and Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
| | - Yu-Feng Zhang
- Department of Chemistry and Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
| | - Pei-Qiang Huang
- Department of Chemistry and Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
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14
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Wade Downey C, Ingersoll JA, Glist HM, Dombrowski CM, Barnett AT. One-Pot Silyl Ketene Acetal-Formation Mukaiyama-Mannich Additions to Imines Mediated by Trimethylsilyl Trifluoromethanesulfonate. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500958] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Just J, Deans BJ, Olivier WJ, Paull B, Bissember AC, Smith JA. New Method for the Rapid Extraction of Natural Products: Efficient Isolation of Shikimic Acid from Star Anise. Org Lett 2015; 17:2428-30. [DOI: 10.1021/acs.orglett.5b00936] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jeremy Just
- School of Physical Sciences
− Chemistry and ‡Australian Centre for Research on
Separation Science (ACROSS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Bianca J. Deans
- School of Physical Sciences
− Chemistry and ‡Australian Centre for Research on
Separation Science (ACROSS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Wesley J. Olivier
- School of Physical Sciences
− Chemistry and ‡Australian Centre for Research on
Separation Science (ACROSS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Brett Paull
- School of Physical Sciences
− Chemistry and ‡Australian Centre for Research on
Separation Science (ACROSS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Alex C. Bissember
- School of Physical Sciences
− Chemistry and ‡Australian Centre for Research on
Separation Science (ACROSS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Jason A. Smith
- School of Physical Sciences
− Chemistry and ‡Australian Centre for Research on
Separation Science (ACROSS), University of Tasmania, Hobart, Tasmania 7001, Australia
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16
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Ye JL, Zhang YF, Liu Y, Zhang JY, Ruan YP, Huang PQ. Studies on the asymmetric synthesis of pandamarilactonines: an unexpected syn-selective vinylogous Mannich reaction of N-tert-butanesulfinimines. Org Chem Front 2015. [DOI: 10.1039/c5qo00098j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Through an unanticipatedsyn-selective VMR, a highly enantioselective total synthesis of (−)-pandamarilactonine-A has been achieved.
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Affiliation(s)
- Jian-Liang Ye
- Department of Chemistry
- Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Yu-Feng Zhang
- Department of Chemistry
- Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Yang Liu
- Department of Chemistry
- Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Jin-Yuan Zhang
- Department of Chemistry
- Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Yuan-Ping Ruan
- Department of Chemistry
- Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Pei-Qiang Huang
- Department of Chemistry
- Fujian Provincial Key Laboratory of Chemical Biology
- iChEM (Collaborative Innovation Center of Chemistry for Energy Materials)
- College of Chemistry and Chemical Engineering
- Xiamen University
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17
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A short synthetic pathway via three-component coupling reaction to tamiphosphor possessing anti-influenza activity. Tetrahedron 2015. [DOI: 10.1016/j.tet.2014.11.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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