1
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Mathez G, Cagno V. Small Molecules Targeting Viral RNA. Int J Mol Sci 2023; 24:13500. [PMID: 37686306 PMCID: PMC10487773 DOI: 10.3390/ijms241713500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The majority of antivirals available target viral proteins; however, RNA is emerging as a new and promising antiviral target due to the presence of highly structured RNA in viral genomes fundamental for their replication cycle. Here, we discuss methods for the identification of RNA-targeting compounds, starting from the determination of RNA structures either from purified RNA or in living cells, followed by in silico screening on RNA and phenotypic assays to evaluate viral inhibition. Moreover, we review the small molecules known to target the programmed ribosomal frameshifting element of SARS-CoV-2, the internal ribosomal entry site of different viruses, and RNA elements of HIV.
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Affiliation(s)
| | - Valeria Cagno
- Institute of Microbiology, University Hospital of Lausanne, University of Lausanne, 1011 Lausanne, Switzerland
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2
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Nizi MG, Persoons L, Corona A, Felicetti T, Cernicchi G, Massari S, Manfroni G, Vangeel L, Barreca ML, Esposito F, Jochmans D, Milia J, Cecchetti V, Schols D, Neyts J, Tramontano E, Sabatini S, De Jonghe S, Tabarrini O. Discovery of 2-Phenylquinolines with Broad-Spectrum Anti-coronavirus Activity. ACS Med Chem Lett 2022; 13:855-864. [PMID: 35571875 PMCID: PMC9088073 DOI: 10.1021/acsmedchemlett.2c00123] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
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A selection of compounds
from a proprietary library, based on chemical
diversity and various biological activities, was evaluated as potential
inhibitors of the Severe Acute Respiratory Syndrome Coronavirus 2
(SARS-CoV-2) in a phenotypic-based screening assay. A compound based
on a 2-phenylquinoline scaffold emerged as the most promising
hit, with EC50 and CC50 values of 6 and 18 μM,
respectively. The subsequent selection of additional analogues, along
with the synthesis of ad hoc derivatives, led to compounds that maintained
low μM activity as inhibitors of SARS-CoV-2 replication and
lacked cytotoxicity at 100 μM. In addition, the most promising
congeners also show pronounced antiviral activity against the human
coronaviruses HCoV-229E and HCoV-OC43, with EC50 values
ranging from 0.2 to 9.4 μM. The presence of a 6,7-dimethoxytetrahydroisoquinoline
group at the C-4 position of the 2-phenylquinoline core gave
compound 6g that showed potent activity against SARS-CoV-2
helicase (nsp13), a highly conserved enzyme, highlighting a potentiality
against emerging HCoVs outbreaks.
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Affiliation(s)
- Maria Giulia Nizi
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Leentje Persoons
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Giada Cernicchi
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Serena Massari
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Laura Vangeel
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | | | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Dirk Jochmans
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jessica Milia
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Dominique Schols
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
| | - Steven De Jonghe
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
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3
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Ritu, Kumar S, Chauhan P, Jain N. Photoredox halogenation of quinolones: the dual role of halo-fluorescein dyes. Org Biomol Chem 2021; 19:4585-4592. [PMID: 33955445 DOI: 10.1039/d1ob00538c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An efficient C-3 halogenation of quinolin-4-ones is reported with halogenated fluorescein dyes which serve both as a halogen source and photocatalyst. This reaction shows broad substrate scope and gives good to excellent yields of C-3 brominated/iodinated quinolones with eosin Y/rose bengal in green light under ambient conditions. The mechanistic investigations suggest a radical pathway involving the oxidative dehalogenation of the dye in the presence of air.
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Affiliation(s)
- Ritu
- Department of Chemistry, Indian Institute of Technology, New Delhi-110016, India.
| | - Sharvan Kumar
- Department of Chemistry, Indian Institute of Technology, New Delhi-110016, India.
| | - Parul Chauhan
- Department of Chemistry, Indian Institute of Technology, New Delhi-110016, India.
| | - Nidhi Jain
- Department of Chemistry, Indian Institute of Technology, New Delhi-110016, India.
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4
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Shantharjun B, Rajeswari R, Vani D, Unnava R, Sridhar B, Reddy KR. Metal‐Free, One‐Pot Oxidative Triple Functionalization of Azaarenes with Methyl Arenes Mediated by Molecular Iodine/TBHP: Synthesis of N‐Benzylated Iodo(iso)quinolinones. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bangarigalla Shantharjun
- Catalysis and Fine Chemicals DivisionCSIR- Indian Institute of Chemical Technology Tarnaka Hyderabad- 500007 India
- Academy of Scientific and Innovative Research New Delhi- 110025 India
| | - Radhakrishnan Rajeswari
- Catalysis and Fine Chemicals DivisionCSIR- Indian Institute of Chemical Technology Tarnaka Hyderabad- 500007 India
| | - Damera Vani
- Catalysis and Fine Chemicals DivisionCSIR- Indian Institute of Chemical Technology Tarnaka Hyderabad- 500007 India
- Academy of Scientific and Innovative Research New Delhi- 110025 India
| | - Ramanjaneyulu Unnava
- Catalysis and Fine Chemicals DivisionCSIR- Indian Institute of Chemical Technology Tarnaka Hyderabad- 500007 India
| | - Balasubramanian Sridhar
- X-ray Crystallography DivisionCSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad- 500007 India
| | - Kallu Rajender Reddy
- Catalysis and Fine Chemicals DivisionCSIR- Indian Institute of Chemical Technology Tarnaka Hyderabad- 500007 India
- Academy of Scientific and Innovative Research New Delhi- 110025 India
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5
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Wang R, Xu K, Shi W. Quinolone derivatives: Potential anti‐HIV agent—development and application. Arch Pharm (Weinheim) 2019; 352:e1900045. [DOI: 10.1002/ardp.201900045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/28/2019] [Accepted: 05/01/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Ruo Wang
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Kai Xu
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
| | - Weixiong Shi
- College of ChemistryFuzhou University Fuzhou Fujian People's Republic of China
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6
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Chauhan P, Ritu, Preeti, Kumar S, Jain N. Metal-Free and Visible-Light-Promoted C-3 Thiocyanation of 2-Arylquinolin-4-ones. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Parul Chauhan
- Department of Chemistry; Indian Institute of Technology; -110016 New Delhi India
| | - Ritu
- Department of Chemistry; Indian Institute of Technology; -110016 New Delhi India
| | - Preeti
- Department of Chemistry; Indian Institute of Technology; -110016 New Delhi India
| | - Sharvan Kumar
- Department of Chemistry; Indian Institute of Technology; -110016 New Delhi India
| | - Nidhi Jain
- Department of Chemistry; Indian Institute of Technology; -110016 New Delhi India
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7
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Desantis J, Massari S, Sosic A, Manfroni G, Cannalire R, Felicetti T, Pannecouque C, Gatto B, Tabarrini O. Design and Synthesis of WM5 Analogues as HIV-1 TAR RNA Binders. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2019. [DOI: 10.2174/1874104501913010016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The 6-aminoquinolone WM5, previously identified by us, is among the most selective small molecules known as TAR RNA binders to show anti-HIV activity.
Methods:
Starting from WM5, a series of analogues modified at N-1, C-6 or C-7 position was prepared by inserting guanidine or amidine groups as well as other protonable moieties intended to electrostatically bind the phosphate backbone of TAR. All the compounds were tested for their ability to inhibit HIV-1 replication in MT-4 cells and in parallel for their cytotoxicity. The active compounds were also evaluated for their ability to interfere with the formation of the Tat-TAR complex using a Fluorescence Quenching Assay (FQA).
Results:
Some of the synthesized compounds showed an anti-HIV-1 activity in the sub-micromolar range with the naphthyridone derivatives being the most potent. Three of the synthesized derivatives were able to interact with the Tat-TAR complex formation presenting Ki values improved as compared to the values obtained with WM5.
Conclusion:
The addition of a pyridine-based protonable side chain at the N-1 position of the quinolone/naphthyridone core imparted to the compounds the ability to interfere with Tat-TAR complex formation and HIV-1 replication.
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8
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Synthesis, alkaline phosphatase inhibition studies and molecular docking of novel derivatives of 4-quinolones. Eur J Med Chem 2017; 126:408-420. [DOI: 10.1016/j.ejmech.2016.11.036] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 11/17/2022]
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9
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Seixas RSGR, Almeida AIS, Pereira SIG, Cavaleiro JAS, Silva AMS. Diastereoselective syntheses of (Z)- and (E)-3-styrylquinolin-4(1H)-ones. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-014-1263-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Ranjan N, Kumar S, Watkins D, Wang D, Appella DH, Arya DP. Recognition of HIV-TAR RNA using neomycin-benzimidazole conjugates. Bioorg Med Chem Lett 2013; 23:5689-93. [PMID: 24012122 PMCID: PMC4048829 DOI: 10.1016/j.bmcl.2013.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
Synthesis of a novel class of compounds and their biophysical studies with TAR-RNA are presented. The synthesis of these compounds was achieved by conjugating neomycin, an aminoglycoside, with benzimidazoles modeled from a B-DNA minor groove binder, Hoechst 33258. The neomycin-benzimidazole conjugates have varying linkers that connect the benzimidazole and neomycin units. The linkers of varying length (5-23 atoms) in these conjugates contain one to three triazole units. The UV thermal denaturation experiments showed that the conjugates resulted in greater stabilization of the TAR-RNA than either neomycin or benzimidazole used in the synthesis of conjugates. These results were corroborated by the FID displacement and tat-TAR inhibition assays. The binding of ligands to the TAR-RNA is affected by the length and composition of the linker. Our results show that increasing the number of triazole groups and the linker length in these compounds have diminishing effect on the binding to TAR-RNA. Compounds that have shorter linker length and fewer triazole units in the linker displayed increased affinity towards the TAR RNA.
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Affiliation(s)
- Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
| | - Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
| | - Derrick Watkins
- NUBAD LLC, 900 B West Faris Road, Greenville, SC 29630, United States
| | - Deyun Wang
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health,Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health,Bethesda, Maryland 20892, United States
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina , United States 29634
- NUBAD LLC, 900 B West Faris Road, Greenville, SC 29630, United States
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11
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Sosic A, Frecentese F, Perissutti E, Sinigaglia L, Santagada V, Caliendo G, Magli E, Ciano A, Zagotto G, Parolin C, Gatto B. Design, synthesis and biological evaluation of TAR and cTAR binders as HIV-1 nucleocapsid inhibitors. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00212h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Warui DM, Baranger AM. Identification of small molecule inhibitors of the HIV-1 nucleocapsid-stem-loop 3 RNA complex. J Med Chem 2012; 55:4132-41. [PMID: 22480197 DOI: 10.1021/jm2007694] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Stem-loop 3 RNA (SL3) in ψ-RNA is a highly conserved motif in different strains of HIV-1 and serves as a principle determinant for viral packaging. Viral encapsulation is critical for viral replication, and disruption of the nucleocapsid-ψ-RNA complex interferes with viral replication. We have used SL3 RNA as a target for identification of small molecule inhibitors of the interactions of nucleocapsid protein (NCp7) and ψ-RNA. We report the use of computational and high-throughput screening approaches to identify 16 compounds that bind SL3 RNA with micromolar affinities. Among the identified ligands, two molecules, compounds 7 and 17, bind with higher affinity to SL3 RNA than to double- and single-stranded RNAs. Four of the 16 SL3 RNA ligands inhibit interactions between SL3 RNA and NCp7 with micromolar inhibition constants. In general, the identified SL3 ligands have simple molecular structures and low molecular weights and are, therefore, possible lead compounds for the development of ligands that target the elements of ψ-RNA of HIV-1 with high affinity and specificity.
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Affiliation(s)
- Douglas M Warui
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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13
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Victoriano AFB, Okamoto T. Transcriptional control of HIV replication by multiple modulators and their implication for a novel antiviral therapy. AIDS Res Hum Retroviruses 2012; 28:125-38. [PMID: 22077140 DOI: 10.1089/aid.2011.0263] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Transcriptional regulation is critical for the human immunodeficiency virus 1 (HIV-1) life cycle and is the only step at which the virus amplifies the content of its genetic information. Numerous known and still unknown transcriptional factors, both host and viral, regulate HIV-1 gene expression and latency. This article is a comprehensive review of transcription factors involved in HIV-1 gene expression and presents the significant implications of nuclear factor kappa B (NF-κB) and the HIV-1 transactivator of transcription (Tat) protein. We include recent findings on chromatin remodeling toward HIV transcription and its therapeutic implication is also discussed. The current status of small-molecular-weight compounds that affect HIV transcription is also described.
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Affiliation(s)
- Ann Florence B. Victoriano
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School for Medical Sciences, Nagoya, Japan
- Japanese Foundation for AIDS Prevention, Tokyo, Japan
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School for Medical Sciences, Nagoya, Japan
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14
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Abstract
The current anti-HIV treatments fail to completely eradicate the virus in HIV-infected individuals, mainly as a result of a small pool of latently infected cells. This issue, together with the emergence of multidrug-resistant viruses, clearly highlights the need to find additional strategies. An overview of the Tat-mediated transcription inhibitors 6-desfluoroquinolones (6-DFQs), identified by our group, is given in this review along with a critical appraisal of their advantages and drawbacks. Attempts are also made to place them within the context of new potential anti-HIV therapeutics. Due to their innovative mechanism of action, the 6-DFQs could be interesting candidates for use in association with the currently used cocktail of drugs. Their potential as antivirals deserves further investigation.
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Gianoncelli A, Basili S, Scalabrin M, Sosic A, Moro S, Zagotto G, Palumbo M, Gresh N, Gatto B. Rational Design, Synthesis, and DNA Binding Properties of Novel Sequence-Selective Peptidyl Congeners of Ametantrone. ChemMedChem 2010; 5:1080-91. [DOI: 10.1002/cmdc.201000106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Heterocyclic analogs of thioflavones: synthesis and NMR spectroscopic investigations. Molecules 2009; 14:3814-32. [PMID: 19783958 PMCID: PMC6255036 DOI: 10.3390/molecules14093814] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 09/11/2009] [Accepted: 09/21/2009] [Indexed: 12/02/2022] Open
Abstract
The synthesis of several hitherto unknown heterocyclic ring systems derived from thioflavone is described. Coupling of various o-haloheteroarenecarbonyl chlorides with phenylacetylene gives 1-(o-haloheteroaryl)-3-phenylprop-2-yn-1-ones, which were treated with NaSH in refluxing ethanol to yield the corresponding bi- and tricyclic annelated 2-phenylthiopyran-4-ones. Detailed NMR spectroscopic investigations of the ring systems and their precursors are presented.
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