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Wall BJ, Sharma KK, O’Brien EA, Donovan A, VanVeller B. General Installation of (4 H)-Imidazolone cis-Amide Bioisosteres Along the Peptide Backbone. J Am Chem Soc 2024; 146:11648-11656. [PMID: 38629317 PMCID: PMC11062833 DOI: 10.1021/jacs.3c13825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Imidazolones represent an important class of heterocycles present in a wide range of pharmaceuticals, metabolites, and bioactive natural products and serve as the active chromophore in green fluorescent protein. Recently, imidazolones have received attention for their ability to act as a nonaromatic amide bond bioisotere which improves pharmacological properties. Herein, we present a tandem amidine installation and cyclization with an adjacent ester to yield (4H)-imidazolone products. Using amino acid building blocks, we can access the first examples of α-chiral imidazolones that have been previously inaccessible. Additionally, our method is amenable to on-resin installation which can be seamlessly integrated into existing solid-phase peptide synthesis protocols. Finally, we show that peptide imidazolones are potent cis-amide bond surrogates that preorganize linear peptides for head-to-tail macrocyclization. This work represents the first general approach to the backbone and side-chain insertion of imidazolone bioisosteres at various positions in linear and cyclic peptides.
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Affiliation(s)
- Brendan J. Wall
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | | | | | - Aaron Donovan
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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2
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Byerly-Duke J, O'Brien EA, Wall BJ, VanVeller B. Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres. Methods Enzymol 2024; 698:27-55. [PMID: 38886036 DOI: 10.1016/bs.mie.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them. The first robust and general procedure for the introduction of amidines into peptide backbones exploits the utility of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. Further, amidines formed on-resin can be reacted to form (4H)-imidazolone heteorcycles which have recently been shown to act as cis-amide isosteres. General methods for heterocyclic installation capable of geometrically restricting peptide conformation are also under-developed. This work is significant because it describes a generally applicable and divergent approach to access unexplored peptide designs and architectures.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Emily A O'Brien
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brendan J Wall
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, IA, United States.
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3
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Lindberg MF, Deau E, Miege F, Greverie M, Roche D, George N, George P, Merlet L, Gavard J, Brugman SJT, Aret E, Tinnemans P, de Gelder R, Sadownik J, Verhofstad E, Sleegers D, Santangelo S, Dairou J, Fernandez-Blanco Á, Dierssen M, Krämer A, Knapp S, Meijer L. Chemical, Biochemical, Cellular, and Physiological Characterization of Leucettinib-21, a Down Syndrome and Alzheimer's Disease Drug Candidate. J Med Chem 2023; 66:15648-15670. [PMID: 38051674 DOI: 10.1021/acs.jmedchem.3c01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Leucettinibs are substituted 2-aminoimidazolin-4-ones (inspired by the marine sponge natural product Leucettamine B) developed as pharmacological inhibitors of DYRK1A (dual-specificity, tyrosine phosphorylation-regulated kinase 1A), a therapeutic target for indications such as Down syndrome and Alzheimer's disease. Leucettinib-21 was selected as a drug candidate following extensive structure/activity studies and multiparametric evaluations. We here report its physicochemical properties (X-ray powder diffraction, differential scanning calorimetry, stability, solubility, crystal structure) and drug-like profile. Leucettinib-21's selectivity (analyzed by radiometric, fluorescence, interaction, thermal shift, residence time assays) reveals DYRK1A as the first target but also some "off-targets" which may contribute to the drug's biological effects. Leucettinib-21 was cocrystallized with CLK1 and modeled in the DYRK1A structure. Leucettinib-21 inhibits DYRK1A in cells (demonstrated by direct catalytic activity and phosphorylation levels of Thr286-cyclin D1 or Thr212-Tau). Leucettinib-21 corrects memory disorders in the Down syndrome mouse model Ts65Dn and is now entering safety/tolerance phase 1 clinical trials.
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Affiliation(s)
- Mattias F Lindberg
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Emmanuel Deau
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Frédéric Miege
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Marie Greverie
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Didier Roche
- Edelris, Bâtiment Bioserra 1, 60 Avenue Rockefeller, 69008 Lyon, France
| | - Nicolas George
- Oncodesign, 25-27 Avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
| | - Laura Merlet
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 8 Quai Moncousu, 44007 Nantes Cedex 1, France
- Equipe Labellisée Ligue Contre le Cancer, 75013 Paris, France
| | - Julie Gavard
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 8 Quai Moncousu, 44007 Nantes Cedex 1, France
- Equipe Labellisée Ligue Contre le Cancer, 75013 Paris, France
- Institut de Cancérologie de l'Ouest (ICO), Boulevard Professeur Jacques Monod, 44800 Saint-Herblain, France
| | | | - Edwin Aret
- Symeres, Peelterbaan 2, 6002 NK Weert, The Netherlands
| | - Paul Tinnemans
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - René de Gelder
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Jan Sadownik
- Symeres, Peelterbaan 2, 6002 NK Weert, The Netherlands
| | | | | | | | - Julien Dairou
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, CNRS, 45 rue des Saints Pères, 75006 Paris, France
| | - Álvaro Fernandez-Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08036, Spain
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08036, Spain
| | - Andreas Krämer
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Strasse 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von Laue Strasse 15, 60438 Frankfurt am Main, Germany
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Laurent Meijer
- Perharidy Research Center, Perha Pharmaceuticals, 29680 Roscoff, Bretagne, France
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Jackson JJ, Siegmund AC, Bai WJ, Reed AB, Birkholz AB, Campuzano IDG, Créquer-Grandhomme A, Hu R, Modak RV, Sudom A, Javier N, Sanders C, Lo MC, Xie F, Cee VJ, Manzanillo P, Allen JG. Imidazolone as an Amide Bioisostere in the Development of β-1,3- N-Acetylglucosaminyltransferase 2 (B3GNT2) Inhibitors. J Med Chem 2023; 66:16120-16140. [PMID: 37988652 DOI: 10.1021/acs.jmedchem.3c01517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
B3GNT2 is responsible for elongation of cell surface long-chain polylactosamine, which influences the regulation of the immune response, making it an attractive target for immunomodulation. In the development of amide containing B3GNT2 inhibitors guided by structure-based drug design, imidazolones were found to successfully serve as amide bioisosteres. This novel imidazolone isosteric strategy alleviated torsional strain of the amide bond on binding to B3GNT2 and improved potency, isoform selectivity, as well as certain physicochemical and pharmacokinetic properties. Herein, we present the synthesis, SAR, X-ray cocrystal structures, and in vivo PK properties of imidazol-4-ones in the context of B3GNT2 inhibition.
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Affiliation(s)
- Jeffrey J Jackson
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Aaron C Siegmund
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Wen-Ju Bai
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Anthony B Reed
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Adam B Birkholz
- Center for Research Acceleration by Digital Innovation, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Center for Research Acceleration by Digital Innovation, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Amandine Créquer-Grandhomme
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Ruozhen Hu
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Rucha V Modak
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Athena Sudom
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Noelle Javier
- Lead Discovery & Characterization, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Christiana Sanders
- Lead Discovery & Characterization, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Mei-Chu Lo
- Lead Discovery & Characterization, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Fang Xie
- Pharmacokinetics & Drug Metabolism, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - Victor J Cee
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Paolo Manzanillo
- Inflammation, Amgen Research, Amgen Inc., 750 Gateway Blvd, Ste 100, South San Francisco, California 94080, United States
| | - John G Allen
- Small Molecule Therapeutic Discovery, Amgen Research, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
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Hodyna D, Kovalishyn V, Kachaeva M, Shulha Y, Klipkov A, Shaitanova E, Kobzar O, Shablykin O, Metelytsia L. In Silico, in Vitro and in Vivo Study of Substituted Imidazolidinone Sulfonamides as Antibacterial Agents. Chem Biodivers 2023; 20:e202301267. [PMID: 37943002 DOI: 10.1002/cbdv.202301267] [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: 08/21/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/10/2023]
Abstract
New substituted imidazolidinone sulfonamides have been developed using a rational drug design strategy. Predictive QSAR models for the search of new antibacterials were created using the OCHEM platform. Regression models were applied to verify a virtual chemical library of new imidazolidinone derivatives designed to have antibacterial activity. A number of substituted imidazolidinone sulfonamides as effective antibacterial agents were identified by QSAR prediction, synthesized and characterized by spectral and elemental, and tested in vitro. Six studied compounds have shown the highest in vitro antibacterial activity against Gram-negative E. coli and Gram-positive S. aureus multidrug-resistant strains. The in vivo acute toxicity of these imidazolidinone sulfonamides based on the LC50 value ranged from 16.01 to 44.35 mg/L (slightly toxic compounds class). The results of molecular docking suggest that the antibacterial mechanism of the compounds can be associated with the inhibition of post-translational modification processes of bacterial peptides and proteins.
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Affiliation(s)
- Diana Hodyna
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Vasyl Kovalishyn
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Maryna Kachaeva
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Yurii Shulha
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Anton Klipkov
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Elena Shaitanova
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Oleksandr Kobzar
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Oleh Shablykin
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
| | - Larysa Metelytsia
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Sciences of Ukraine, 02094, Academician Kukhar Str, 1, Kyiv, Ukraine
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Belen’kii LI, Gazieva GA, Evdokimenkova YB, Soboleva NO. The literature of heterocyclic chemistry, Part XX, 2020. ADVANCES IN HETEROCYCLIC CHEMISTRY 2022. [DOI: 10.1016/bs.aihch.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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7
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Kovács E, Cseri L, Jancsó A, Terényi F, Fülöp A, Rózsa B, Galbács G, Mucsi Z. Synthesis and Fluorescence Mechanism of the Aminoimidazolone Analogues of the Green Fluorescent Protein: Towards Advanced Dyes with Enhanced Stokes Shift, Quantum Yield and Two‐Photon Absorption. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ervin Kovács
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
- Institute of Materials and Environmental Chemistry Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Levente Cseri
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
- Department of Chemical Engineering & Analytical Science The University of Manchester The Mill, Sackville Street Manchester M1 3BB United Kingdom
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry University of Szeged Dóm tér 8 Szeged 6720 Hungary
| | - Ferenc Terényi
- Department of Inorganic and Analytical Chemistry University of Szeged Dóm tér 8 Szeged 6720 Hungary
| | - Anna Fülöp
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
| | - Balázs Rózsa
- Two-Photon Measurement Technology Research Group The Faculty of Information Technology Pázmány Péter Catholic University Práter u. 50/A Budapest 1083 Hungary
- Laboratory of 3D Functional Imaging of Neuronal Networks and Dendritic Integration Institute of Experimental Medicine Szigony utca 43 Budapest 1083 Hungary
| | - Gábor Galbács
- Department of Inorganic and Analytical Chemistry University of Szeged Dóm tér 8 Szeged 6720 Hungary
| | - Zoltán Mucsi
- Department of Chemistry Femtonics Inc. Tűzoltó u. 58 1094 Budapest Hungary
- Institute of Chemistry Faculty of Materials Science and Engineering University of Miskolc Egyetem út 1 Miskolc 3515 Hungary
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Abstract
N-heterocycles, both saturated and unsaturated, are ubiquitous biologically active molecules that are extremely appealing scaffolds in drug discovery programs. Although classical synthetic methods have been developed to access many relevant N-heterocyclic scaffolds, representing well-established and reliable routes, some do not meet the needs of sustainability. In this context, several advances have been made towards the sustainable synthesis of N-heterocycles. This review focuses on the most recent examples from the last five years of catalytic synthesis of several heterocyclic compounds of medicinal relevance. Thus, the synthesis of isoindoloquinazolines, quinazolines and azaindoles, among others, are covered. The synthetic methods selected include the use of homogeneous and heterogeneous catalysts and the use of alternative and sustainable methods such as, for example, metal-catalyzed acceptorless coupling and one-pot reactions. The green aspects of the individual synthetic approaches are highlighted, and the scope of each methodology is described.
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Desai NC, Wadekar KR, Mehta HK, Pandit UP. Design, Synthesis, and Antimicrobial Activity of Novel
Fluorine-Containing Imidazolones. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021060142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Keel KL, Tepe JJ. Total Synthesis of Nortopsentin D via a Late-Stage Pinacol-like Rearrangement. Org Lett 2021; 23:5368-5372. [PMID: 34170714 DOI: 10.1021/acs.orglett.1c01681] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nortopsentin D is part of a class of bis(indole) alkaloids known for their biological activity, including inhibitory activity in tumoral cells and antifungal activity. Herein we describe the first total synthesis of nortopsentin D, in which amidine and dione undergo a pivotal condensation and subsequent cyclization via a pinacol-like rearrangement. This synthesis represents a unique strategy for the formation of 5,5-disubstituted (4H)-imidazol-4-one containing natural products, many of which have yet to succumb to total synthesis.
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Affiliation(s)
- Katarina L Keel
- Michigan State University, Department of Chemistry, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jetze J Tepe
- Michigan State University, Department of Chemistry, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
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Ikejiri M, Miyashita K, Watanabe A, Katsuda M, Funakoshi M, Fujisaka A. Acetate/Acetic Acid-Assisted One-Pot Synthesis of (Diarylmethylene)imidazolone from Amide or Thioamide. HETEROCYCLES 2021. [DOI: 10.3987/com-20-14396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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