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Taha I, Keshk EM, Khalil AGM, Fekri A. Benzocaine as a precursor of promising derivatives: synthesis, reactions, and biological activity. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01808-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schulz R, Atef A, Becker D, Gottschalk F, Tauber C, Wagner S, Arkona C, Abdel-Hafez AA, Farag HH, Rademann J, Wolber G. Phenylthiomethyl Ketone-Based Fragments Show Selective and Irreversible Inhibition of Enteroviral 3C Proteases. J Med Chem 2018; 61:1218-1230. [PMID: 29328649 DOI: 10.1021/acs.jmedchem.7b01440] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lead structure discovery mainly focuses on the identification of noncovalently binding ligands. Covalent linkage, however, is an essential binding mechanism for a multitude of successfully marketed drugs, although discovered by serendipity in most cases. We present a concept for the design of fragments covalently binding to proteases. Covalent linkage enables fragment binding unrelated to affinity to shallow protein binding sites and at the same time allows differentiated targeted hit verification and binding location verification through mass spectrometry. We describe a systematic and rational computational approach for the identification of covalently binding fragments from compound collections inhibiting enteroviral 3C protease, a target with high therapeutic potential. By implementing reactive groups potentially forming covalent bonds as a chemical feature in our 3D pharmacophore methodology, covalent binders were discovered by high-throughput virtual screening. We present careful experimental validation of the virtual hits using enzymatic assays and mass spectrometry unraveling a novel, previously unknown irreversible inhibition of the 3C protease by phenylthiomethyl ketone-based fragments. Subsequent synthetic optimization through fragment growing and reactivity analysis against catalytic and noncatalytic cysteines revealed specific irreversible 3C protease inhibition.
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Affiliation(s)
- Robert Schulz
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Amira Atef
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University , Assiut 71526, Egypt
| | - Daniel Becker
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Franziska Gottschalk
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Carolin Tauber
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Stefan Wagner
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Christoph Arkona
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Atef A Abdel-Hafez
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University , Assiut 71526, Egypt
| | - Hassan H Farag
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University , Assiut 71526, Egypt
| | - Jörg Rademann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin , Königin-Luise Straße 2+4, Berlin 14195, Germany
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Vodolazhenko MA, Mykhailenko AE, Gorobets NY, Desenko SM. One-pot Synthesis of Benzo[4,5]imidazo[1,2- a]pyridine Derivatives in Aqueous Conditions. J Heterocycl Chem 2016. [DOI: 10.1002/jhet.2617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maria A. Vodolazhenko
- Department of Chemistry of Heterocyclic Compounds; SSI “Institute for Single Crystals” of National Academy of Sciences of Ukraine; Nauky Avenue 60 Kharkiv 61001 Ukraine
| | - Anastasiia E. Mykhailenko
- Department of Chemistry of Heterocyclic Compounds; SSI “Institute for Single Crystals” of National Academy of Sciences of Ukraine; Nauky Avenue 60 Kharkiv 61001 Ukraine
| | - Nikolay Yu. Gorobets
- Department of Chemistry of Heterocyclic Compounds; SSI “Institute for Single Crystals” of National Academy of Sciences of Ukraine; Nauky Avenue 60 Kharkiv 61001 Ukraine
| | - Sergey M. Desenko
- Department of Chemistry of Heterocyclic Compounds; SSI “Institute for Single Crystals” of National Academy of Sciences of Ukraine; Nauky Avenue 60 Kharkiv 61001 Ukraine
- Faculty of Chemistry; V.N. Karazin Kharkiv National University; Svobody Sq. 4 Kharkiv 61077 Ukraine
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Vodolazhenko MA, Gorobets NY, Zhikol OA, Desenko SM, Shishkin OV. A quantum chemical approach towards understanding stability and tautomerism of 2-imino-2H-pyran derivatives. RSC Adv 2016. [DOI: 10.1039/c6ra08873b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The ring-chain tautomerism of 2-imino-2H-pyran derivatives annelated with an aromatic or aliphatic ring and their transformation into corresponding 2-pyridons were studied based on the relative stabilities of two series of model isomers calculated by the DFT method.
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Affiliation(s)
| | | | - Oleg A. Zhikol
- SSI “Institute for Single Crystals”
- NAS of Ukraine
- 61001 Kharkiv
- Ukraine
| | - Sergey M. Desenko
- SSI “Institute for Single Crystals”
- NAS of Ukraine
- 61001 Kharkiv
- Ukraine
| | - Oleg V. Shishkin
- SSI “Institute for Single Crystals”
- NAS of Ukraine
- 61001 Kharkiv
- Ukraine
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Loidreau Y, Melissen S, Levacher V, Logé C, Graton J, Le Questel JY, Besson T. Study of N1-alkylation of indoles from the reaction of 2(or 3)-aminoindole-3-(or 2)carbonitriles with DMF-dialkylacetals. Org Biomol Chem 2012; 10:4916-25. [DOI: 10.1039/c2ob25747e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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