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Rampias T, Antoniou T, Stevaert A, Kravariti L, Van Loy B, Vandeput J, Sgrignani J, Filippidou N, Locatelli P, Samiotaki M, Tzakos EP, Cavalli A, Naesens L, Sideris DC, Tzakos AG. Exploration of isatin-based inhibitors of SARS-CoV-2 Nsp15 endoribonuclease. Eur J Med Chem 2024; 279:116886. [PMID: 39312834 DOI: 10.1016/j.ejmech.2024.116886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 09/10/2024] [Accepted: 09/14/2024] [Indexed: 09/25/2024]
Abstract
The global health crisis caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) urges the development of new antiviral agents with broad coronavirus coverage. Due to its key role in viral evasion from the host innate immune response, the coronavirus Nsp15 uridine-specific endoribonuclease (EndoU) is of high interest as a drug target. Considering that the isatin scaffold is well-known for its versatile pharmacological properties, we synthesized and evaluated a series of compounds carrying an isatin core. The initial compounds were selected on the basis of in silico predictions. After biochemical assays showed moderate inhibition of SARS-CoV-2 EndoU-mediated RNA cleavage, structural analogues were rationally designed to enhance the interaction with the target. This included the incorporation of a nitrile group since this dipole can improve ADME and facilitate polar interactions with proteins and can operate as hydroxy or carboxy surrogate. A straightforward solvent free and green, microwave-assisted synthetic process was established to achieve the development of the different target compounds. The best compound exhibited inhibitory activity in enzymatic EndoU assays, and reduced the SARS-CoV-2 viral RNA load by almost 68,000-fold in the low micromolar range similarly to the established antiviral agent GS-441524.
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Affiliation(s)
- Theodoros Rampias
- Biomedical Research Foundation Academy of Athens, 4 Soranou Efesiou, 115 27, Athens, Greece
| | - Thomas Antoniou
- University of Ioannina, Department of Chemistry, Section of Organic Chemistry and Biochemistry, Ioannina, GR-45110, Greece
| | - Annelies Stevaert
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Lara Kravariti
- National and Kapodistrian University of Athens, Section of Biochemistry and Molecular Biology, Department of Biology, Panepistimiopolis, 15701, Athens, Greece
| | - Benjamin Van Loy
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Julie Vandeput
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Jacopo Sgrignani
- Institute for Research In Biochemistry (IRB), Universita' della Svizzera Italiana, Via Chiesa 5, Bellinzona, 6500, Switzerland
| | - Natalia Filippidou
- Biomedical Research Foundation Academy of Athens, 4 Soranou Efesiou, 115 27, Athens, Greece
| | - Patrizia Locatelli
- Institute for Research In Biochemistry (IRB), Universita' della Svizzera Italiana, Via Chiesa 5, Bellinzona, 6500, Switzerland
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming, 16672, Vari, Greece
| | - Eleftherios Paraskevas Tzakos
- National and Kapodistrian University of Athens, Section of Biochemistry and Molecular Biology, Department of Biology, Panepistimiopolis, 15701, Athens, Greece
| | - Andrea Cavalli
- Institute for Research In Biochemistry (IRB), Universita' della Svizzera Italiana, Via Chiesa 5, Bellinzona, 6500, Switzerland
| | - Lieve Naesens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Diamantis C Sideris
- National and Kapodistrian University of Athens, Section of Biochemistry and Molecular Biology, Department of Biology, Panepistimiopolis, 15701, Athens, Greece.
| | - Andreas G Tzakos
- University of Ioannina, Department of Chemistry, Section of Organic Chemistry and Biochemistry, Ioannina, GR-45110, Greece.
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Song L, Gao S, Ye B, Yang M, Cheng Y, Kang D, Yi F, Sun JP, Menéndez-Arias L, Neyts J, Liu X, Zhan P. Medicinal chemistry strategies towards the development of non-covalent SARS-CoV-2 M pro inhibitors. Acta Pharm Sin B 2024; 14:87-109. [PMID: 38239241 PMCID: PMC10792984 DOI: 10.1016/j.apsb.2023.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 01/22/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an attractive target in anti-COVID-19 therapy for its high conservation and major role in the virus life cycle. The covalent Mpro inhibitor nirmatrelvir (in combination with ritonavir, a pharmacokinetic enhancer) and the non-covalent inhibitor ensitrelvir have shown efficacy in clinical trials and have been approved for therapeutic use. Effective antiviral drugs are needed to fight the pandemic, while non-covalent Mpro inhibitors could be promising alternatives due to their high selectivity and favorable druggability. Numerous non-covalent Mpro inhibitors with desirable properties have been developed based on available crystal structures of Mpro. In this article, we describe medicinal chemistry strategies applied for the discovery and optimization of non-covalent Mpro inhibitors, followed by a general overview and critical analysis of the available information. Prospective viewpoints and insights into current strategies for the development of non-covalent Mpro inhibitors are also discussed.
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Affiliation(s)
- Letian Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Shenghua Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Bing Ye
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Mianling Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yusen Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Fan Yi
- The Key Laboratory of Infection and Immunity of Shandong Province, Department of Pharmacology, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas & Autonomous University of Madrid), Madrid 28049, Spain
| | - Johan Neyts
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven 3000, Belgium
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
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3
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Du YD, Wang S, Du HW, Chang XY, Chen XY, Li YL, Shu W. Organophotocatalysed synthesis of 2-piperidinones in one step via [1 + 2 + 3] strategy. Nat Commun 2023; 14:5339. [PMID: 37660185 PMCID: PMC10475035 DOI: 10.1038/s41467-023-40197-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 07/13/2023] [Indexed: 09/04/2023] Open
Abstract
Six-membered N-containing heterocycles, such as 2-piperidinone derivatives, with diverse substitution patterns are widespread in natural products, drug molecules and serve as key precursors for piperidines. Thus, the development of stereoselective synthesis of multi-substituted 2-piperidinones are attractive. However, existing methods heavily rely on modification of pre-synthesized backbones which require tedious multi-step procedure and suffer from limited substitution patterns. Herein, an organophotocatalysed [1 + 2 + 3] strategy was developed to enable the one-step access to diverse substituted 2-piperidinones from easily available inorganic ammonium salts, alkenes, and unsaturated carbonyl compounds. This mild protocol exhibits exclusive chemoselectivity over two alkenes, tolerating both terminal and internal alkenes with a wide range of functional groups.
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Affiliation(s)
- Yi-Dan Du
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, P. R. China
| | - Shan Wang
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, P. R. China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 300071, Tianjin, P. R. China
| | - Hai-Wu Du
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, P. R. China
| | - Xiao-Yong Chang
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, P. R. China
| | - Xiao-Yi Chen
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, P. R. China
| | - Yu-Long Li
- College of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, 643000, Zigong, P. R. China
| | - Wei Shu
- Shenzhen Grubbs Institute and Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, P. R. China.
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 300071, Tianjin, P. R. China.
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