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Felicetti T, Sarnari C, Gaito R, Tabarrini O, Manfroni G. Recent Progress toward the Discovery of Small Molecules as Novel Anti-Respiratory Syncytial Virus Agents. J Med Chem 2024; 67:11543-11579. [PMID: 38970494 DOI: 10.1021/acs.jmedchem.4c00630] [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: 07/08/2024]
Abstract
Respiratory syncytial virus (RSV) stands as the foremost cause of infant hospitalization globally, ranking second only to malaria in terms of infant mortality. Although three vaccines have recently been approved for the prophylaxis of adults aged 60 and above, and pregnant women, there is currently no effective antiviral drug for treating RSV infections. The only preventive measure for infants at high risk of severe RSV disease is passive immunization through monoclonal antibodies. This Perspective offers an overview of the latest advancements in RSV drug discovery of small molecule antivirals, with particular focus on the promising findings from agents targeting the fusion and polymerase proteins. A comprehensive reflection on the current state of RSV research is also given, drawing inspiration from the lessons gleaned from HCV and HIV, while also considering the impact of the recent approval of the three vaccines.
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Affiliation(s)
- Tommaso Felicetti
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Chiara Sarnari
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Roberta Gaito
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo, 1-06123, Perugia, Italy
| | - Giuseppe Manfroni
- Department of Pharmaceutical Sciences, University of Perugia, Via Del Liceo, 1-06123, Perugia, Italy
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2
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Shtro AA, Klabukov AM, Garshinina AV, Galochkina AV, Nikolaeva YV, Khomenko TM, Bobkov DE, Lozhkov AA, Sivak KV, Yakovlev KS, Komissarov AB, Borisevich SS, Volcho KP, Salakhutdinov NF. Identification and Study of the Action Mechanism of Small Compound That Inhibits Replication of Respiratory Syncytial Virus. Int J Mol Sci 2023; 24:12933. [PMID: 37629115 PMCID: PMC10454904 DOI: 10.3390/ijms241612933] [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: 07/10/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Respiratory syncytial virus (RSV) is known to cause annual epidemics of respiratory infections; however, the lack of specific treatment options for this disease poses a challenge. In light of this, there has been a concerted effort to identify small molecules that can effectively combat RSV. This article focuses on the mechanism of action of compound K142, which was identified as a primary screening leader in the earlier stages of the project. The research conducted demonstrates that K142 significantly reduces the intensity of virus penetration into the cells, as well as the formation of syncytia from infected cells. These findings show that the compound's interaction with the surface proteins of RSV is a key factor in its antiviral activity. Furthermore, pharmacological modeling supports that K142 effectively interacts with the F-protein. However, in vivo studies have shown only weak antiviral activity against RSV infection, with a slight decrease in viral load observed in lung tissues. As a result, there is a need to enhance the bioavailability or antiviral properties of this compound. Based on these findings, we hypothesize that further modifications of the compound under study could potentially increase its antiviral activity.
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Affiliation(s)
- Anna A Shtro
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Artem M Klabukov
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Anzhelika V Garshinina
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Anastasia V Galochkina
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Yulia V Nikolaeva
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Tatyana M Khomenko
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev av. 9, 630090 Novosibirsk, Russia
| | - Danila E Bobkov
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
- Institute of Cytology Russian Academy of Science, Tikhoretsky av., 4, 194064 St. Petersburg, Russia
| | - Aleksey A Lozhkov
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Konstantin V Sivak
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Kirill S Yakovlev
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Andrey B Komissarov
- Smorodintsev Research Institute of Influenza, Professora Popova str, 15/17, 197376 St. Petersburg, Russia
| | - Sophia S Borisevich
- Ufa Chemistry Institute of the Ufa Federal Research Center, 71 Octyabrya pr., 450054 Ufa, Russia
| | - Konstantin P Volcho
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev av. 9, 630090 Novosibirsk, Russia
| | - Nariman F Salakhutdinov
- Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentyev av. 9, 630090 Novosibirsk, Russia
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Khomenko TM, Zakharenko AL, Kornienko TE, Chepanova AA, Dyrkheeva NS, Artemova AO, Korchagina DV, Achara C, Curtis A, Reynisson J, Volcho KP, Salakhutdinov NF, Lavrik OI. New 5-Hydroxycoumarin-Based Tyrosyl-DNA Phosphodiesterase I Inhibitors Sensitize Tumor Cell Line to Topotecan. Int J Mol Sci 2023; 24:ijms24119155. [PMID: 37298106 DOI: 10.3390/ijms24119155] [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: 03/29/2023] [Revised: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Tyrosyl-DNA-phosphodiesterase 1 (TDP1) is an important enzyme in the DNA repair system. The ability of the enzyme to repair DNA damage induced by a topoisomerase 1 poison such as the anticancer drug topotecan makes TDP1 a promising target for complex antitumor therapy. In this work, a set of new 5-hydroxycoumarin derivatives containing monoterpene moieties was synthesized. It was shown that most of the conjugates synthesized demonstrated high inhibitory properties against TDP1 with an IC50 in low micromolar or nanomolar ranges. Geraniol derivative 33a was the most potent inhibitor with IC50 130 nM. Docking the ligands to TDP1 predicted a good fit with the catalytic pocket blocking access to it. The conjugates used in non-toxic concentration increased cytotoxicity of topotecan against HeLa cancer cell line but not against conditionally normal HEK 293A cells. Thus, a new structural series of TDP1 inhibitors, which are able to sensitize cancer cells to the topotecan cytotoxic effect has been discovered.
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Affiliation(s)
- Tatyana M Khomenko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Tatyana E Kornienko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Arina A Chepanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Anastasia O Artemova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dina V Korchagina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Chigozie Achara
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK
| | - Anthony Curtis
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Newcastle-under-Lyme, Staffordshire ST5 5BG, UK
| | - Konstantin P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Nariman F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Khomenko TM, Shtro AA, Galochkina AV, Nikolaeva YV, Garshinina AV, Borisevich SS, Korchagina DV, Volcho KP, Salakhutdinov NF. New Inhibitors of Respiratory Syncytial Virus (RSV) Replication Based on Monoterpene-Substituted Arylcoumarins. Molecules 2023; 28:molecules28062673. [PMID: 36985645 PMCID: PMC10054240 DOI: 10.3390/molecules28062673] [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: 01/13/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
Respiratory syncytial virus (RSV) causes annual epidemics of respiratory infection. Usually harmless to adults, the RSV infection can be dangerous to children under 3 years of age and elderly people over 65 years of age, often causing serious problems, even death. At present, there are no vaccines and specific chemotherapeutic agents for the treatment of this disease, so the search for low-molecular weight compounds to combat RSV is a challenge. In this work, we have shown, for the first time, that monoterpene-substituted arylcoumarins are efficient RSV replication inhibitors at low micromolar concentrations. The most active compound has a selectivity index of about 200 and acts most effectively at the early stages of infection. The F protein of RSV is a potential target for these compounds, which is also confirmed by molecular docking and molecular dynamics simulation data.
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Affiliation(s)
- Tatyana M. Khomenko
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentjev Ave. 9, 630090 Novosibirsk, Russia
| | - Anna A. Shtro
- Laboratory of Chemotherapy for Viral Infections, Smorodintsev Research Intitute of Influenza, 197376 Saint-Petersburg, Russia
| | - Anastasia V. Galochkina
- Laboratory of Chemotherapy for Viral Infections, Smorodintsev Research Intitute of Influenza, 197376 Saint-Petersburg, Russia
| | - Yulia V. Nikolaeva
- Laboratory of Chemotherapy for Viral Infections, Smorodintsev Research Intitute of Influenza, 197376 Saint-Petersburg, Russia
| | - Anzhelika V. Garshinina
- Laboratory of Chemotherapy for Viral Infections, Smorodintsev Research Intitute of Influenza, 197376 Saint-Petersburg, Russia
| | - Sophia S. Borisevich
- Laboratory of Physical Chemistry, Ufa Chemistry Institute of the Ufa Federal Research Center, 71 Octyabrya pr., 450054 Ufa, Russia
- Institute of Cyber Intelligence Systems, National Research Nuclear University MEPhI, 115409 Moscow, Russia
| | - Dina V. Korchagina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentjev Ave. 9, 630090 Novosibirsk, Russia
| | - Konstantin P. Volcho
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentjev Ave. 9, 630090 Novosibirsk, Russia
- Correspondence:
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentjev Ave. 9, 630090 Novosibirsk, Russia
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El‐Deeb AA, Zablotskaya SS, Rubel MS, Nour MAY, Kozlovskaya LI, Shtro AA, Komissarov AB, Kolpashchikov DM. Toward a Home Test for COVID-19 Diagnosis: DNA Machine for Amplification-Free SARS-CoV-2 Detection in Clinical Samples. ChemMedChem 2022; 17:e202200382. [PMID: 36031581 PMCID: PMC9538286 DOI: 10.1002/cmdc.202200382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/26/2022] [Indexed: 11/08/2022]
Abstract
Nucleic acid-based detection of RNA viruses requires an annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structures of folded viral RNA. In this study, we designed a protein-enzyme-free nano-construction, named four-armed DNA machine (4DNM), that requires neither an amplification stage nor a high-temperature annealing step for SARS-CoV-2 detection. It uses a binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with a total of four RNA-binding arms. Additional arms were found to improve the limit of detection at least 10-fold. The sensor distinguished SARS-CoV-2 from other respiratory viruses and correctly identified five positive and six negative clinical samples verified by quantitative polymerase chain reaction (RT-qPCR). The strategy reported here can be used for the detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.
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Affiliation(s)
- Ahmed A. El‐Deeb
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Sofia S. Zablotskaya
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Maria S. Rubel
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Moustapha A. Y. Nour
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
| | - Liubov I. Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological ProductsRussian Academy of SciencesInstitute of PoliomyelitisMoscowRussia
| | - Anna A. Shtro
- Smorodintsev Research Institute of Influenza197376Saint PetersburgRussia
| | | | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor MaterialsSCAMT InstituteITMO University191002Saint PetersburgRussia
- Chemistry DepartmentUniversity of Central FloridaOrlandoFL 32816USA
- Burnett School of Biomedical SciencesUniversity of Central FloridaOrlandoFL 32827USA
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Nemolochnova AG, Rogachev AD, Salnikova OP, Khomenko TM, Volcho KP, Yarovaya OI, Fatianova AV, Pokrovsky AG, Salakhutdinov NF. Stability Study, Quantification Method and Pharmacokinetics Investigation of a Coumarin-Monoterpene Conjugate Possessing Antiviral Properties against Respiratory Syncytial Virus. Pharmaceuticals (Basel) 2022; 15:1158. [PMID: 36145379 PMCID: PMC9504583 DOI: 10.3390/ph15091158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
The stability of a new coumarin derivative, agent K-142, bearing α-pinene residue and possessing antiviral activity against respiratory syncytial virus (RSV) was studied in whole mice blood in vitro, and a method for its quantification in this matrix was developed and validated. The sample preparation method was precipitation of whole blood with a mixture of 0.2 M ZnSO4 with MeOH (2:8 v/v) containing 2-adamantylamine hydrochloride as an internal standard (IS). Analysis was carried out by HPLC-MS/MS using reversed phase chromatography and a triple quadrupole mass spectrometer 6500 QTRAP (SCIEX) in multiple reaction monitoring (MRM) mode. The transitions 351.2 → 217.1 Da and 152.2 → 93.1/107.2 Da were monitored for K-142 and the IS, respectively. The method was validated in terms of selectivity, calibration curve, LLOQ, accuracy and precision, stability, recovery and carry over. The developed method was used for a pharmacokinetics study of the compound after its oral administration to mice at a dose of 20 mg/kg.
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Affiliation(s)
- Arina G. Nemolochnova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent’ev ave, 9, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov St. 2, 630090 Novosibirsk, Russia
| | - Artem D. Rogachev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent’ev ave, 9, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov St. 2, 630090 Novosibirsk, Russia
| | - Olga P. Salnikova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent’ev ave, 9, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov St. 2, 630090 Novosibirsk, Russia
| | - Tatyana M. Khomenko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent’ev ave, 9, 630090 Novosibirsk, Russia
| | - Konstantin P. Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent’ev ave, 9, 630090 Novosibirsk, Russia
| | - Olga I. Yarovaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent’ev ave, 9, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov St. 2, 630090 Novosibirsk, Russia
| | - Alina V. Fatianova
- Faculty of Natural Sciences, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov St. 2, 630090 Novosibirsk, Russia
| | - Andrey G. Pokrovsky
- Faculty of Natural Sciences, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov St. 2, 630090 Novosibirsk, Russia
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent’ev ave, 9, 630090 Novosibirsk, Russia
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