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Kamzeeva P, Dagaev N, Lizunova S, Khodarovich Y, Sogomonyan A, Kolchanova A, Pokrovsky V, Alferova V, Chistov A, Eshtukov-Shcheglov A, Eshtukova-Shcheglova E, Belyaev E, Skvortsov D, Varizhuk A, Aralov A. Synthesis and Biological Evaluation of Benzo [4,5]- and Naphtho[2',1':4,5]imidazo[1,2-c]pyrimidinone Derivatives. Biomolecules 2023; 13:1669. [PMID: 38002351 PMCID: PMC10669118 DOI: 10.3390/biom13111669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Azacarbazoles have attracted significant interest due to their valuable properties, such as anti-pathogenic and antitumor activity. In this study, a series of structurally related tricyclic benzo[4,5]- and tertacyclic naphtho[2',1':4,5]imidazo[1,2-c]pyrimidinone derivatives with one or two positively charged tethers were synthesized and evaluated for anti-proliferative activity. Lead tetracyclic derivative 5b with two amino-bearing arms inhibited the metabolic activity of A549 lung adenocarcinoma cells with a CC50 value of 3.6 μM, with remarkable selectivity (SI = 17.3) over VA13 immortalized fibroblasts. Cell-cycle assays revealed that 5b triggers G2/M arrest without signs of apoptosis. A study of its interaction with various DNA G4s and duplexes followed by dual luciferase and intercalator displacement assays suggests that intercalation, rather than the modulation of G4-regulated oncogene expression, might contribute to the observed activity. Finally, a water-soluble salt of 5b was shown to cause no acute toxic effects, changes in mice behavior, or any decrease in body weight after a 72 h treatment at concentrations up to 20 mg/kg. Thus, 5b is a promising candidate for studies in vivo; however, further investigations are needed to elucidate its molecular target(s).
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Affiliation(s)
- Polina Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.)
| | - Nikolai Dagaev
- Department of Chemistry and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; (N.D.)
| | - Sofia Lizunova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Yuri Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.)
- Research and Educational Resource Center for Cellular Technologies, The Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Anna Sogomonyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.)
| | - Anastasia Kolchanova
- Department of Chemistry and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; (N.D.)
| | - Vadim Pokrovsky
- N.N. Blokhin Cancer Research Center, 115478 Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, RUDN University, 117198 Moscow, Russia
| | - Vera Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.)
| | - Alexey Chistov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.)
| | - Artur Eshtukov-Shcheglov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.)
| | | | - Evgeny Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dmitry Skvortsov
- Department of Chemistry and Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; (N.D.)
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- G4_Interact, USERN, University of Pavia, 27100 Pavia, Italy
| | - Andrey Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.)
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- G4_Interact, USERN, University of Pavia, 27100 Pavia, Italy
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Knizhnik E, Chumakov S, Svetlova J, Pavlova I, Khodarovich Y, Brylev V, Severov V, Alieva R, Kozlovskaya L, Andreev D, Aralov A, Varizhuk A. Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication. Biomolecules 2023; 13:1660. [PMID: 38002341 PMCID: PMC10668963 DOI: 10.3390/biom13111660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtained and compared three types of such antiviral candidates, namely locked nucleic acids (LNA), LNA-DNA gapmers, and G-clamp-containing phosphorothioates (CPSs) complementary to PK stems. Using optical and electrophoretic methods, we showed that stem 2-targeting oligonucleotide analogs induced PK unfolding at nanomolar concentrations, and this effect was particularly pronounced in the case of LNA. For the leading PK-unfolding LNA and CPS oligonucleotide analogs, we also demonstrated dose-dependent RSF inhibition in dual luciferase assays (DLAs). Finally, we showed that the leading oligonucleotide analogs reduced SARS-CoV-2 replication at subtoxic concentrations in the nanomolar range in two human cell lines. Our findings highlight the promise of PK targeting, illustrate the advantages and limitations of various types of DNA modifications and may promote the future development of oligonucleotide-based antivirals.
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Affiliation(s)
- Ekaterina Knizhnik
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Stepan Chumakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
| | - Julia Svetlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
| | - Iulia Pavlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yuri Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
- Research and Educational Resource Center for Cellular Technologies of The Peoples’ Friendship University of Russia, 117198 Moscow, Russia
| | - Vladimir Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
| | - Vjacheslav Severov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
| | - Rugiya Alieva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Raman Spectroscopy Laboratory, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Liubov Kozlovskaya
- Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia;
| | - Dmitry Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia;
| | - Andrey Aralov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (S.C.); (Y.K.); (V.B.); (D.A.)
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (I.P.); (V.S.)
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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Kamzeeva P, Petushkov I, Knizhnik E, Snoeck R, Khodarovich Y, Ryabukhina E, Alferova V, Eshtukov-Shcheglov A, Belyaev E, Svetlova J, Vedekhina T, Kulbachinskiy A, Varizhuk A, Andrei G, Aralov A. Phenotypic Test of Benzo[4,5]imidazo[1,2-c]pyrimidinone-Based Nucleoside and Non-Nucleoside Derivatives against DNA and RNA Viruses, Including Coronaviruses. Int J Mol Sci 2023; 24:14540. [PMID: 37834006 PMCID: PMC10572855 DOI: 10.3390/ijms241914540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/16/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023] Open
Abstract
Emerging and re-emerging viruses periodically cause outbreaks and epidemics around the world, which ultimately lead to global events such as the COVID-19 pandemic. Thus, the urgent need for new antiviral drugs is obvious. Over more than a century of antiviral development, nucleoside analogs have proven to be promising agents against diversified DNA and RNA viruses. Here, we present the synthesis and evaluation of the antiviral activity of nucleoside analogs and their deglycosylated derivatives based on a hydroxybenzo[4,5]imidazo[1,2-c]pyrimidin-1(2H)-one scaffold. The antiviral activity was evaluated against a panel of structurally and phylogenetically diverse RNA and DNA viruses. The leader compound showed micromolar activity against representatives of the family Coronaviridae, including SARS-CoV-2, as well as against respiratory syncytial virus in a submicromolar range without noticeable toxicity for the host cells. Surprisingly, methylation of the aromatic hydroxyl group of the leader compound resulted in micromolar activity against the varicella-zoster virus without any significant impact on cell viability. The leader compound was shown to be a weak inhibitor of the SARS-CoV-2 RNA-dependent RNA polymerase. It also inhibited biocondensate formation important for SARS-CoV-2 replication. The active compounds may be considered as a good starting point for further structure optimization and mechanistic and preclinical studies.
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Affiliation(s)
- Polina Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Ivan Petushkov
- Institute of Molecular Genetics, National Research Centre ‘Kurchatov Institute’, 123182 Moscow, Russia; (I.P.); (A.K.)
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ekaterina Knizhnik
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (R.S.); (G.A.)
| | - Yuri Khodarovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Ekaterina Ryabukhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Vera Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Artur Eshtukov-Shcheglov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
| | - Evgeny Belyaev
- Frumkin Institute of Physical Chemistry and Electrochemistry, RAS, 119071 Moscow, Russia;
| | - Julia Svetlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
| | - Tatiana Vedekhina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Centre ‘Kurchatov Institute’, 123182 Moscow, Russia; (I.P.); (A.K.)
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.K.); (J.S.); (T.V.); (A.V.)
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (R.S.); (G.A.)
| | - Andrey Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (P.K.); (E.R.); (V.A.); (A.E.-S.)
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