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Chistov AA, Chumakov SP, Mikhnovets IE, Nikitin TD, Slesarchuk NA, Uvarova VI, Rubekina AA, Nikolaeva YV, Radchenko EV, Khvatov EV, Orlov AA, Frolenko VS, Sukhorukov MV, Kolpakova ES, Shustova EY, Galochkina AV, Streshnev PP, Osipov EM, Sapozhnikova KA, Moiseenko AV, Brylev VA, Proskurin GV, Dokukin YS, Kutyakov SV, Aralov AV, Korshun VA, Strelkov SV, Palyulin VA, Ishmukhametov AA, Shirshin EA, Osolodkin DI, Shtro AA, Kozlovskaya LI, Alferova VA, Ustinov AV. 5-(Perylen-3-ylethynyl)uracil as an antiviral scaffold: Potent suppression of enveloped virus reproduction by 3-methyl derivatives in vitro. Antiviral Res 2023; 209:105508. [PMID: 36581049 DOI: 10.1016/j.antiviral.2022.105508] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Amphipathic nucleoside and non-nucleoside derivatives of pentacyclic aromatic hydrocarbon perylene are known as potent non-cytotoxic broad-spectrum antivirals. Here we report 3-methyl-5-(perylen-3-ylethynyl)-uracil-1-acetic acid and its amides, a new series of compounds based on a 5-(perylen-3-ylethynyl)-uracil scaffold. The compounds demonstrate pronounced in vitro activity against arthropod-borne viruses, namely tick-borne encephalitis virus (TBEV) and yellow fever virus (YFV), in plaque reduction assays with EC50 values below 1.9 and 1.3 nM, respectively, and Chikungunya virus (CHIKV) in cytopathic effect inhibition test with EC50 values below 3.2 μM. The compounds are active against respiratory viruses as well: severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in cytopathic effect inhibition test and influenza A virus (IAV) in virus titer reduction experiments are inhibited - EC50 values below 51 nM and 2.2 μM, respectively. The activity stems from the presence of a hydrophobic perylene core, and all of the synthesized compounds exhibit comparable 1O2 generation rates. Nonetheless, activity can vary by orders of magnitude depending on the hydrophilic part of the molecule, suggesting a complex mode of action. A time-of-addition experiment and fluorescent imaging indicate that the compounds inhibit viral fusion in a dose-dependent manner. The localization of the compound in the lipid bilayers and visible damage to the viral envelope suggest the membrane as the primary target. Dramatic reduction of antiviral activity with limited irradiation or under treatment with antioxidants further cements the idea of photoinduced ROS-mediated viral envelope damage being the mode of antiviral action.
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Affiliation(s)
- Alexey A Chistov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Stepan P Chumakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Igor E Mikhnovets
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Timofei D Nikitin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Nikita A Slesarchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Victoria I Uvarova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia
| | - Anna A Rubekina
- Department of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Yulia V Nikolaeva
- Smorodintsev Research Institute of Influenza, St. Petersburg, 197376, Russia
| | - Eugene V Radchenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Evgeny V Khvatov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia
| | - Alexey A Orlov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia; FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia; Skolkovo Institute of Science and Technology, 143026, Moscow Region, Russia
| | - Vasilisa S Frolenko
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia
| | - Maksim V Sukhorukov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia; FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia
| | - Ekaterina S Kolpakova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia
| | - Elena Y Shustova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia
| | | | - Philipp P Streshnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Eugene M Osipov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | | | | | - Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia; Lumiprobe RUS Ltd., Moscow, 121351, Russia
| | - Gleb V Proskurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Yuri S Dokukin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Sergey V Kutyakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Sergei V Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia
| | - Evgeny A Shirshin
- Department of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia
| | - Anna A Shtro
- Smorodintsev Research Institute of Influenza, St. Petersburg, 197376, Russia
| | - Liubov I Kozlovskaya
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia.
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia; Lumiprobe RUS Ltd., Moscow, 121351, Russia.
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Stekhanova TN, Bezsudnova EY, Mardanov AV, Osipov EM, Ravin NV, Skryabin KG, Popov VO. Nicotinamidase from the thermophilic archaeon Acidilobus saccharovorans: structural and functional characteristics. Biochemistry (Mosc) 2014; 79:54-61. [PMID: 24512664 DOI: 10.1134/s0006297914010088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nicotinamidase is involved in the maintenance of NAD+ homeostasis and in the NAD+ salvage pathway of most prokaryotes, and it is considered as a possible drug target. The gene (ASAC_0847) encoding a hypothetical nicotinamidase has been found in the genome of the thermophilic archaeon Acidilobus saccharovorans. The product of this gene, NA_As0847, has been expressed in Escherichia coli, isolated, and characterized as a Fe(2+)-containing nicotinamidase (k(cat)/K(m) = 427 mM(-1)·sec(-1))/pyrazinamidase (k(cat)/K(m) = 331 mM(-1)·sec(-1)). NA_As0847 is a homodimer with molecular mass 46.4 kDa. The enzyme has high thermostability (T(1/2) (60°C) = 180 min, T(1/2) (80°C) = 35 min) and thermophilicity (T(opt) = 90°C, E(a) = 30.2 ± 1.0 kJ/mol) and broad pH interval of activity, with the optimum at pH 7.5. Special features of NA_As0847 are the presence of Fe2+ instead of Zn2+ in the active site of the enzyme and inhibition of the enzyme activity by Zn2+ at micromolar concentrations. Analysis of the amino acid sequence revealed a new motif of the metal-binding site (DXHXXXDXXEXXXWXXH) for homological archaeal nicotinamidases.
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Affiliation(s)
- T N Stekhanova
- Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 119071, Russia.
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