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Yarovaya OI, Shcherbakov DN, Borisevich SS, Sokolova AS, Gureev MA, Khamitov EM, Rudometova NB, Zybkina AV, Mordvinova ED, Zaykovskaya AV, Rogachev AD, Pyankov OV, Maksyutov RA, Salakhutdinov NF. Borneol Ester Derivatives as Entry Inhibitors of a Wide Spectrum of SARS-CoV-2 Viruses. Viruses 2022; 14:v14061295. [PMID: 35746766 PMCID: PMC9228966 DOI: 10.3390/v14061295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
In the present work we studied the antiviral activity of the home library of monoterpenoid derivatives using the pseudoviral systems of our development, which have glycoproteins of the SARS-CoV-2 virus strains Wuhan and Delta on their surface. We found that borneol derivatives with a tertiary nitrogen atom can exhibit activity at the early stages of viral replication. In order to search for potential binding sites of ligands with glycoprotein, we carried out additional biological tests to study the inhibition of the re-receptor-binding domain of protein S. For the compounds that showed activity on the pseudoviral system, a study using three strains of the infectious SARS-CoV-2 virus was carried out. As a result, two leader compounds were found that showed activity on the Wuhan, Delta, and Omicron strains. Based on the biological results, we searched for the potential binding site of the leader compounds using molecular dynamics and molecular docking methods. We suggested that the compounds can bind in conserved regions of the central helices and/or heptad repeats of glycoprotein S of SARS-CoV-2 viruses.
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Affiliation(s)
- Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
- Correspondence:
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics Ufa Institute of Chemistry, Ufa Federal Research Center, RAS, Octyabrya pr., 71, 450054 Ufa, Russia; (S.S.B.); (E.M.K.)
| | - Anastasiya S. Sokolova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
| | - Maxim A. Gureev
- Research Center “Digital Biodesign and Personalized Healthcare”, I.M. Sechenov First Moscow State Medical University, Trubetskaya str., 8/2, 119991 Moscow, Russia;
- Department of Computational Biology, Sirius University of Science and Technology, Olympic Ave., 1, 354340 Sochi, Russia
| | - Edward M. Khamitov
- Laboratory of Chemical Physics Ufa Institute of Chemistry, Ufa Federal Research Center, RAS, Octyabrya pr., 71, 450054 Ufa, Russia; (S.S.B.); (E.M.K.)
| | - Nadezda B. Rudometova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Anastasiya V. Zybkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Ekaterina D. Mordvinova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Artem D. Rogachev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Rinat A. Maksyutov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.B.R.); (A.V.Z.); (A.V.Z.); (O.V.P.); (R.A.M.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrentiev ave., 9, 630090 Novosibirsk, Russia; (A.S.S.); (E.D.M.); (A.D.R.); (N.F.S.)
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Sokolova AS, Putilova VP, Yarovaya OI, Zybkina AV, Mordvinova ED, Zaykovskaya AV, Shcherbakov DN, Orshanskaya IR, Sinegubova EO, Esaulkova IL, Borisevich SS, Bormotov NI, Shishkina LN, Zarubaev VV, Pyankov OV, Maksyutov RA, Salakhutdinov NF. Synthesis and Antiviral Activity of Camphene Derivatives against Different Types of Viruses. Molecules 2021; 26:2235. [PMID: 33924393 PMCID: PMC8070564 DOI: 10.3390/molecules26082235] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/25/2022] Open
Abstract
To date, the 'one bug-one drug' approach to antiviral drug development cannot effectively respond to the constant threat posed by an increasing diversity of viruses causing outbreaks of viral infections that turn out to be pathogenic for humans. Evidently, there is an urgent need for new strategies to develop efficient antiviral agents with broad-spectrum activities. In this paper, we identified camphene derivatives that showed broad antiviral activities in vitro against a panel of enveloped pathogenic viruses, including influenza virus A/PR/8/34 (H1N1), Ebola virus (EBOV), and the Hantaan virus. The lead-compound 2a, with pyrrolidine cycle in its structure, displayed antiviral activity against influenza virus (IC50 = 45.3 µM), Ebola pseudotype viruses (IC50 = 0.12 µM), and authentic EBOV (IC50 = 18.3 µM), as well as against pseudoviruses with Hantaan virus Gn-Gc glycoprotein (IC50 = 9.1 µM). The results of antiviral activity studies using pseudotype viruses and molecular modeling suggest that surface proteins of the viruses required for the fusion process between viral and cellular membranes are the likely target of compound 2a. The key structural fragments responsible for efficient binding are the bicyclic natural framework and the nitrogen atom. These data encourage us to conduct further investigations using bicyclic monoterpenoids as a scaffold for the rational design of membrane-fusion targeting inhibitors.
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Affiliation(s)
- Anastasiya S. Sokolova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
| | - Valentina P. Putilova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
| | - Olga I. Yarovaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
| | - Anastasiya V. Zybkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Ekaterina D. Mordvinova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Iana R. Orshanskaya
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Ekaterina O. Sinegubova
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Iana L. Esaulkova
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 71 Pr. Oktyabrya, 450078 Ufa, Russia;
| | - Nikolay I. Bormotov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Larisa N. Shishkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Vladimir V. Zarubaev
- Pasteur Institute of Epidemiology and Microbiology, 14 Mira str., 197101 St. Petersburg, Russia; (I.R.O.); (E.O.S.); (I.L.E.); (V.V.Z.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Rinat A. Maksyutov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Novosibirsk, Russia; (A.V.Z.); (A.V.Z.); (D.N.S.); (N.I.B.); (L.N.S.); (O.V.P.); (R.A.M.)
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Lavrent’ev av., 9, 630090 Novosibirsk, Russia; (V.P.P.); (O.I.Y.); (E.D.M.); (N.F.S.)
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Volkova NV, Pyankov OV, Ivanova AV, Isaeva AA, Zybkina AV, Kazachinskaya EI, Shcherbakov DN. Prototype of a DNA Vaccine against Marburg Virus. Bull Exp Biol Med 2021; 170:475-478. [PMID: 33713231 DOI: 10.1007/s10517-021-05091-w] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Indexed: 11/29/2022]
Abstract
The preparation and study of the biological properties of the pVAKS-GPVM DNA immunogen containing a gene encoding Marburgvirus glycoprotein are described. The specificity of blood serum antibodies of guinea pigs immunized with DNA immunogen was analyzed by ELISA. Inactivated viral preparation, recombinant glycoprotein (GP) obtained in the prokaryotic system and virus-like particles based on the recombinant vesicular stomatitis virus exhibiting Marburgvirus GP were used as the antigens. The neutralizing activity of antibodies of immunized animals was tested in vitro using a pseudovirus system. It was demonstrated that the developed immunogen administered to guinea pigs induced the production of specific antibodies that neutralize virus-like particles and Marburgvirus in cultured Vero cells.
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Affiliation(s)
- N V Volkova
- State Research Centre of Virology and Biotechnology "Vector", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia.
| | - O V Pyankov
- State Research Centre of Virology and Biotechnology "Vector", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A V Ivanova
- State Research Centre of Virology and Biotechnology "Vector", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A A Isaeva
- State Research Centre of Virology and Biotechnology "Vector", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - A V Zybkina
- State Research Centre of Virology and Biotechnology "Vector", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - E I Kazachinskaya
- State Research Centre of Virology and Biotechnology "Vector", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
| | - D N Shcherbakov
- State Research Centre of Virology and Biotechnology "Vector", Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, Koltsovo, Novosibirsk region, Russia
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Sokolova AS, Yarovaya OI, Zybkina AV, Mordvinova ED, Shcherbakova NS, Zaykovskaya AV, Baev DS, Tolstikova TG, Shcherbakov DN, Pyankov OV, Maksyutov RA, Salakhutdinov NF. Monoterpenoid-based inhibitors of filoviruses targeting the glycoprotein-mediated entry process. Eur J Med Chem 2020; 207:112726. [PMID: 32905862 DOI: 10.1016/j.ejmech.2020.112726] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 05/28/2020] [Revised: 07/21/2020] [Accepted: 08/03/2020] [Indexed: 01/25/2023]
Abstract
In this study, we screened a large library of (+)-camphor and (-)-borneol derivatives to assess their filovirus entry inhibition activities using pseudotype systems. Structure-activity relationship studies revealed several compounds exhibiting submicromolar IC50 values. These compounds were evaluated for their effect against natural Ebola virus (EBOV) and Marburg virus. Compound 3b (As-358) exhibited the good antiviral potency (IC50 = 3.7 μM, SI = 118) against Marburg virus, while the hydrochloride salt of this compound 3b·HCl had a strong inhibitory effect against Ebola virus (IC50 = 9.1 μM, SI = 31) and good in vivo safety (LD50 > 1000 mg/kg). The results of molecular docking and in vitro mutagenesis analyses suggest that the synthesized compounds bind to the active binding site of EBOV glycoprotein similar to the known inhibitor toremifene.
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Affiliation(s)
- Anastasiya S Sokolova
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090, Novosibirsk, Lavrent'ev Av., 9, Russia.
| | - Olga I Yarovaya
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090, Novosibirsk, Lavrent'ev Av., 9, Russia; Novosibirsk State University, 630090, Novosibirsk, Pirogova St., 1, Russia
| | - Anastasiya V Zybkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Koltsovo, Novosibirsk Region, Russia
| | - Ekaterina D Mordvinova
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090, Novosibirsk, Lavrent'ev Av., 9, Russia; State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Koltsovo, Novosibirsk Region, Russia
| | - Nadezhda S Shcherbakova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Koltsovo, Novosibirsk Region, Russia
| | - Anna V Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Koltsovo, Novosibirsk Region, Russia
| | - Dmitriy S Baev
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090, Novosibirsk, Lavrent'ev Av., 9, Russia
| | - Tatyana G Tolstikova
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090, Novosibirsk, Lavrent'ev Av., 9, Russia; Novosibirsk State University, 630090, Novosibirsk, Pirogova St., 1, Russia
| | - Dmitriy N Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Koltsovo, Novosibirsk Region, Russia
| | - Oleg V Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Koltsovo, Novosibirsk Region, Russia
| | - Rinat A Maksyutov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Koltsovo, Novosibirsk Region, Russia
| | - Nariman F Salakhutdinov
- N.N.Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090, Novosibirsk, Lavrent'ev Av., 9, Russia
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