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Mollaamin F. Structural and Functional Characterization of Medicinal Plants as Selective Antibodies towards Therapy of COVID-19 Symptoms. Antibodies (Basel) 2024; 13:38. [PMID: 38804306 PMCID: PMC11130808 DOI: 10.3390/antib13020038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/23/2023] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Considering the COVID-19 pandemic, this research aims to investigate some herbs as probable therapies for this disease. Achillea millefolium (Yarrow), Alkanet, Rumex patientia (Patience dock), Dill, Tarragon, and sweet fennel, including some principal chemical compounds of achillin, alkannin, cuminaldehyde, dillapiole, estragole, and fenchone have been selected. The possible roles of these medicinal plants in COVID-19 treatment have been investigated through quantum sensing methods. The formation of hydrogen bonding between the principal substances selected in anti-COVID natural drugs and Tyr-Met-His (the database amino acids fragment), as the active area of the COVID protein, has been evaluated. The physical and chemical attributes of nuclear magnetic resonance, vibrational frequency, the highest occupied molecular orbital energy and the lowest unoccupied molecular orbital energy, partial charges, and spin density have been investigated using the DFT/TD-DFT method and 6-311+G (2d,p) basis set by the Gaussian 16 revision C.01 program toward the industry of drug design. This research has exhibited that there is relative agreement among the results that these medicinal plants could be efficient against COVID-19 symptoms.
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Affiliation(s)
- Fatemeh Mollaamin
- Department of Biomedical Engineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu 37150, Turkey
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2
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Freidel MR, Armen RS. Research Progress on Spike-Dependent SARS-CoV-2 Fusion Inhibitors and Small Molecules Targeting the S2 Subunit of Spike. Viruses 2024; 16:712. [PMID: 38793593 PMCID: PMC11125925 DOI: 10.3390/v16050712] [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: 03/01/2024] [Revised: 04/07/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the beginning of the COVID-19 pandemic, extensive drug repurposing efforts have sought to identify small-molecule antivirals with various mechanisms of action. Here, we aim to review research progress on small-molecule viral entry and fusion inhibitors that directly bind to the SARS-CoV-2 Spike protein. Early in the pandemic, numerous small molecules were identified in drug repurposing screens and reported to be effective in in vitro SARS-CoV-2 viral entry or fusion inhibitors. However, given minimal experimental information regarding the exact location of small-molecule binding sites on Spike, it was unclear what the specific mechanism of action was or where the exact binding sites were on Spike for some inhibitor candidates. The work of countless researchers has yielded great progress, with the identification of many viral entry inhibitors that target elements on the S1 receptor-binding domain (RBD) or N-terminal domain (NTD) and disrupt the S1 receptor-binding function. In this review, we will also focus on highlighting fusion inhibitors that target inhibition of the S2 fusion function, either by disrupting the formation of the postfusion S2 conformation or alternatively by stabilizing structural elements of the prefusion S2 conformation to prevent conformational changes associated with S2 function. We highlight experimentally validated binding sites on the S1/S2 interface and on the S2 subunit. While most substitutions to the Spike protein to date in variants of concern (VOCs) have been localized to the S1 subunit, the S2 subunit sequence is more conserved, with only a few observed substitutions in proximity to S2 binding sites. Several recent small molecules targeting S2 have been shown to have robust activity over recent VOC mutant strains and/or greater broad-spectrum antiviral activity for other more distantly related coronaviruses.
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Affiliation(s)
| | - Roger S. Armen
- Department of Pharmaceutical Sciences, College of Pharmacy, Thomas Jefferson University, 901 Walnut St. Suite 918, Philadelphia, PA 19170, USA;
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3
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Sokolova AS, Yarovaya OI, Artyushin OI, Sharova EV, Baev DS, Mordvinova ED, Shcherbakov DN, Shnaider TA, Nikitina TV, Esaulkova IL, Ilyina PA, Zarubaev VV, Brel VK, Tolstikova TG, Salakhutdinov NF. Design, synthesis and antiviral evaluation of novel conjugates of the 1,7,7-trimethylbicyclo[2.2.1]heptane scaffold and saturated N-heterocycles via 1,2,3-triazole linker. Arch Pharm (Weinheim) 2024; 357:e2300549. [PMID: 38036303 DOI: 10.1002/ardp.202300549] [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: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
A new series of heterocyclic derivatives with a 1,7,7-trimethylbicyclo[2.2.1]heptane fragment was designed, synthesised and biologically evaluated. Synthesis of the target compounds was performed using the Cu(I) catalysed cycloaddition reaction. The key starting substances in the click reaction were an alkyne containing a 1,7,7-trimethylbicyclo[2.2.1]heptane fragment and a series of azides with saturated nitrogen-containing heterocycles. Some of the derivatives were found to exhibit strong antiviral activity against Marburg and Ebola pseudotype viruses. Lysosomal trapping assays revealed the derivatives to possess lysosomotropic properties. The molecular modelling study demonstrated the binding affinity between the compounds investigated and the possible active site to be mainly due to hydrophobic interactions. Thus, combining a natural hydrophobic structural fragment and a lysosome-targetable heterocycle may be an effective strategy for designing antiviral agents.
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Affiliation(s)
- Anastasiya S Sokolova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Olga I Yarovaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Oleg I Artyushin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elena V Sharova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitriy S Baev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, Koltsovo, Russian Federation
| | - Ekaterina D Mordvinova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk Region, Russian Federation
| | - Dmitriy N Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, Koltsovo, Novosibirsk Region, Russian Federation
| | - Tatiana A Shnaider
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Tatiana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russian Federation
| | - Iana L Esaulkova
- Pasteur Institute of Epidemiology and Microbiology, St. Petersburg, Russian Federation
| | - Polina A Ilyina
- Pasteur Institute of Epidemiology and Microbiology, St. Petersburg, Russian Federation
| | - Vladimir V Zarubaev
- Pasteur Institute of Epidemiology and Microbiology, St. Petersburg, Russian Federation
| | - Valery K Brel
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatyana G Tolstikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russian Federation
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4
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Yarovaya OI, Filimonov AS, Baev DS, Borisevich SS, Zaykovskaya AV, Chirkova VY, Marenina MK, Meshkova YV, Belenkaya SV, Shcherbakov DN, Gureev MA, Luzina OA, Pyankov OV, Salakhutdinov NF, Khvostov MV. The Potential of Usnic-Acid-Based Thiazolo-Thiophenes as Inhibitors of the Main Protease of SARS-CoV-2 Viruses. Viruses 2024; 16:215. [PMID: 38399993 PMCID: PMC10893357 DOI: 10.3390/v16020215] [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: 11/27/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (-)-usnic acid and studied their ability to inhibit the main protease of SARS-CoV-2. Substances containing unsubstituted thiophene groups or methyl- or bromo-substituted thiophene moieties showed moderate activity. Derivatives containing nitro substituents in the thiophene heterocycle-just as pure (+)- and (-)-usnic acids-showed no anti-3CLpro activity. Kinetic parameters of the most active compound, (+)-3e, were investigated, and molecular modeling of the possible interaction of the new thiazolo-thiophenes with the active site of the main protease was carried out. We evaluated the binding energies of the ligand and protein in a ligand-protein complex. Active compound (+)-3e was found to bind with minimum free energy; the binding of inactive compound (+)-3g is characterized by higher values of minimum free energy; the positioning of pure (+)-usnic acid proved to be unstable and is accompanied by the formation of intermolecular contacts with many amino acids of the catalytic binding site. Thus, the molecular dynamics results were consistent with the experimental data. In an in vitro antiviral assay against six strains (Wuhan, Delta, and four Omicron sublineages) of SARS-CoV-2, (+)-3e demonstrated pronounced antiviral activity against all the strains.
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Affiliation(s)
- Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Aleksandr S. Filimonov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Dmitriy S. Baev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
| | - Sophia S. Borisevich
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis SB RAS, 630559 Koltsovo, Russia;
- Laboratory of Chemical Physics, Ufa Institute of Chemistry, Ufa Federal Research Centre, 450078 Ufa, Russia
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Varvara Yu. Chirkova
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Mariya K. Marenina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Yulia V. Meshkova
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Svetlana V. Belenkaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Dmitriy N. Shcherbakov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
- Institute of Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia;
| | - Maxim A. Gureev
- Laboratory of Bio- and Cheminformatics, St. Petersburg School of Physics, Mathematics and Computer Science, HSE University, 194100 St. Peterburg, Russia;
| | - Olga A. Luzina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (A.V.Z.); (O.V.P.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
| | - Mikhail V. Khvostov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia; (A.S.F.); (D.S.B.); (M.K.M.); (Y.V.M.); (S.V.B.); (D.N.S.); (O.A.L.); (N.F.S.); (M.V.K.)
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Kazakova O, Ma X, Tretyakova E, Smirnova I, Slita A, Sinegubova E, Zarubaev V, Jin H, Zhou D, Xiao S. Evaluation of A-ring hydroxymethylene-amino- triterpenoids as inhibitors of SARS-CoV-2 spike pseudovirus and influenza H1N1. J Antibiot (Tokyo) 2024; 77:39-49. [PMID: 38001284 DOI: 10.1038/s41429-023-00677-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023]
Abstract
A set of triterpene A-ring hydroxymethylene-amino-derivatives was synthesized and their antiviral activity was studied. The synthesized compounds were tested for their potential inhibition of SARS-CoV-2 pseudovirus in BHK-21-hACE2 cells and influenza A/PuertoRico/8/34 (H1N1) virus in MDCK cell culture. Compounds 6, 8 and 19 showed significant anti-SARS-CoV-2 pseudovirus activity with EC50 value of 3.20-11.13 µM, which is comparable to the positive control amodiaquine (EC50 3.17 µM). Among them, 28-O-imidazolyl-azepano-betulin 6 and C3-hydroxymethylene-amino-glycyrrhetol-11,13-diene 19 were identified as the lead compounds with SI values of 7 and 10. The binding mode of compound 6 into the RBD domain of SARS-CoV-2 spike glycoprotein (PDB code: 7DK3) by docking and molecular dynamics simulation was investigated.
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Affiliation(s)
- Oxana Kazakova
- Ufa Institute of Chemistry UFRC RAS, pr. Oktyabrya 71, 450054, Ufa, Russia.
| | - Xinyuan Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Elena Tretyakova
- Ufa Institute of Chemistry UFRC RAS, pr. Oktyabrya 71, 450054, Ufa, Russia
| | - Irina Smirnova
- Ufa Institute of Chemistry UFRC RAS, pr. Oktyabrya 71, 450054, Ufa, Russia
| | - Alexander Slita
- Department of Virology, St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Experimental Virology Laboratory, 14 Mira St., St. Petersburg, 197001, Russia
| | - Ekaterina Sinegubova
- Department of Virology, St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Experimental Virology Laboratory, 14 Mira St., St. Petersburg, 197001, Russia
| | - Vladimir Zarubaev
- Department of Virology, St. Petersburg Pasteur Institute of Epidemiology and Microbiology, Experimental Virology Laboratory, 14 Mira St., St. Petersburg, 197001, Russia
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Demin Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Sulong Xiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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Borisevich SS, Zarubaev VV, Shcherbakov DN, Yarovaya OI, Salakhutdinov NF. Molecular Modeling of Viral Type I Fusion Proteins: Inhibitors of Influenza Virus Hemagglutinin and the Spike Protein of Coronavirus. Viruses 2023; 15:v15040902. [PMID: 37112882 PMCID: PMC10142020 DOI: 10.3390/v15040902] [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: 03/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
The fusion of viral and cell membranes is one of the basic processes in the life cycles of viruses. A number of enveloped viruses confer fusion of the viral envelope and the cell membrane using surface viral fusion proteins. Their conformational rearrangements lead to the unification of lipid bilayers of cell membranes and viral envelopes and the formation of fusion pores through which the viral genome enters the cytoplasm of the cell. A deep understanding of all the stages of conformational transitions preceding the fusion of viral and cell membranes is necessary for the development of specific inhibitors of viral reproduction. This review systematizes knowledge about the results of molecular modeling aimed at finding and explaining the mechanisms of antiviral activity of entry inhibitors. The first section of this review describes types of viral fusion proteins and is followed by a comparison of the structural features of class I fusion proteins, namely influenza virus hemagglutinin and the S-protein of the human coronavirus.
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Affiliation(s)
- Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 450078 Ufa, Russia
- Correspondence: (S.S.B.); (O.I.Y.)
| | - Vladimir V. Zarubaev
- Laboratory of Experimental Virology, Saint-Petersburg Pasteur Institute, 197101 Saint Petersburg, Russia;
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia;
| | - Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
- Correspondence: (S.S.B.); (O.I.Y.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia;
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Yarovaya OI, Baranova DV, Sokolova AS, Nemolochnova AG, Sal’nikova OP, Fat’anova AV, Rogachev AD, Volobueva AS, Zarubaev VV, Pokrovsky AG, Salakhutdinov NF. Synthesis of N-heterocyclic amides based on (+)-camphoric acid and study of their antiviral activity and pharmacokinetics. Russ Chem Bull 2023; 72:807-818. [PMID: 37089866 PMCID: PMC10105540 DOI: 10.1007/s11172-023-3845-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 04/25/2023]
Abstract
Efficient conditions for the synthesis of nitrogen-containing heterocyclic derivatives of (1R,3S)(+)-camphoric acid were selected. A series of heterocyclic compounds based on (+)-camphoric acid bearing pharmacophoric fragments was synthesized using the developed methodology. The compounds were tested for their antiviral activity against SARS-CoV-2 and H1N1 influenza viruses, and efficient inhibitors were identified that are of significant interest for further studies. The stability of the compounds and pharmaco-kinetics of the leader compound were studied when administered intragastrically and intramuscularly to mice at a dose of 200 mg kg-1 using the HPLC-MS/MS method.
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Affiliation(s)
- O. I. Yarovaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Akademika Lavrent’eva, 630090 Novosibirsk, Russian Federation
- Novosibirsk State University, 2 ul. Pirogova, 630090 Novosibirsk, Russian Federation
| | - D. V. Baranova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Akademika Lavrent’eva, 630090 Novosibirsk, Russian Federation
| | - A. S. Sokolova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Akademika Lavrent’eva, 630090 Novosibirsk, Russian Federation
| | - A. G. Nemolochnova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Akademika Lavrent’eva, 630090 Novosibirsk, Russian Federation
- Novosibirsk State University, 2 ul. Pirogova, 630090 Novosibirsk, Russian Federation
| | - O. P. Sal’nikova
- Novosibirsk State University, 2 ul. Pirogova, 630090 Novosibirsk, Russian Federation
| | - A. V. Fat’anova
- Novosibirsk State University, 2 ul. Pirogova, 630090 Novosibirsk, Russian Federation
| | - A. D. Rogachev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Akademika Lavrent’eva, 630090 Novosibirsk, Russian Federation
- Novosibirsk State University, 2 ul. Pirogova, 630090 Novosibirsk, Russian Federation
| | - A. S. Volobueva
- Pasteur Institute of Epidemiology and Microbiology, 14 ul. Mira, 197101 St. Petersburg, Russian Federation
| | - V. V. Zarubaev
- Pasteur Institute of Epidemiology and Microbiology, 14 ul. Mira, 197101 St. Petersburg, Russian Federation
| | - A. G. Pokrovsky
- Novosibirsk State University, 2 ul. Pirogova, 630090 Novosibirsk, Russian Federation
| | - N. F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Akademika Lavrent’eva, 630090 Novosibirsk, Russian Federation
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8
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Filimonov AS, Yarovaya OI, Zaykovskaya AV, Rudometova NB, Shcherbakov DN, Chirkova VY, Baev DS, Borisevich SS, Luzina OA, Pyankov OV, Maksyutov RA, Salakhutdinov NF. (+)-Usnic Acid and Its Derivatives as Inhibitors of a Wide Spectrum of SARS-CoV-2 Viruses. Viruses 2022; 14:2154. [PMID: 36298709 PMCID: PMC9611092 DOI: 10.3390/v14102154] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/04/2023] Open
Abstract
In order to test the antiviral activity, a series of usnic acid derivatives were synthesized, including new, previously undescribed compounds. The activity of the derivatives against three strains of SARS-CoV-2 virus was studied. To understand the mechanism of antiviral action, the inhibitory activity of the main protease of SARS-CoV-2 virus was studied using the developed model as well as the antiviral activity against the pseudoviral system with glycoprotein S of SARS-CoV-2 virus on its surface. It was shown that usnic acid exhibits activity against three strains of SARS-CoV-2 virus: Wuhan, Delta, and Omicron. Compounds 10 and 13 also showed high activity against the three strains. The performed biological studies and molecular modeling allowed us to assume that the derivatives of usnic acid bind in the N-terminal domain of the surface glycoprotein S at the binding site of the hemoglobin decay metabolite.
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Affiliation(s)
- Aleksandr S. Filimonov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Olga I. Yarovaya
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Yekaterinburg, Russia
| | - Nadezda B. Rudometova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Yekaterinburg, Russia
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Yekaterinburg, Russia
| | - Varvara Yu. Chirkova
- Department of Physical-Chemistry Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia
| | - Dmitry S. Baev
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 450078 Ufa, Russia
| | - Olga A. Luzina
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Yekaterinburg, Russia
| | - Rinat A. Maksyutov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Yekaterinburg, Russia
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, 630090 Novosibirsk, Russia
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Oreshko VV, Kovaleva KS, Mordvinova ED, Yarovaya OI, Gatilov YV, Shcherbakov DN, Bormotov NI, Serova OA, Shishkina LN, Salakhutdinov NF. Synthesis and Antiviral Properties of Camphor-Derived Iminothiazolidine-4-Ones and 2,3-Dihydrothiazoles. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154761. [PMID: 35897931 PMCID: PMC9331314 DOI: 10.3390/molecules27154761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022]
Abstract
A set of heterocyclic products was synthesized from natural (+)-camphor and semi-synthetic (−)-camphor. Then, 2-Imino-4-thiazolidinones and 2,3-dihydrothiazoles were obtained using a three-step procedure. For the synthesized compounds, their antiviral activity against the vaccinia virus and Marburg virus was studied. New promising agents active against both viruses were found among the tested compounds.
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Affiliation(s)
- Vladislav V. Oreshko
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (V.V.O.); (K.S.K.); (Y.V.G.); (N.F.S.)
- Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogova St., 1, 630090 Novosibirsk, Russia;
| | - Kseniya S. Kovaleva
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (V.V.O.); (K.S.K.); (Y.V.G.); (N.F.S.)
| | - Ekaterina D. Mordvinova
- Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogova St., 1, 630090 Novosibirsk, Russia;
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.I.B.); (O.A.S.); (L.N.S.)
| | - Olga I. Yarovaya
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (V.V.O.); (K.S.K.); (Y.V.G.); (N.F.S.)
- Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogova St., 1, 630090 Novosibirsk, Russia;
- Correspondence: ; Tel.: +7-383-330-88-70
| | - Yuri V. Gatilov
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (V.V.O.); (K.S.K.); (Y.V.G.); (N.F.S.)
| | - Dmitry N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.I.B.); (O.A.S.); (L.N.S.)
| | - Nikolai I. Bormotov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.I.B.); (O.A.S.); (L.N.S.)
| | - Olga A. Serova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.I.B.); (O.A.S.); (L.N.S.)
| | - Larisa N. Shishkina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (D.N.S.); (N.I.B.); (O.A.S.); (L.N.S.)
| | - Nariman F. Salakhutdinov
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 9, 630090 Novosibirsk, Russia; (V.V.O.); (K.S.K.); (Y.V.G.); (N.F.S.)
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