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Dalinger AI, Baev DS, Yarovaya OI, Chirkova VY, Sharlaeva EA, Belenkaya SV, Shcherbakov DN, Salakhutdinov NF, Vatsadze SZ. Synthesis of non-symmetric N-benzylbispidinol amides and study of their inhibitory activity against the main protease of the SARS-CoV-2 virus. Russ Chem Bull 2023; 72:239-247. [PMID: 36817558 PMCID: PMC9926410 DOI: 10.1007/s11172-023-3729-x] [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: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 02/16/2023]
Abstract
Based on the data obtained by molecular modeling of the non-covalent interaction of non-symmetric N-benzylbispidin-9-ol amides with the active site of the main protease 3CLpro of the SARS-CoV-2 virus, a series of compounds was synthesized, and their inhibitory activity against 3CLpro was studied and compared with that of the known inhibitor ML188 (IC50 = 1.56±0.55 µmol L-1). It was found that only compound 1g containing the 1,4-dihydroindeno[1,2-c]pyrazole fragment showed moderate activity (IC50 = 100±5.7µmol L-1) and was characterized by the highest calculated binding energy among the studied bispidine derivatives according to molecular docking data.
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Affiliation(s)
- A. I. Dalinger
- Lomonosov Moscow State University, Build. 3, 1 Leninskie Gory, 119991 Moscow, Russian Federation
| | - D. S. Baev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Acad. Lavrentieva, 630090 Novosibirsk, Russian Federation
| | - O. I. Yarovaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Acad. Lavrentieva, 630090 Novosibirsk, Russian Federation
| | - V. Yu. Chirkova
- Altai State University, 61 prosp. Lenina, 656049 Barnaul, Russian Federation
| | - E. A. Sharlaeva
- Altai State University, 61 prosp. Lenina, 656049 Barnaul, Russian Federation
| | - S. V. Belenkaya
- Novosibirsk State University, 2 ul. Pirogova, 630090 Novosibirsk, Russian Federation
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Novosibirsk region, Russian Federation
| | - D. N. Shcherbakov
- Altai State University, 61 prosp. Lenina, 656049 Barnaul, Russian Federation
- Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, State Research Center of Virology and Biotechnology VECTOR, 630559 Koltsovo, Novosibirsk region, Russian Federation
| | - N. F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9 prosp. Acad. Lavrentieva, 630090 Novosibirsk, Russian Federation
| | - S. Z. Vatsadze
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
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2
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Kurskova AO, Dotsenko VV, Frolov KA, Aksenov NA, Aksenova IV, Krivokolysko BS, Peresypkina AA, Chigorina EA, Krivokolysko SG. Synthesis and Aminomethylation of 2-Amino-4-(2-chlorophenyl)-6-(dicyanomethyl)-1,4-dihydropyridine-3,5-dicarbonitrile N-Methylmorpholinium Salt. RUSS J GEN CHEM+ 2022; 92:779-790. [PMID: 35729943 PMCID: PMC9197094 DOI: 10.1134/s1070363222050061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/01/2022]
Abstract
Sequential reaction of 2-chlorobenzaldehyde, cyanothioacetamide, and malononitrile dimer in the presence of an excess of N-methylmorpholine resulted in the formation of N-methylmorphlinium salt of 2-amino-4-(2-chlorophenyl)-6-(dicyanomethyl)-1,4-dihydropyridine-3,5-dicarbonitrile. The resulting salt reacts under Mannich conditions with primary amines and an excess of formaldehyde to form substituted 2-alkylamino-4-(dicyanomethylene)-3,7-diazabicyclo[3.3.1]non-2-ene-1,5-dicarbonitriles. Structure of the key compound was confirmed by single crystal X-ray diffraction analysis.
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Affiliation(s)
- A O Kurskova
- ChemEx Laboratory, V. Dahl Lugansk State University, 91034 Lugansk, Ukraine
| | - V V Dotsenko
- Kuban State University, 350040 Krasnodar, Russia.,North Caucasian Federal University, 355009 Stavropol, Russia
| | - K A Frolov
- ChemEx Laboratory, V. Dahl Lugansk State University, 91034 Lugansk, Ukraine
| | - N A Aksenov
- North Caucasian Federal University, 355009 Stavropol, Russia
| | - I V Aksenova
- North Caucasian Federal University, 355009 Stavropol, Russia
| | - B S Krivokolysko
- Lugansk State Medical University named after St. Luke, 91045 Lugansk, Ukraine
| | - A A Peresypkina
- Belgorod State National Research University, 308015 Belgorod, Russia
| | - E A Chigorina
- National Research Center "Kurchatov Institute" - IREA, 107076 Moscow, Russia.,National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - S G Krivokolysko
- ChemEx Laboratory, V. Dahl Lugansk State University, 91034 Lugansk, Ukraine.,Lugansk State Medical University named after St. Luke, 91045 Lugansk, Ukraine
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Dalinger AI, Churakov AV, Vatsadze SZ. Formation of Spirocyclic Quaternary Ammonium Salts of N-Benzyl-1,5-Dimethyl-3,7-Diazabicyclo[3.3.1]nonan-9-ol due to Its Interaction with Terminal Dibromoalkanes. DOKLADY CHEMISTRY 2022. [DOI: 10.1134/s0012500821090019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Shcherbakov D, Baev D, Kalinin M, Dalinger A, Chirkova V, Belenkaya S, Khvostov A, Krut’ko D, Medved’ko A, Volosnikova E, Sharlaeva E, Shanshin D, Tolstikova T, Yarovaya O, Maksyutov R, Salakhutdinov N, Vatsadze S. Design and Evaluation of Bispidine-Based SARS-CoV-2 Main Protease Inhibitors. ACS Med Chem Lett 2022; 13:140-147. [PMID: 35043075 PMCID: PMC8491553 DOI: 10.1021/acsmedchemlett.1c00299] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/27/2021] [Indexed: 12/31/2022] Open
Abstract
For the first time, derivatives of 3,7-diazabicyclo[3.3.1]nonane (bispidine) were proposed as potential inhibitors of the SARS-CoV-2 main viral protease (3-chymotrypsin-like, 3CLpro). Based on the created pharmacophore model of the active site of the protease, a group of compounds were modeled and tested for activity against 3CLpro. The 3CLpro activity was measured using the fluorogenic substrate Dabcyl-VNSTLQSGLRK(FAM)MA; the efficiency of the proposed approach was confirmed by comparison with literature data for ebselen and disulfiram. The results of the experiments performed with bispidine compounds showed that 14 compounds exhibited activity in the concentration range 1-10 μM, and 3 samples exhibited submicromolar activity. The structure-activity relationship studies showed that the molecules containing a carbonyl group in the ninth position of the bicycle exhibited the maximum activity. Based on the experimental and theoretical results obtained, further directions for the development of this topic were proposed.
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Affiliation(s)
- Dmitriy Shcherbakov
- State
Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Russia, Koltsovo, Novosibirsk Region, Russian Federation
- Altay
State University, 656049, Barnaul, Leninski pr.
61, Russian Federation
| | - Dmitriy Baev
- N.N.
Vorozhtsov Novosibirsk Institute of Organic chemistry SB RAS, Lavrent’ev
av., 630090, Russia, Novosibirsk, Russian Federation
| | - Mikhail Kalinin
- N.D.
Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninski pr., 47, 119991 Moscow, Russian Federation
- Department
of Chemistry, M.V. Lomonosov Moscow State
University, Leninskie Gory, 1-3, 119991 Moscow, Russian Federation
| | - Alexander Dalinger
- Department
of Chemistry, M.V. Lomonosov Moscow State
University, Leninskie Gory, 1-3, 119991 Moscow, Russian Federation
| | - Varvara Chirkova
- Altay
State University, 656049, Barnaul, Leninski pr.
61, Russian Federation
| | - Svetlana Belenkaya
- State
Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Russia, Koltsovo, Novosibirsk Region, Russian Federation
- Novosibirsk
State University, Novosibirsk
Pirogova 1, 630090 Novosibirsk, Russian Federation
| | - Aleksei Khvostov
- Department
of Chemistry, M.V. Lomonosov Moscow State
University, Leninskie Gory, 1-3, 119991 Moscow, Russian Federation
| | - Dmitry Krut’ko
- Department
of Chemistry, M.V. Lomonosov Moscow State
University, Leninskie Gory, 1-3, 119991 Moscow, Russian Federation
| | - Aleksei Medved’ko
- N.D.
Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninski pr., 47, 119991 Moscow, Russian Federation
| | - Ekaterina Volosnikova
- State
Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Russia, Koltsovo, Novosibirsk Region, Russian Federation
| | - Elena Sharlaeva
- Altay
State University, 656049, Barnaul, Leninski pr.
61, Russian Federation
| | - Daniil Shanshin
- State
Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Russia, Koltsovo, Novosibirsk Region, Russian Federation
| | - Tatyana Tolstikova
- N.N.
Vorozhtsov Novosibirsk Institute of Organic chemistry SB RAS, Lavrent’ev
av., 630090, Russia, Novosibirsk, Russian Federation
| | - Olga Yarovaya
- N.N.
Vorozhtsov Novosibirsk Institute of Organic chemistry SB RAS, Lavrent’ev
av., 630090, Russia, Novosibirsk, Russian Federation
| | - Rinat Maksyutov
- State
Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559, Russia, Koltsovo, Novosibirsk Region, Russian Federation
| | - Nariman Salakhutdinov
- N.N.
Vorozhtsov Novosibirsk Institute of Organic chemistry SB RAS, Lavrent’ev
av., 630090, Russia, Novosibirsk, Russian Federation
| | - Sergey Vatsadze
- N.D.
Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninski pr., 47, 119991 Moscow, Russian Federation
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5
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Antipin IS, Alfimov MV, Arslanov VV, Burilov VA, Vatsadze SZ, Voloshin YZ, Volcho KP, Gorbatchuk VV, Gorbunova YG, Gromov SP, Dudkin SV, Zaitsev SY, Zakharova LY, Ziganshin MA, Zolotukhina AV, Kalinina MA, Karakhanov EA, Kashapov RR, Koifman OI, Konovalov AI, Korenev VS, Maksimov AL, Mamardashvili NZ, Mamardashvili GM, Martynov AG, Mustafina AR, Nugmanov RI, Ovsyannikov AS, Padnya PL, Potapov AS, Selektor SL, Sokolov MN, Solovieva SE, Stoikov II, Stuzhin PA, Suslov EV, Ushakov EN, Fedin VP, Fedorenko SV, Fedorova OA, Fedorov YV, Chvalun SN, Tsivadze AY, Shtykov SN, Shurpik DN, Shcherbina MA, Yakimova LS. Functional supramolecular systems: design and applications. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5011] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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7
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Churakov AV, Medved’ko AV, Prikhodchenko PV, Krut’ko DP, Vatsadze SZ. First example of peroxosolvate of iodine-containing organic molecule. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Churakov AV, Medved’ko AV, Prikhodchenko PV, Krut’ko DP, Vatsadze SZ. First example of peroxosolvate of iodine-containing organic molecule. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Vatsadze SZ, Medved’ko AV, Bodunov AA, Lyssenko KA. Bispidine-based bis-azoles as a new family of supramolecular receptors: the theoretical approach. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.05.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Makhova NN, Belen’kii LI, Gazieva GA, Dalinger IL, Konstantinova LS, Kuznetsov VV, Kravchenko AN, Krayushkin MM, Rakitin OA, Starosotnikov AM, Fershtat LL, Shevelev SA, Shirinian VZ, Yarovenko VN. Progress in the chemistry of nitrogen-, oxygen- and sulfur-containing heterocyclic systems. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4914] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Ananikov VP. Organic-Inorganic Hybrid Nanomaterials. NANOMATERIALS 2019; 9:nano9091197. [PMID: 31454924 PMCID: PMC6780615 DOI: 10.3390/nano9091197] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 11/16/2022]
Abstract
The paramount progress in the field of organic–inorganic hybrid nanomaterials was stimulated by numerous applications in chemistry, physics, life sciences, medicine, and technology. Currently, in the field of hybrid materials, researchers may choose either to mimic complex natural materials or to compete with nature by constructing new artificial materials. The deep mechanistic understanding and structural insight achieved in recent years will guide a new wave in the design of hybrid materials at the atomic and molecular levels.
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Affiliation(s)
- Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia.
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