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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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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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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: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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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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Medved'ko AV, Dalinger AI, Nuriev VN, Semashko VS, Filatov AV, Ezhov AA, Churakov AV, Howard JAK, Shiryaev AA, Baranchikov AE, Ivanov VK, Vatsadze SZ. Supramolecular Organogels Based on N-Benzyl, N'-Acylbispidinols. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E89. [PMID: 30641896 PMCID: PMC6359647 DOI: 10.3390/nano9010089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 12/24/2018] [Accepted: 01/03/2019] [Indexed: 12/12/2022]
Abstract
The acylation of unsymmetrical N-benzylbispidinols in aromatic solvents without an external base led to the formation of supramolecular gels, which possess different thicknesses and degrees of stability depending on the substituents in para-positions of the benzylic group as well as on the nature of the acylating agent and of the solvent used. Structural features of the native gels as well as of their dried forms were studied by complementary techniques including Fourier-transform infrared (FTIR) and attenuated total reflection (ATR) spectroscopy, atomic force microscopy (AFM), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and small-angle X-ray scattering and diffraction (SAXS). Structures of the key crystalline compounds were established by X-ray diffraction. An analysis of the obtained data allowed speculation on the crucial structural and condition factors that governed the gel formation. The most important factors were as follows: (i) absence of base, either external or internal; (ii) presence of HCl; (iii) presence of carbonyl and hydroxyl groups to allow hydrogen bonding; and (iv) presence of two (hetero)aromatic rings at both sides of the molecule. The hydrogen bonding involving amide carbonyl, hydroxyl at position 9, and, very probably, ammonium N-H⁺ and Cl- anion appears to be responsible for the formation of infinite molecular chains required for the first step of gel formation. Subsequent lateral cooperation of molecular chains into fibers occurred, presumably, due to the aromatic π-π-stacking interactions. Supercritical carbon dioxide drying of the organogels gave rise to aerogels with morphologies different from that of air-dried samples.
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Affiliation(s)
- Alexey V Medved'ko
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | | | - Vyacheslav N Nuriev
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Vera S Semashko
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Andrei V Filatov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Alexander A Ezhov
- Faculty of Physics, Lomonosov Moscow State University, 119991 Moscow, Russia.
- Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 119991 Moscow, Russia.
| | | | - Andrey A Shiryaev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119071 Moscow, Russia.
- Institute of Geology of Ore Deposits, Petrography, Mineralogy and Geochemistry, Russian Academy of Sciences, 119017 Moscow, Russia.
| | - Alexander E Baranchikov
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Vladimir K Ivanov
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 119991 Moscow, Russia.
- Faculty of Material Science, Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Sergey Z Vatsadze
- Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
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6
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Vereshchagin AN. Classical and interdisciplinary approaches to the design of organic and hybrid molecular systems. Russ Chem Bull 2018. [DOI: 10.1007/s11172-017-1950-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Synthesis of hybrid compounds composed of daunorubicin covalently linked with Cp 2 Fe and CpMn(CO) 3. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Vatsadze SZ, Manaenkova MA, Vasilev EV, Venskovsky NU, Khrustalev VN. Crystal structures and supra-molecular features of 9,9-dimethyl-3,7-di-aza-bicyclo-[3.3.1]nonane-2,4,6,8-tetra-one, 3,7-di-aza-spiro-[bi-cyclo-[3.3.1]nonane-9,1'-cyclo-penta-ne]-2,4,6,8-tetra-one and 9-methyl-9-phenyl-3,7-di-aza-bicyclo-[3.3.1]nonane-2,4,6,8-tetra-one di-methyl-formamide monosolvate. Acta Crystallogr E Crystallogr Commun 2017; 73:1097-1101. [PMID: 28775891 PMCID: PMC5499299 DOI: 10.1107/s2056989017009458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 06/25/2017] [Indexed: 11/10/2022]
Abstract
Compounds (I), C9H10N2O4, (II), C11H12N2O4, and (III), C14H12N2O4·C3H7NO represent 9,9-disubstituted-3,7-di-aza-bicyclo-[3.3.1]nonane-2,4,6,8-tetra-one deriv-atives with very similar mol-ecular geometries for the bicyclic framework: the dihedral angle between the planes of the imide groups is 74.87 (6), 73.86 (3) and 74.83 (6)° in (I)-(III), respectively. The dimethyl derivative (I) is positioned on a crystallographic twofold axis and its overall geometry deviates only slightly from idealized C2v symmetry. The spiro-cyclo-pentane derivative (II) and the phen-yl/methyl analog (III) retain only inter-nal Cs symmetry, which in the case of (II) coincides with crystallographic mirror symmetry. The cyclo-pentane moiety in (II) adopts an envelope conformation, with the spiro C atom deviating from the mean plane of the rest of the ring by 0.548 (2) Å. In compound (III), an N-H⋯O hydrogen bond is formed with the di-methyl-formamide solvent mol-ecule. In the crystal, both (I) and (II) form similar zigzag hydrogen-bonded ribbons through double inter-molecular N-H⋯O hydrogen bonds. However, whereas in (I) the ribbons are formed by two trans-arranged O=C-N-H amide fragments, the amide fragments are cis-positioned in (II). The formation of ribbons in (III) is apparently disrupted by participation of one of its N-H groups in hydrogen bonding with the solvent mol-ecule. As a result, the mol-ecules of (III) form zigzag chains rather than the ribbons through inter-molecular N-H⋯O hydrogen bonds. The crystal of (I) was a pseudo-merohedral twin.
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Affiliation(s)
- Sergey Z. Vatsadze
- Department of Chemistry, Moscow State University, 1 Leninskie Gory, Moscow 119991, Russian Federation
| | - Marina A. Manaenkova
- Department of Chemistry, Moscow State University, 1 Leninskie Gory, Moscow 119991, Russian Federation
| | - Evgeny V. Vasilev
- Department of Chemistry, Moscow State University, 1 Leninskie Gory, Moscow 119991, Russian Federation
| | - Nikolai U. Venskovsky
- Inorganic Chemistry Department, Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklay St., Moscow 117198, Russian Federation
| | - Victor N. Khrustalev
- Inorganic Chemistry Department, Faculty of Science, Peoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklay St., Moscow 117198, Russian Federation
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