1
|
Medvedev AG, Medved'ko AV, Vener MV, Churakov AV, Prikhodchenko PV, Vatsadze SZ. Dioxygen-halogen bonding exemplified by crystalline peroxosolvates of N, N'-bis(haloacetyl) bispidines. Phys Chem Chem Phys 2024; 26:5195-5206. [PMID: 38261463 DOI: 10.1039/d3cp05834d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The halogen bonding in molecular crystals and supramolecular assemblies has been widely investigated. Special attention is given to the molecular structures capable of simultaneously exhibiting different types of non-covalent interactions, including conventional hydrogen bonds and halogen bonds. This paper systematically analyzes crystalline peroxosolvates of bispidine-based bis-amide derivatives, containing haloacetic acid residues, namely previously reported 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodooethanone) peroxosolvate C13H20I2N2O2·H2O2 (1) and four new crystalline compounds, 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O2·H2O2 (2), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodoethanone) peroxosolvate C13H20I2N2O5·0.5H2O2 (3), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O5·H2O2 (4), and 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-chloroethanone) peroxosolvate C13H20Cl2N2O5·H2O2 (5). Compounds 2-5 were synthesized for the first time and their crystal structures were determined by single-crystal X-ray diffractometry (SCXRD). To the best of our knowledge, 3-5 are unprecedented crystalline hydrogen peroxide adducts of organic hydroperoxides (R-OOH). Short intermolecular contacts between halogen and hydroperoxo oxygen atoms were found in 1-3. The halogen bonding of C-I(Br) fragments with dioxygen species in compounds 1-3 as well as in the previously reported cocrystal of diacetone diperoxide with triodotrinitrobenzene (6) was identified through reduced density gradient analysis, Hirshfeld surface analysis, and Bader analysis of crystalline electron density. The interactions were quantified using the electron density topological properties acquired from the periodic DFT calculations and evaluated to lie in the range of 9-19 kJ mol-1. A distinctive spectral feature was revealed for this type of interaction, involving a red shift of the characteristic O-O stretching vibration by about 6 cm-1, which appeared in IR spectra as a narrow low-intensity band in the region 837-872 cm-1.
Collapse
Affiliation(s)
- Alexander G Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Aleksei V Medved'ko
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Mikhail V Vener
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Andrei V Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Petr V Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| | - Sergey Z Vatsadze
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Krut’ko DP, Medved’ko AV, Lyssenko KA, Churakov AV, Dalinger AI, Kalinin MA, Gudovannyy AO, Ponomarev KY, Suslov EV, Vatsadze SZ. Bispidine Platform as a Tool for Studying Amide Configuration Stability. Molecules 2022; 27:430. [PMID: 35056748 PMCID: PMC8779339 DOI: 10.3390/molecules27020430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this work, the solution conformations of seventeen 3,7-diacyl bispidines were studied by means of NMR spectroscopy including VT NMR experiments. The acyl groups included alkyl, alkenyl, aryl, hetaryl, and ferrocene moieties. The presence of syn/anti-isomers and their ratios were estimated, and some reasons explaining experimental facts were formulated. In particular, all aliphatic and heterocyclic units in the acylic R(CO) fragments led to an increased content of the syn-form in DMSO-d6 solutions. In contrast, only the anti-form was detected in DMSO-d6 and CDCl3 in the case when R = Ph, ferrocenyl, (R)-myrtenyl. In the case of a chiral compound derived from the natural terpene myrtene, a new dynamic process was found in addition to the expected inversion around the amide N-C(O) bond. Here, rotation around the CO-C=C bond in the acylic R fragment was detected, and its energy was estimated. For this compound, ΔG for amide N-C(O) inversion was found to be equal to 15.0 ± 0.2 kcal/mol, and for the rotation around the N(CO)-C2' bond, it was equal to 15.6 ± 0.3 kcal/mol. NMR analysis of the chiral bispidine-based bis-amide was conducted for the first time. Two X-ray structures are reported. For the first time, the unique syn-form was found in the crystal of an acyclic bispidine-based bis-amide. Quantum chemical calculations revealed the unexpected mechanism for amide bond inversion. It was found that the reaction does not proceed as direct N-C(O) bond inversion in the double-chair (CC) conformation but rather requires the conformational transformation into the chair-boat (CB) form first. The amide bond inversion in the latter requires less energy than in the CC form.
Collapse
Affiliation(s)
- Dmitry P. Krut’ko
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | | | - Konstantin A. Lyssenko
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry, 119991 Moscow, Russia;
| | - Alexander I. Dalinger
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| | - Mikhail A. Kalinin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia;
| | - Alexey O. Gudovannyy
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
- High Chemical College, Mendeleev University of Chemical Technology of Russia, 125047 Moscow, Russia
| | - Konstantin Y. Ponomarev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 630090 Novosibirsk, Russia; (K.Y.P.); (E.V.S.)
| | - Eugeny V. Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 630090 Novosibirsk, Russia; (K.Y.P.); (E.V.S.)
| | - Sergey Z. Vatsadze
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia; (D.P.K.); (K.A.L.); (A.I.D.); (M.A.K.); (A.O.G.)
| |
Collapse
|
4
|
Buldashov IA, Medvedev AG, Mikhaylov AA, Churakov AV, Lev O, Prikhodchenko PV. Non-covalent interactions of the hydroperoxo group in crystalline adducts of organic hydroperoxides and their potassium salts. CrystEngComm 2022. [DOI: 10.1039/d2ce01017h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray diffraction of three new stable cocrystals of potassium salts of organic hydroperoxides with molecular hydroperoxides reveals strong charge-assisted ROO−⋯HOOR H-bonds.
Collapse
Affiliation(s)
- Ivan A. Buldashov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
- Faculty of Chemistry, National Research University Higher School of Economics, Miasnitskaya Str. 20, Moscow 101000, Russia
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| | - Ovadia Lev
- The Casali Center, The Institute of Chemistry, and The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow 119991, Russia
| |
Collapse
|