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Sobornova VV, Belov KV, Krestyaninov MA, Khodov IA. Influence of Solvent Polarity on the Conformer Ratio of Bicalutamide in Saturated Solutions: Insights from NOESY NMR Analysis and Quantum-Chemical Calculations. Int J Mol Sci 2024; 25:8254. [PMID: 39125824 PMCID: PMC11311660 DOI: 10.3390/ijms25158254] [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: 06/21/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The study presents a thorough and detailed analysis of bicalutamide's structural and conformational properties. Quantum chemical calculations were employed to explore the conformational properties of the molecule, identifying significant energy differences between conformers. Analysis revealed that hydrogen bonds stabilise the conformers, with notable variations in torsion angles. Conformers were classified into 'closed' and 'open' types based on the relative orientation of the cyclic fragments. NOE spectroscopy in different solvents (CDCl3 and DMSO-d6) was used to study the conformational preferences of the molecule. NOESY experiments provided the predominance of 'closed' conformers in non-polar solvents and a significant presence of 'open' conformers in polar solvents. The proportions of open conformers were 22.7 ± 3.7% in CDCl3 and 59.8 ± 6.2% in DMSO-d6, while closed conformers accounted for 77.3 ± 3.7% and 40.2 ± 6.2%, respectively. This comprehensive study underscores the solvent environment's impact on its structural behaviour. The findings significantly contribute to a deeper understanding of conformational dynamics, stimulating further exploration in drug development.
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Affiliation(s)
| | | | | | - Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo 153045, Russia
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2
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Belov K, Brel V, Sobornova V, Fedorova I, Khodov I. Conformational Analysis of 1,5-Diaryl-3-Oxo-1,4-Pentadiene Derivatives: A Nuclear Overhauser Effect Spectroscopy Investigation. Int J Mol Sci 2023; 24:16707. [PMID: 38069031 PMCID: PMC10706324 DOI: 10.3390/ijms242316707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
1,5-Diaryl-3-Oxo-1,4-Pentadiene derivatives are intriguing organic compounds with a unique structure featuring a pentadiene core, aryl groups, and a ketone group. This study investigates the influence of fluorine atoms on the conformational features of these derivatives in deuterated chloroform (CDCl3) solution. Through nuclear magnetic resonance (NMR) spectroscopy and quantum chemical calculations, we discerned variations in interatomic distances and established predominant conformer proportions. The findings suggest that the non-fluorinated entity exhibits a uniform distribution across various conformer groups. The introduction of a fluorine atom induces substantial alterations, resulting in the predominance of a specific conformer group. This structural insight may hold the key to their diverse anticancer activities, previously reported in the literature.
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Affiliation(s)
- Konstantin Belov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia; (K.B.); (V.S.); (I.F.)
| | - Valery Brel
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Valentina Sobornova
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia; (K.B.); (V.S.); (I.F.)
| | - Irina Fedorova
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia; (K.B.); (V.S.); (I.F.)
| | - Ilya Khodov
- G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia; (K.B.); (V.S.); (I.F.)
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3
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Khodov IA, Belov KV, Krestyaninov MA, Dyshin AA, Kiselev MG. Investigation of the Spatial Structure of Flufenamic Acid in Supercritical Carbon Dioxide Media via 2D NOESY. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16041524. [PMID: 36837153 PMCID: PMC9961892 DOI: 10.3390/ma16041524] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 02/09/2023] [Indexed: 05/13/2023]
Abstract
The search for new forms of already known drug compounds is an urgent problem of high relevance as more potent drugs with fewer side effects are needed. The trifluoromethyl group in flufenamic acid renders its chemical structure differently from other fenamates. This modification is responsible for a large number of conformational polymorphs. Therefore, flufenamic acid is a promising structural modification of well-known drug molecules. An effective approach in this field is micronization, employing "green" supercritical fluid technologies. This research raises some key questions to be answered on how to control polymorphic forms during the micronization of drug compounds. The results presented in this work demonstrate the ability of two-dimensional nuclear Overhauser effect spectroscopy to determine conformational preferences of small molecular weight drug compounds in solutions and fluids, which can be used to predict the polymorphic form during the micronization. Quantitative analysis was carried out to identify the conformational preferences of flufenamic acid molecules in dimethyl sulfoxide-d6 medium at 25 °C and 0.1 MPa, and in mixed solvent medium containing supercritical carbon dioxide at 45 °C and 9 MPa. The data presented allows predictions of the flufenamic acid conformational preferences of poorly soluble drug compounds to obtain new micronized forms.
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Conformational Screening of Arbidol Solvates: Investigation via 2D NOESY. Pharmaceutics 2023; 15:pharmaceutics15010226. [PMID: 36678855 PMCID: PMC9865235 DOI: 10.3390/pharmaceutics15010226] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/31/2022] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Understanding of the nucleation process's fundamental principles in saturated solutions is an urgent task. To do this task, it is necessary to control the formation of polymorphic forms of biologically active compounds. In certain cases, a compound can exist in a single polymorphic form, but have several solvates which can appear in different crystal forms, depending on the medium and conditions of formation, and show different pharmaceutical activity. In the present paper, we report on the analysis of Arbidol conformational preferences in two solvents of different polarities-deuterated chloroform and dimethyl sulfoxide-at 25 °C, using the 2D NOESY method. The Arbidol molecule has various solvate forms depending on the molecular conformation. The method based on the nuclear Overhauser effect spectroscopy was shown to be efficient in the analysis of complex heterocyclic compounds possessing conformation-dependent pseudo-polymorphism. It is one of the types of polymorphism observed in compounds forming crystal solvates. Combined use of NMR methods and X-ray data allowed determining of conformer populations of Arbidol in CDCl3 and DMSO-d6 which were found to be 8/92% and 37/63%, respectively. The preferred conformation in solution is the same that appears in stable crystal solvates of Arbidol.
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Belov KV, Batista de Carvalho LAE, Dyshin AA, Kiselev MG, Sobornova VV, Khodov IA. Conformational Analysis of Mefenamic Acid in scCO2-DMSO by the 2D NOESY Method. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793122070028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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6
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Khodov I, Belov K, Dyshin A, Krestyaninov M, Kiselev M. Pressure effect on lidocaine conformational equilibria in scCO2: A study by 2D NOESY. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Structures Controlled by Entropy: The Flexibility of Strychnine as Example. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227987. [PMID: 36432085 PMCID: PMC9692940 DOI: 10.3390/molecules27227987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
To study the flexibility of strychnine, we performed molecular dynamics simulations with orientational tensorial constraints (MDOC). Tensorial constraints are derived from nuclear magnetic resonance (NMR) interaction tensors, for instance, from residual dipolar couplings (RDCs). Used as orientational constraints, they rotate the whole molecule and molecular parts with low rotational barriers. Since the NMR parameters are measured at ambient temperatures, orientational constraints generate conformers that populate the whole landscape of Gibbs free energy. In MDOC, structures are populated that are not only controlled by energy but by the entropy term TΔS of the Gibbs free energy. In the case of strychnine, it is shown that ring conformers are populated, which has not been discussed in former investigations. These conformer populations are not only in accordance with RDCs but fulfill nuclear Overhauser effect (NOE)-derived distance constraints and 3JHH couplings as well.
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Belov KV, Batista de Carvalho LAE, Dyshin AA, Efimov SV, Khodov IA. The Role of Hidden Conformers in Determination of Conformational Preferences of Mefenamic Acid by NOESY Spectroscopy. Pharmaceutics 2022; 14:2276. [PMID: 36365095 PMCID: PMC9696638 DOI: 10.3390/pharmaceutics14112276] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 12/25/2023] Open
Abstract
Mefenamic acid has been used as a non-steroidal anti-inflammatory drug for a long time. However, its practical use is quite limited due to a number of side effects on the intestinal organs. Conformational polymorphism provides mefenamic acid with unique properties regarding possible modifications obtained during the micronization process, which can improve pharmacokinetics and minimize side effects. Micronization can be performed by decompression of supercritical fluids; methods such as rapid expansion of the supercritical solution have proven their efficiency. However, this group of methods is poorly applicable for compounds with low solubility, and the modification of the method using a pharmaceutically suitable co-solvent may be useful. In our case, addition of only 2 mol% dimethyl sulfoxide increased the solubility remarkably. Information on the conformational state may be critically important for carrying out micronization. In this work, structural analysis and estimate of conformational preferences of mefenamic acid in dimethyl sulfoxide-d6 (at 25 °C and 0.1 MPa) and in a mixed solvent supercritical carbon dioxide + dimethyl sulfoxide-d6 (45 °C, 9 MPa) were performed based on nuclear Overhauser effect spectroscopy. Results show changes in the conformation fractions depending on the medium used. The importance of allowing for hidden conformers in estimating the conformational state was demonstrated in the analysis. Obtained results may be useful for improving micronization parameters.
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Affiliation(s)
- Konstantin V. Belov
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | | | - Alexey A. Dyshin
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - Sergey V. Efimov
- Institute of Physics, Kazan Federal University, 420008 Kazan, Russia
| | - Ilya A. Khodov
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
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Belov KV, Dyshin AA, Kiselev MG, Krestyaninov MA, Sobornova VV, Khodov IA. Determination of the Spatial Structure of Lidocaine in SC-CO2 by the 2D NOESY Method. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2022. [DOI: 10.1134/s1990793121080145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Spatial structure and conformations of hydrazones derived from pyridoxal 5′-phosphate and 2-, 3-pyridinecarbohydrazide in the light of NMR study and quantum chemical calculations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Exposing Hidden Conformations of Carbamazepine Appearing Due to Interaction With the Solid Phase by 2D 1H- 15N HMBC NMR Spectroscopy. J Pharm Sci 2021; 110:1533-1539. [PMID: 33421434 DOI: 10.1016/j.xphs.2021.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 11/20/2022]
Abstract
Two-dimensional 1H-15N HMBC NMR spectra of the well-known anticonvulsant carbamazepine dissolved in different organic solvents, recorded on an NMR spectrometer prove the existence of hidden conformers in saturated solutions. Obtained conformer distribution arises due to the presence of the solid phase in saturated solution. A weak influence of ring currents was revealed for different molecular conformations of carbamazepine dissolved in a saturated solution, which provides a simple approach to discovering hidden conformations. Hidden conformers were found in three different solvents: dimethyl sulfoxide, chloroform, and dichloromethane.
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12
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Lazovskiy DA, Mamardashvili GM, Khodov IA, Mamardashvili NZ. Water soluble porphyrin-fluorescein triads: Design, DFT calculation and pH-change-triggered fluorescence response. J Photochem Photobiol A Chem 2020. [DOI: https://doi.org/10.1016/j.jphotochem.2020.112832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Mamardashvili GM, Kaigorodova EY, Simonova OR, Lazovskiy DA, Mamardashvili NZ. Interaction of the Sn(IV)-tetra(4-sulfonatophenyl)porphyrin axial complexes with cetyltrimethylammonium bromide: Aggregation and location in micelles, fluorescence properties and photochemical stability. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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14
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Mamardashvili GM, Kaigorodova EY, Simonova OR, Lazovskiy DA, Mamardashvili NZ. Interaction of the Sn(IV)-tetra(4-sulfonatophenyl)porphyrin axial complexes with cetyltrimethylammonium bromide: Aggregation and location in micelles, fluorescence properties and photochemical stability. J Mol Liq 2020. [DOI: https://doi.org/10.1016/j.molliq.2020.113988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Lazovskiy DA, Mamardashvili GM, Khodov IA, Mamardashvili NZ. Water soluble porphyrin-fluorescein triads: Design, DFT calculation and pH-change-triggered fluorescence response. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112832] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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16
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Hussaini SR, Kuta A, Pal A, Wang Z, Eastman MA, Duran R. Application of NMR Spectroscopy for the Detection of Equilibrating E- Z Diastereomers. ACS OMEGA 2020; 5:24848-24853. [PMID: 33015503 PMCID: PMC7528312 DOI: 10.1021/acsomega.0c03554] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Conjugation can lower the energy barrier for unsaturated C-C bond rotations, resulting in a mixture of equilibrating diastereomers at room temperature. Therefore, methods claiming diastereoselective synthesis of conjugated double bonds often require proof that the observed diastereomeric ratio is not because of the diastereomeric equilibration of the product. Variable-temperature (VT) NMR experiments are commonly used to distinguish between the two possibilities. However, the VT technique requires accessories for the NMR spectrometer and more setup time. Here, we show that the rarely used application of 1-D and 2-D nuclear Overhauser effect spectroscopy experiments for the detection of the equilibrating diastereomers is a convenient alternative to the VT technique.
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Affiliation(s)
- Syed Raziullah Hussaini
- Department
of Chemistry and Biochemistry, The University
of Tulsa, 800 S. Tucker Drive, Tulsa, Oklahoma 74104, United
States
| | - Adama Kuta
- Department
of Chemistry and Biochemistry, The University
of Tulsa, 800 S. Tucker Drive, Tulsa, Oklahoma 74104, United
States
| | - Arpan Pal
- Department
of Chemistry and Biochemistry, The University
of Tulsa, 800 S. Tucker Drive, Tulsa, Oklahoma 74104, United
States
| | - Zhiguo Wang
- Department
of Chemistry and Biochemistry, The University
of Tulsa, 800 S. Tucker Drive, Tulsa, Oklahoma 74104, United
States
| | - Margaret A. Eastman
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74074, United States
| | - Ramon Duran
- Department
of Chemistry and Biochemistry, The University
of Tulsa, 800 S. Tucker Drive, Tulsa, Oklahoma 74104, United
States
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Khodov I, Dyshin A, Efimov S, Ivlev D, Kiselev M. High-pressure NMR spectroscopy in studies of the conformational composition of small molecules in supercritical carbon dioxide. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113113] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Efimov S, Dubinin M, Kobchikova P, Zgadzay Y, Khodov I, Belosludtsev K, Klochkov V. Comparison of cyclosporin variants B–E based on their structural properties and activity in mitochondrial membranes. Biochem Biophys Res Commun 2020; 526:1054-1060. [DOI: 10.1016/j.bbrc.2020.03.184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
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Mamardashvili GM, Kaigorodova EY, Khodov IA, Scheblykin I, Mamardashvili NZ, Koifman OI. Micelles encapsulated Cо(III)-tetra(4-sulfophenyl)porphyrin in aqueous CTAB solutions: Micelle formation, imidazole binding and redox Co(III)/Co(II) processes. J Mol Liq 2019. [DOI: https://doi.org/10.1016/j.molliq.2019.111471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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20
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Mamardashvili GM, Kaigorodova EY, Khodov IA, Scheblykin I, Mamardashvili NZ, Koifman OI. Micelles encapsulated Cо(III)-tetra(4-sulfophenyl)porphyrin in aqueous CTAB solutions: Micelle formation, imidazole binding and redox Co(III)/Co(II) processes. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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21
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Spatial structure, thermodynamics and kinetics of formation of hydrazones derived from pyridoxal 5′-phosphate and 2-furoic, thiophene-2-carboxylic hydrazides in solution. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.125] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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Mamardashvili GM, Maltceva OV, Lazovskiy DA, Khodov IA, Borovkov V, Mamardashvili NZ, Koifman OI. Medium viscosity effect on fluorescent properties of Sn(IV)-tetra(4-sulfonatophenyl)porphyrin complexes in buffer solutions. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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23
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Mamardashvili GM, Maltceva OV, Lazovskiy DA, Khodov IA, Borovkov V, Mamardashvili NZ, Koifman OI. Medium viscosity effect on fluorescent properties of Sn(IV)-tetra(4-sulfonatophenyl)porphyrin complexes in buffer solutions. J Mol Liq 2019. [DOI: https://doi.org/10.1016/j.molliq.2018.12.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Budkov Y, Kolesnikov A, Ivlev D, Kalikin N, Kiselev M. Possibility of pressure crossover prediction by classical DFT for sparingly dissolved compounds in scCO2. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Manin AN, Voronin AP, Drozd KV, Churakov AV, Perlovich GL. Pharmaceutical salts of emoxypine with dicarboxylic acids. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2018; 74:797-806. [PMID: 29973419 DOI: 10.1107/s2053229618007386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/16/2018] [Indexed: 02/01/2023]
Abstract
New salt forms of the antioxidant drug emoxypine (EMX, 2-ethyl-6-methylpyridin-3-ol) with pharmaceutically acceptable maleic (Mlt), malonic (Mln) and adipic (Adp) acids were obtained {emoxypinium maleate, C8H12NO+·C4H3O4-, [EMX+Mlt], emoxypinium malonate, C8H12NO+·C3H3O4-, [EMX+Mln], and emoxypinium adipate, C8H12NO+·C6H9O4-, [EMX+Adp]} and their crystal structures determined. The molecular packing in the three EMX salts was studied by means of solid-state density functional theory (DFT), followed by QTAIMC (quantum theory of atoms in molecules and crystals) analysis. It was found that the major contribution to the packing energy comes from pyridine-carboxylate and hydroxy-carboxylate heterosynthons forming infinite one-dimensional ribbons, with [EMX+Adp] additionally stabilized by hydrogen-bonded C(9) chains of Adp- ions. The melting processes of the [EMX+Mlt] (1:1), [EMX+Mln] (1:1) and [EMX+Adp] (1:1) salts were studied and the fusion enthalpy was found to increase with the increase of the calculated lattice energy. The dissolution process of the EMX salts in buffer (pH 7.4) was also studied. It was found that the formation of binary crystals of EMX with dicarboxylic acids increases the EMX solubility by more than 30 times compared to its pure form.
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Affiliation(s)
- Alex N Manin
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya St., Ivanovo 153045, Russian Federation
| | - Alexander P Voronin
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya St., Ivanovo 153045, Russian Federation
| | - Ksenia V Drozd
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya St., Ivanovo 153045, Russian Federation
| | - Andrei V Churakov
- Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky Prosp., Moscow 119991, Russian Federation
| | - German L Perlovich
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya St., Ivanovo 153045, Russian Federation
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26
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Theoretical and experimental study of imine-enamine tautomerism of condensation products of propanal with 4-aminobenzoic acid in ethanol. Russ Chem Bull 2017. [DOI: 10.1007/s11172-017-1701-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Khodov IA, Maltceva OV, Klochkov VV, Koifman OI, Mamardashvili NZ. N-Confused porphyrins: complexation and 1H NMR studies. NEW J CHEM 2017. [DOI: 10.1039/c7nj01814b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The complexation of 2-aza-21-carba-tetraphenylporphyrin and 2-aza-2-methyl-5,10,15,20-tetraphenyl-21-carbaporphyrin with nickel and zinc acetates in organic solvents has been investigated by UV-Vis spectroscopy and 1H NMR.
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Affiliation(s)
- Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
- Kazan Federal University
- Kazan
| | - Olga V. Maltceva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
| | | | - Oscar I. Koifman
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- Ivanovo
- Russia
- Research Institute of Macroheterocycles
- Ivanovo State University of Chemistry and Technology
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Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:293-300. [PMID: 27589857 DOI: 10.1007/s00249-016-1167-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong dαα NOE effects between residues R18 and F12, V14, and V16. These "inconsistent" with monomer structure NOEs appears due to formation of an additional antiparallel β-sheet between two monomers. It was also suggested that there is a possible association of protegrins dimers to form octameric or decameric β-barrels in an oligomer state. In order to investigate a more detailed oligomerization process of protegrins, in the present article we report the monomer (PDB ID: 2NC7) and octamer pore structures of the protegrin-5 (PG-5) in the presence of DPC micelles studied by solution NMR spectroscopy. In contrast to PG-1, PG-2, and PG-3 studies, for PG-5 we observed not only dimer NOEs but also several additional NOEs between side chains, which allows us to calculate an octamer pore structure of PG-5 that was in good agreement with previous AFM and PMF data.
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Corrigendum to “The importance of suppressing spin diffusion effects in the accurate determination of the spatial structure of a flexible molecule by nuclear Overhauser effect spectroscopy” [J. Mol. Struct. 1106 (2016) 373–381]. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Khodov IA, Kiselev MG, Efimov SV, Klochkov VV. Comment on "Conformational analysis of small organic molecules using NOE and RDC data: A discussion of strychnine and α-methylene-γ-butyrolactone". JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 266:67-68. [PMID: 26924224 DOI: 10.1016/j.jmr.2016.02.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Affiliation(s)
- I A Khodov
- Laboratory of NMR-spectroscopy and Numerical Investigation Methods of Liquids, G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St. 1, Ivanovo 153045, Russian Federation; Institute of Physics, Kazan Federal University, Kremlevskaya St. 18, Kazan 420008, Russian Federation.
| | - M G Kiselev
- Laboratory of NMR-spectroscopy and Numerical Investigation Methods of Liquids, G.A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St. 1, Ivanovo 153045, Russian Federation
| | - S V Efimov
- Institute of Physics, Kazan Federal University, Kremlevskaya St. 18, Kazan 420008, Russian Federation
| | - V V Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya St. 18, Kazan 420008, Russian Federation
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