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Advances in NMR Spectroscopy for Bioactive Small Molecules

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: 15 August 2024 | Viewed by 36510

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Special Issue Editor

Dr. Ilya A. Khodov

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Guest Editor

1. Laboratory of "Liquid and Fluid State NMR", G.A. Krestov Institute of Solution Chemistry of RAS (ISC RAS), Akademicheskaya St., Ivanovo 153045, Russia
2. Laboratory of NMR-Spectroscopy and Numerical Investigation Methods of Liquids, G.A. Krestov Institute of Solution Chemistry of RAS (ISC RAS), Akademicheskaya St., Ivanovo 153045, Russia
Interests: molecular structure; conformational analysis; nuclear magnetic resonance (NMR) spectroscopy; diffusion of liquids; drug design; polymorphism; tautomeric forms; supercritical fluids; model cell membranes; non-covalent interactions

Special Issue Information

Dear Colleagues,

Nuclear magnetic resonance spectroscopy is a critical tool for determining the spatial structure of small molecules and their interactions. It is widely used in medicine, physics, and biochemistry to study a wide range of pharmacological and functional materials research topics, such as micronization, impregnation, and adsorption. As such, it is important to develop new methods to improve the accuracy of the determination of NMR spectral parameters in order to gain better insights into the structure and interactions of bioactive small molecules. To this end, this Special Issue, titled “Advances in NMR Spectroscopy for Bioactive Small Molecules”, will provide an opportunity for researchers to share their most recent discoveries in the field of high-quality experimental NMR studies of the structure and lipid interaction studies of bioactive small molecules. We invite authors to submit original research articles as well as review articles that address the latest advances in the NMR spectroscopy of bioactive small molecules. Potential topics include, but are not limited to: NMR methodologies for bioactive small molecules; NMR strategies for structural elucidation of bioactive small molecules; NMR techniques for the study of bioactive small molecules in solution; NMR studies of bioactive small molecules in biological systems; NMR studies of bioactive small molecules in membrane environments; and NMR spectroscopy of small molecule lipid interactions We look forward to receiving your submissions.

Dr. Ilya A. Khodov
Guest Editor

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Published Papers (7 papers)

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Research

15 pages, 5655 KiB

Open AccessArticle

NMR Study of Water-Soluble Carotenoid Crocin: Formation of Mixed Micelles, Interaction with Lipid Membrane and Antioxidant Activity

by Wenjing Su, Anna V. Mastova, Maya A. Ul’yanova, Polina A. Kononova, Olga Yu. Selyutina, Veronika I. Evseenko, Elizaveta S. Meteleva, Alexander V. Dushkin, Weike Su and Nikolay E. Polyakov

Int. J. Mol. Sci. 2024, 25(6), 3194; https://doi.org/10.3390/ijms25063194 - 11 Mar 2024

Viewed by 3800

Abstract

Crocin is a unique water-soluble carotenoid found in crocus and gardenia flowers. Crocin has been shown to have a variety of pharmacological activities, such as antioxidant, anti-cancer, memory improvement, antidepressant, anti-ischemia, blood pressure lowering and aphrodisiac, gene protection and detoxification activities. Due to their amphiphilicity, crocin molecules form concentration-dependent self-associates (micelles) in a water solution. In the present study, using various NMR techniques (T₂ relaxation and selective gradient NOESY), we have demonstrated that crocin forms mixed micelles with water-soluble drug delivery system glycyrrhizin and linoleic acid molecules. Note, that the spin–spin T₂ relaxation time and NOESY spectroscopy are very sensitive to intermolecular interactions and molecular diffusion mobility. The second purpose of this work was the elucidation of the interaction of crocin with a model lipid membrane using NMR techniques and a molecular dynamics simulation and its effects on lipid oxidation. It was shown that the crocin molecule is located near the surface of the lipid bilayer and effectively protects lipids from oxidation by peroxyl radicals. The role of glycyrrhizin and vitamin C in metal-induced lipid oxidation was also elucidated. The results of this study may be useful for expanding the field of application of crocin in medicine and in the food industry. Full article

(This article belongs to the Special Issue Advances in NMR Spectroscopy for Bioactive Small Molecules)

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9 pages, 894 KiB

Open AccessArticle

Assessment of the Long-Range NMR C,H Coupling of a Series of Carbazolequinone Derivatives

by Matías Monroy-Cárdenas, José A. Gavín and Ramiro Araya-Maturana

Int. J. Mol. Sci. 2023, 24(24), 17450; https://doi.org/10.3390/ijms242417450 - 14 Dec 2023

Viewed by 719

Abstract

Synthesis, the complete ¹H- and ¹³C-NMR assignments, and the long-range C,H coupling constants (ⁿJ_C,H) of some hydrogen-deficient carbazolequinones, assessed by a J-HMBC experiment, are reported. In these molecules, the protons, used as entry points for assignments, are separated by several bonds with non-protonated atom carbons. Therefore, the use of long-range NMR experiments for the assignment of the spectra is mandatory; we used HSQC and HMBC. On the other hand, the measured heteronuclear (C,H) coupling constants ²J to ⁵J) allow us to choose the value of the long-range delay used in the HMBC experiment less arbitrarily in order to visualize a desired correlation in the spectrum. The chemical shifts and the coupling constant values can be used as input for assignments in related chemical structures. Full article

(This article belongs to the Special Issue Advances in NMR Spectroscopy for Bioactive Small Molecules)

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19 pages, 4960 KiB

Open AccessArticle

Conformational Analysis of 1,5-Diaryl-3-Oxo-1,4-Pentadiene Derivatives: A Nuclear Overhauser Effect Spectroscopy Investigation

by Konstantin Belov, Valery Brel, Valentina Sobornova, Irina Fedorova and Ilya Khodov

Int. J. Mol. Sci. 2023, 24(23), 16707; https://doi.org/10.3390/ijms242316707 - 24 Nov 2023

Cited by 1 | Viewed by 10157

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. Full article

(This article belongs to the Special Issue Advances in NMR Spectroscopy for Bioactive Small Molecules)

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15 pages, 2502 KiB

Open AccessArticle

Weak, Broken, but Working—Intramolecular Hydrogen Bond in 2,2′-bipyridine

by Ilya G. Shenderovich

Int. J. Mol. Sci. 2023, 24(12), 10390; https://doi.org/10.3390/ijms241210390 - 20 Jun 2023

Cited by 1 | Viewed by 2152

Abstract

From an academic and practical point of view, it is desirable to be able to assess the possibility of the proton exchange of a given molecular system just by knowing the positions of the proton acceptor and the proton donor. This study addresses the difference between intramolecular hydrogen bonds in 2,2′-bipyridinium and 1,10-phenanthrolinium. Solid-state ¹⁵N NMR and model calculations show that these hydrogen bonds are weak; their energies are 25 kJ/mol and 15 kJ/mol, respectively. Neither these hydrogen bonds nor N-H stretches can be responsible for the fast reversible proton transfer observed for 2,2′-bipyridinium in a polar solvent down to 115 K. This process must have been caused by an external force, which was a fluctuating electric field present in the solution. However, these hydrogen bonds are the grain that tips the scales precisely because they are an integral part of a large system of interactions, including both intramolecular interactions and environmental influence. Full article

(This article belongs to the Special Issue Advances in NMR Spectroscopy for Bioactive Small Molecules)

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19 pages, 8403 KiB

Open AccessArticle

Intramolecular Hydrogen Bonding in N⁶-Substituted 2-Chloroadenosines: Evidence from NMR Spectroscopy

by Maria Ya. Berzina, Barbara Z. Eletskaya, Alexei L. Kayushin, Elena V. Dorofeeva, Olga I. Lutonina, Ilya V. Fateev, Olga N. Zhavoronkova, Arthur R. Bashorin, Alexandra O. Arnautova, Olga S. Smirnova, Konstantin V. Antonov, Alexander S. Paramonov, Maxim A. Dubinnyi, Roman S. Esipov, Anatoly I. Miroshnikov and Irina D. Konstantinova

Int. J. Mol. Sci. 2023, 24(11), 9697; https://doi.org/10.3390/ijms24119697 - 2 Jun 2023

Viewed by 1301

Abstract

Two forms were found in the NMR spectra of N⁶-substituted 2-chloroadenosines. The proportion of the mini-form was 11–32% of the main form. It was characterized by a separate set of signals in COSY, ¹⁵N-HMBC and other NMR spectra. We assumed that the mini-form arises due to the formation of an intramolecular hydrogen bond between the N7 atom of purine and the N⁶–CH proton of the substituent. The ¹H,¹⁵N-HMBC spectrum confirmed the presence of a hydrogen bond in the mini-form of the nucleoside and its absence in the main form. Compounds incapable of forming such a hydrogen bond were synthesized. In these compounds, either the N7 atom of the purine or the N⁶–CH proton of the substituent was absent. The mini-form was not found in the NMR spectra of these nucleosides, confirming the importance of the intramolecular hydrogen bond in its formation. Full article

(This article belongs to the Special Issue Advances in NMR Spectroscopy for Bioactive Small Molecules)

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18 pages, 6429 KiB

Open AccessArticle

Extent of N-Terminus Folding of Semenogelin 1 Cleavage Product Determines Tendency to Amyloid Formation

by Daria A. Osetrina, Aleksandra M. Kusova, Aydar G. Bikmullin, Evelina A. Klochkova, Aydar R. Yulmetov, Evgenia A. Semenova, Timur A. Mukhametzyanov, Konstantin S. Usachev, Vladimir V. Klochkov and Dmitriy S. Blokhin

Int. J. Mol. Sci. 2023, 24(10), 8949; https://doi.org/10.3390/ijms24108949 - 18 May 2023

Viewed by 1100

Abstract

It is known that four peptide fragments of predominant protein in human semen Semenogelin 1 (SEM1) (SEM1(86–107), SEM1(68–107), SEM1(49–107) and SEM1(45–107)) are involved in fertilization and amyloid formation processes. In this work, the structure and dynamic behavior of SEM1(45–107) and SEM1(49–107) peptides and their N-domains were described. According to ThT fluorescence spectroscopy data, it was shown that the amyloid formation of SEM1(45–107) starts immediately after purification, which is not observed for SEM1(49–107). Seeing that the peptide amino acid sequence of SEM1(45–107) differs from SEM1(49–107) only by the presence of four additional amino acid residues in the N domain, these domains of both peptides were obtained via solid-phase synthesis and the difference in their dynamics and structure was investigated. SEM1(45–67) and SEM1(49–67) showed no principal difference in dynamic behavior in water solution. Furthermore, we obtained mostly disordered structures of SEM1(45–67) and SEM1(49–67). However, SEM1(45–67) contains a helix (E58-K60) and helix-like (S49-Q51) fragments. These helical fragments may rearrange into β-strands during amyloid formation process. Thus, the difference in full-length peptides’ (SEM1(45–107) and SEM1(49–107)) amyloid-forming behavior may be explained by the presence of a structured helix at the SEM1(45–107) N-terminus, which contributes to an increased rate of amyloid formation. Full article

(This article belongs to the Special Issue Advances in NMR Spectroscopy for Bioactive Small Molecules)

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17 pages, 3629 KiB

Open AccessArticle

Exploring the Conformational Equilibrium of Mefenamic Acid Released from Silica Aerogels via NMR Analysis

by Ilya Khodov, Valentina Sobornova, Valeriya Mulloyarova, Konstantin Belov, Alexey Dyshin, Luís Batista de Carvalho, Peter Tolstoy and Michael Kiselev

Int. J. Mol. Sci. 2023, 24(8), 6882; https://doi.org/10.3390/ijms24086882 - 7 Apr 2023

Cited by 6 | Viewed by 16143

Abstract

This study examines the influence of mefenamic acid on the physical and chemical properties of silica aerogels, as well as its effect on the sorption characteristics of the composite material. Solid state magic angle spinning nuclear magnetic resonance (MAS NMR) and high-pressure ¹³C NMR kinetic studies were conducted to identify the presence of mefenamic acid and measure the kinetic rates of CO₂ sorption. Additionally, a high-pressure T₁–T₂ relaxation-relaxation correlation spectroscopy (RRCOSY) study was conducted to estimate the relative amount of mefenamic acid in the aerogel’s pores, and a high-pressure nuclear Overhauser effect spectoscopy (NOESY) study was conducted to investigate the conformational preference of mefenamic acid released from the aerogel. The results indicate that mefenamic acid is affected by the chemical environment of the aerogel, altering the ratio of mefenamic acid conformers from 75% to 25% in its absence to 22% to 78% in the presence of aerogel. Full article

(This article belongs to the Special Issue Advances in NMR Spectroscopy for Bioactive Small Molecules)

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