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New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 4557

Special Issue Editor

Dr. Igor Zhukov

E-Mail Website
Guest Editor
Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland
Interests: NMR spectroscopy; protein structure; NMR relaxation; molecular dynamic processes; membrane proteins; neurodegenerative diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

NMR spectroscopy has evolved significantly over many years, and recent advancements have introduced exciting possibilities for chemical and biomolecular research. Understanding these new trends is crucial for staying at the forefront of structural analysis and metabolomic/pharmaceutical studies. We demonstrate the latest achievements in NMR spectroscopy, specifically applications that may revolutionize scientific research on biomolecular systems. We are interested in introducing the newest NMR techniques, including dynamic nuclear polarization (DNP-NMR), and solid-state NMR. We plan to explore how NMR spectroscopy is employed in metabolomics, drug discovery, and pharmaceutical research. We will highlight NMR applications, such as intrinsically disordered proteins, protein–ligand interactions, and membrane proteins. We will discuss the challenges in NMR-based research and speculate on future directions and innovations that may shape the field in the coming years. By understanding and embracing these trends, we aim to present knowledge required to advance structural analysis and metabolomic/pharmaceutical research. This Special Issue will be a valuable resource for up-to-date developments in NMR and their applications.

Dr. Igor Zhukov
Guest Editor

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Keywords

  • NMR spectroscopy
  • metabolomics
  • pharmaceutical studies
  • solid-state NMR
  • 19F NMR spectroscopy
  • peptide
  • IDP proteins

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Published Papers (5 papers)

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Research

20 pages, 3409 KiB  
Article
Metabolomic Profiling of Osteoblasts in Rat Subchondral Bone Following Anterior Cruciate Ligament Injury
by Xu Qiu, Huili Deng, Xuchang Zhou, Guoxin Ni, Caihua Huang and Donghai Lin
Molecules 2025, 30(11), 2255; https://doi.org/10.3390/molecules30112255 - 22 May 2025
Abstract
Objectives: Osteoarthritis (OA) is a prevalent chronic degenerative joint disorder marked by cartilage degradation, subchondral bone remodeling, and synovial inflammation. Despite its widespread occurrence, effective pharmacological interventions to halt or reverse OA progression remain elusive. Thus, an in-depth understanding of its pathogenesis is [...] Read more.
Objectives: Osteoarthritis (OA) is a prevalent chronic degenerative joint disorder marked by cartilage degradation, subchondral bone remodeling, and synovial inflammation. Despite its widespread occurrence, effective pharmacological interventions to halt or reverse OA progression remain elusive. Thus, an in-depth understanding of its pathogenesis is imperative for developing novel therapeutic strategies. Methods: Sixty-four male Sprague-Dawley rats (8 weeks old, weighing 180–220 g) were randomly assigned to two groups: the anterior cruciate ligament transection (ACLT) group and the sham-operated group. Primary osteoblasts were isolated from the subchondral bone at 0, 4, 8, and 12 weeks after ACLT. Nuclear magnetic resonance (NMR)-based metabolomics was used to elucidate metabolic changes and the underlying mechanisms in osteoblasts. Results: A total of 26 metabolites were identified from the NMR spectra of osteoblasts. Distinct metabolic profiles were observed in the ACLT group at 0, 4, 8, and 12 weeks after surgery. In particular, several differential metabolites were identified, including glucose, lactate, NADP+, phosphocreatine, and alanine, as well as eight perturbed pathways, such as alanine, aspartate, and glutamate metabolism, phenylalanine metabolism, and taurine metabolism. Conclusions: Key energy-related metabolites, including glucose, lactate, creatine phosphate, and creatine, were identified as key markers of osteoblast dysfunction in OA, underscoring the profound metabolic perturbations induced by ACL injury. These disturbances in energy homeostasis are strongly implicated in the progression of OA. In addition, branched-chain amino acids emerged as potential biomarkers, further highlighting the metabolic dysregulation associated with the disease. Taken together, the metabolic changes observed in rat osteoblasts following ACL injury reveal a complex interplay between energy and amino acid metabolism, providing critical insights into the pathogenesis of post-traumatic OA and highlighting potential therapeutic targets. Full article
(This article belongs to the Special Issue New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies)
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24 pages, 3520 KiB  
Article
Nuclear Magnetic Resonance Analysis Seeking for Metabolic Markers of Hypertension in Human Serum
by Adriana Sousa, Nádia Oliveira, Ricardo Conde, Elisabete Morais, Ana Paula Amaral, Nieves Embade, Oscar Millet and Ignacio Verde
Molecules 2025, 30(10), 2145; https://doi.org/10.3390/molecules30102145 - 13 May 2025
Viewed by 226
Abstract
Hypertension is a highly prevalent medical condition that occurs when blood pressure is too high, which greatly increases the risk of developing other cardiovascular diseases and is generally associated with higher rates of morbidity and mortality. Due to the silent/asymptomatic nature of hypertension, [...] Read more.
Hypertension is a highly prevalent medical condition that occurs when blood pressure is too high, which greatly increases the risk of developing other cardiovascular diseases and is generally associated with higher rates of morbidity and mortality. Due to the silent/asymptomatic nature of hypertension, although the methods currently available to diagnose it are easy, they generally do not allow for an early diagnosis and an efficient prognosis to avoid irreversible damage in the medium or long term. In fact, an early diagnosis of hypertension would be crucial to decrease hypertension-associated mortality. Since metabolomics using NMR can provide a global measurement of various serum metabolites, it is very suitable for detecting novel biomarkers. We therefore analyzed serum metabolomic profiles among normotensive and hypertensive elderly individuals by NMR and identified new potential biomarkers for hypertension and associated diseases. We found higher levels of acetate, formate, and glycerol, and lower levels of glutamine, glycine, and sarcosine in individuals with hypertension. Therefore, these metabolites could be used for early diagnosis of hypertension to avoid comorbidities derived from hypertension and associated mortality. Full article
(This article belongs to the Special Issue New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies)
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18 pages, 3654 KiB  
Article
Quantitative 1H and 13C NMR and Chemometric Assessment of 13C NMR Data: Application to Anabolic Steroid Formulations
by Stéphane Balayssac, Gaëtan Assemat, Saïda Danoun, Myriam Malet-Martino and Véronique Gilard
Molecules 2025, 30(9), 2060; https://doi.org/10.3390/molecules30092060 - 6 May 2025
Viewed by 233
Abstract
This study investigates the potential of 1H and 13C NMR for the characterization and classification of anabolic androgenic steroids (AASs) in various formulations. First, twenty AAS formulations, including tablets, capsules, and injectable solutions, were analyzed using 1H NMR for the [...] Read more.
This study investigates the potential of 1H and 13C NMR for the characterization and classification of anabolic androgenic steroids (AASs) in various formulations. First, twenty AAS formulations, including tablets, capsules, and injectable solutions, were analyzed using 1H NMR for the qualitative identification and quantification of active compounds. The results revealed discrepancies between the labeled and detected substances in several samples, highlighting issues related to product mislabeling and potential health risks. Then, twelve oil-based injectable formulations were examined using 13C NMR, demonstrating its effectiveness in differentiating and quantifying closely related steroid structures that cannot be discriminated with 1H NMR. A chemometric approach from 13C NMR data, based on a principal component analysis (PCA) and hierarchical cluster analysis (HCA), enabled the classification of samples and the identification of key active ingredients. Full article
(This article belongs to the Special Issue New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies)
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18 pages, 4881 KiB  
Article
DPPA as a Potential Cell Membrane Component Responsible for Binding Amyloidogenic Protein Human Cystatin C
by Igor Zhukov, Emilia Sikorska, Marta Orlikowska, Magdalena Górniewicz-Lorens, Mariusz Kepczynski and Przemyslaw Jurczak
Molecules 2024, 29(15), 3446; https://doi.org/10.3390/molecules29153446 - 23 Jul 2024
Cited by 1 | Viewed by 1472
Abstract
A phospholipid bilayer is a typical structure that serves crucial functions in various cells and organelles. However, it is not unusual for it to take part in pathological processes. The cell membrane may be a binding target for amyloid-forming proteins, becoming a factor [...] Read more.
A phospholipid bilayer is a typical structure that serves crucial functions in various cells and organelles. However, it is not unusual for it to take part in pathological processes. The cell membrane may be a binding target for amyloid-forming proteins, becoming a factor modulating the oligomerization process leading to amyloid deposition—a hallmark of amyloidogenic diseases—e.g., Alzheimer’s disease. The information on the mechanisms governing the oligomerization influenced by the protein–membrane interactions is scarce. Therefore, our study aims to describe the interactions between DPPA, a cell membrane mimetic, and amyloidogenic protein human cystatin C. Circular dichroism spectroscopy and differential scanning calorimetry were used to monitor (i) the secondary structure of the human cystatin C and (ii) the phase transition temperature of the DPPA, during the protein–membrane interactions. NMR techniques were used to determine the protein fragments responsible for the interactions, and molecular dynamics simulations were applied to provide a molecular structure representing the interaction. The obtained data indicate that the protein interacts with DPPA, submerging itself into the bilayer via the AS region. Additionally, the interaction increases the content of α-helix within the protein’s secondary structure and stabilizes the whole molecule against denaturation. Full article
(This article belongs to the Special Issue New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies)
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15 pages, 2062 KiB  
Article
The Temperature Dependence of Hydrogen Bonds Is More Uniform in Stable Proteins: An Analysis of NMR h3JNC′ Couplings in Four Different Protein Structures
by Andrei T. Alexandrescu and Aurelio J. Dregni
Molecules 2024, 29(13), 2950; https://doi.org/10.3390/molecules29132950 - 21 Jun 2024
Viewed by 1655
Abstract
Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC′, 2JNC′, 3JNCγ, and h3JNC′ couplings. The h3JNC′ couplings are transmitted through hydrogen bonds and their sizes are correlated to [...] Read more.
Long-range HNCO NMR spectra for proteins show crosspeaks due to 1JNC′, 2JNC′, 3JNCγ, and h3JNC′ couplings. The h3JNC′ couplings are transmitted through hydrogen bonds and their sizes are correlated to hydrogen bond lengths. We collected long-range HNCO data at a series of temperatures for four protein structures. P22i and CUS-3i are six-stranded beta-barrel I-domains from phages P22 and CUS-3 that share less than 40% sequence identity. The cis and trans states of the C-terminal domain from pore-forming toxin hemolysin ΙΙ (HlyIIC) arise from the isomerization of a single G404-P405 peptide bond. For P22i and CUS-3i, hydrogen bonds detected by NMR agree with those observed in the corresponding domains from cryoEM structures of the two phages. Hydrogen bond lengths derived from the h3JNC′ couplings, however, are poorly conserved between the distantly related CUS-3i and P22i domains and show differences even between the closely related cis and trans state structures of HlyIIC. This is consistent with hydrogen bond lengths being determined by local differences in structure rather than the overall folding topology. With increasing temperature, hydrogen bonds typically show an apparent increase in length that has been attributed to protein thermal expansion. Some hydrogen bonds are invariant with temperature, however, while others show apparent decreases in length, suggesting they become stabilized with increasing temperature. Considering the data for the three proteins in this study and previously published data for ubiquitin and GB3, lowered protein folding stability and cooperativity corresponds with a larger range of temperature responses for hydrogen bonds. This suggests a partial uncoupling of hydrogen bond energetics from global unfolding cooperativity as protein stability decreases. Full article
(This article belongs to the Special Issue New Trends of Nuclear Magnetic Resonance Spectroscopy (NMR) in Chemical and Biomolecular Studies)
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