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Bütikofer M, Stadler GR, Kadavath H, Cadalbert R, Torres F, Riek R. Rapid Protein-Ligand Affinity Determination by Photoinduced Hyperpolarized NMR. J Am Chem Soc 2024; 146:17974-17985. [PMID: 38957136 PMCID: PMC11228983 DOI: 10.1021/jacs.4c04000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The binding affinity determination of protein-ligand complexes is a cornerstone of drug design. State-of-the-art techniques are limited by lengthy and expensive processes. Building upon our recently introduced novel screening method utilizing photochemically induced dynamic nuclear polarization (photo-CIDNP) NMR, we provide the methodological framework to determine binding affinities within 5-15 min using 0.1 mg of protein. The accuracy of our method is demonstrated for the affinity constants of peptides binding to a PDZ domain and fragment ligands binding to the protein PIN1. The method can also be extended to measure the affinity of nonphoto-CIDNP-polarizable ligands in competition binding experiments. Finally, we demonstrate a strong correlation between the ligand-reduced signals in photo-CIDNP-based NMR fragment screening and the well-established saturation transfer difference (STD) NMR. Thus, our methodology measures protein-ligand affinities in the micro- to millimolar range in only a few minutes and informs on the binding epitope in a single-scan experiment, opening new avenues for early stage drug discovery approaches.
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Affiliation(s)
- Matthias Bütikofer
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Gabriela R Stadler
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Harindranath Kadavath
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Riccardo Cadalbert
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
| | - Felix Torres
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
- NexMR AG, Wiesenstrasse 10A, 8952 Schlieren, Switzerland
| | - Roland Riek
- Institute for Molecular Physical Science, Vladimir Prelog Weg 2, 8093 Zürich, Switzerland
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Cunha RS, Cruz PF, Costa T, Almeida ZL, de Lima MEF, Serpa C, Chaves OA. Revisiting and Updating the Interaction between Human Serum Albumin and the Non-Steroidal Anti-Inflammatory Drugs Ketoprofen and Ketorolac. Molecules 2024; 29:3001. [PMID: 38998953 PMCID: PMC11243439 DOI: 10.3390/molecules29133001] [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: 05/11/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Ketoprofen (KTF) and ketorolac (KTL) are among the most primarily used non-steroidal anti-inflammatory drugs (NSAIDs) in humans to alleviate moderate pain and to treat inflammation. Their binding affinity with albumin (the main globular protein responsible for the biodistribution of drugs in the bloodstream) was previously determined by spectroscopy without considering some conventional pitfalls. Thus, the present work updates the biophysical characterization of the interactions of HSA:KTF and HSA:KTL by 1H saturation-transfer difference nuclear magnetic resonance (1H STD-NMR), ultraviolet (UV) absorption, circular dichroism (CD), steady-state, and time-resolved fluorescence spectroscopies combined with in silico calculations. The binding of HSA:NSAIDs is spontaneous, endothermic, and entropically driven, leading to a conformational rearrangement of HSA with a slight decrease in the α-helix content (7.1% to 7.6%). The predominance of the static quenching mechanism (ground-state association) was identified. Thus, both Stern-Volmer quenching constant (KSV) and binding constant (Kb) values enabled the determination of the binding affinity. In this sense, the KSV and Kb values were found in the order of 104 M-1 at human body temperature, indicating moderate binding affinity with differences in the range of 0.7- and 3.4-fold between KTF and KTL, which agree with the previously reported experimental pharmacokinetic profile. According to 1H STD-NMR data combined with in silico calculations, the aromatic groups in relation to the aliphatic moiety of the drugs interact preferentially with HSA into subdomain IIIA (site II) and are stabilized by interactions via hydrogen bonding and hydrophobic forces. In general, the data obtained in this study have been revised and updated in comparison to those previously reported by other authors who did not account for inner filter corrections, spectral backgrounds, or the identification of the primary mathematical approach for determining the binding affinity of HSA:KTF and HSA:KTL.
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Affiliation(s)
- Rita S. Cunha
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Pedro F. Cruz
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Telma Costa
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Zaida L. Almeida
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Marco Edilson Freire de Lima
- Departament of Organic Chemistry, Institute of Chemistry, Federal Rural University of Rio de Janeiro, Seropédica 23890-000, RJ, Brazil
| | - Carlos Serpa
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
| | - Otávio A. Chaves
- Department of Chemistry, Coimbra Chemistry Centre-Institute of Molecular Sciences (CQC-IMS), University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
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Palmioli A, Airoldi C. An NMR Toolkit to Probe Amyloid Oligomer Inhibition in Neurodegenerative Diseases: From Ligand Screening to Dissecting Binding Topology and Mechanisms of Action. Chempluschem 2024:e202400243. [PMID: 38712695 DOI: 10.1002/cplu.202400243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
The aggregation of amyloid peptides and proteins into toxic oligomers is a hallmark of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Machado-Joseph's disease, and transmissible spongiform encephalopathies. Inhibition of amyloid oligomers formation and interactions with biological counterparts, as well as the triggering of non-toxic amorphous aggregates, are strategies towards preventive interventions against these pathologies. NMR spectroscopy addresses the need for structural characterization of amyloid proteins and their aggregates, their binding to inhibitors, and rapid screening of compound libraries for ligand identification. Here we briefly discuss the solution experiments constituting the NMR spectroscopist's toolkit and provide examples of their application.
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Affiliation(s)
- Alessandro Palmioli
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
| | - Cristina Airoldi
- Department of Biotechnology and Biosciences, University of Milano - Bicocca, P.zza della Scienza 2, 20126, Milan, Italy
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Putko P, Romero JA, Kazimierczuk K. A pH-enhanced resolution in benchtop NMR spectroscopy. Analyst 2024; 149:1998-2003. [PMID: 38421293 DOI: 10.1039/d3an02000b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
NMR spectroscopy is one of the most potent methods in analytical chemistry. NMR titration experiments are particularly useful since they measure molecular binding affinities and other concentration-dependent effects. These experiments, however, require a long series of measurements. An alternative to these serial measurements has recently been presented, exploiting a pH (or generally - a concentration) gradient along the NMR tube. The proposed experiment, although efficient, was based on the sensitivity- and hardware-demanding chemical shift imaging (CSI) method. Thus, it is practically limited to high-resolution NMR spectrometers. This paper proposes modifying and adapting the approach to the popular and cost-efficient benchtop NMR machines. Instead of CSI, we use a device that shifts the NMR tube vertically to measure the spectra of different sample volumes, which have different pH values due to the established gradient along the tube. We demonstrate the potential of the method on the test samples of L-tyrosine and 2,6-lutidine, and two real samples from the food industry - an infant formula and an energy drink. The proposed method boosts spectral resolution and allows for the sampling of a broader range of pH values when compared to the original approach.
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Affiliation(s)
- Paulina Putko
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland.
| | - Javier A Romero
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland.
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Widmalm G. Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy. JACS AU 2024; 4:20-39. [PMID: 38274261 PMCID: PMC10807006 DOI: 10.1021/jacsau.3c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.
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Affiliation(s)
- Göran Widmalm
- Department of Organic Chemistry,
Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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Rocha G, Ramírez-Cárdenas J, Padilla-Pérez MC, Walpole S, Nepravishta R, García-Moreno MI, Sánchez-Fernández EM, Ortiz Mellet C, Angulo J, Muñoz-García JC. Speeding-up the Determination of Protein-Ligand Affinities by STD NMR: The Reduced Data Set STD NMR Approach (rd-STD NMR). Anal Chem 2024; 96:615-619. [PMID: 38165272 PMCID: PMC10853903 DOI: 10.1021/acs.analchem.3c03980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
STD NMR spectroscopy is a powerful ligand-observed NMR tool for screening and characterizing the interactions of small molecules and low molecular weight fragments with a given macromolecule, identifying the main intermolecular contacts in the bound state. It is also a powerful analytical technique for the accurate determination of protein-ligand dissociation constants (KD) of medium-to-weak affinity, of interest in the pharmaceutical industry. However, accurate KD determination and epitope mapping requires a long series of experiments at increasing saturation times to carry out a full analysis using the so-called STD NMR build-up curve approach and apply the "initial slopes approximation". Here, we have developed a new protocol to bypass this important limitation, which allows us to obtain initial slopes by using just two saturation times and, hence, to very quickly determine precise protein-ligand dissociation constants by STD NMR.
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Affiliation(s)
- Gabriel Rocha
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
| | - Jonathan Ramírez-Cárdenas
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
| | - M. Carmen Padilla-Pérez
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Samuel Walpole
- School
of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Ridvan Nepravishta
- School
of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
- Cancer
Research Horizons, The Beatson Institute, Garscube Estate, Switchback Road,
Bearsden, Glasgow G61 1BD, United Kingdom
| | - M. Isabel García-Moreno
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Elena M. Sánchez-Fernández
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Carmen Ortiz Mellet
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Jesús Angulo
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
- School
of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Juan C. Muñoz-García
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
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