1
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Wetton H, Klukowski P, Riek R, Güntert P. Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA. Front Mol Biosci 2023; 10:1244029. [PMID: 37854037 PMCID: PMC10581199 DOI: 10.3389/fmolb.2023.1244029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023] Open
Abstract
Chemical shift transfer (CST) is a well-established technique in NMR spectroscopy that utilizes the chemical shift assignment of one protein (source) to identify chemical shifts of another (target). Given similarity between source and target systems (e.g., using homologs), CST allows the chemical shifts of the target system to be assigned using a limited amount of experimental data. In this study, we propose a deep-learning based workflow, ARTINA-CST, that automates this procedure, allowing CST to be carried out within minutes or hours of computational time and strictly without any human supervision. We characterize the efficacy of our method using three distinct synthetic and experimental datasets, demonstrating its effectiveness and robustness even when substantial differences exist between the source and target proteins. With its potential applications spanning a wide range of NMR projects, including drug discovery and protein interaction studies, ARTINA-CST is anticipated to be a valuable method that facilitates research in the field.
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Affiliation(s)
- Henry Wetton
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
| | - Piotr Klukowski
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
| | - Peter Güntert
- Institute of Molecular Physical Science, ETH Zurich, Zurich, Switzerland
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, Japan
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2
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Torres F, Stadler G, Kwiatkowski W, Orts J. A Benchmark Study of Protein-Fragment Complex Structure Calculations with NMR 2. Int J Mol Sci 2023; 24:14329. [PMID: 37762631 PMCID: PMC10531959 DOI: 10.3390/ijms241814329] [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: 08/04/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Protein-fragment complex structures are particularly sought after in medicinal chemistry to rationally design lead molecules. These structures are usually derived using X-ray crystallography, but the failure rate is non-neglectable. NMR is a possible alternative for the calculation of weakly interacting complexes. Nevertheless, the time-consuming protein signal assignment step remains a barrier to its routine application. NMR Molecular Replacement (NMR2) is a versatile and rapid method that enables the elucidation of a protein-ligand complex structure. It has been successfully applied to peptides, drug-like molecules, and more recently to fragments. Due to the small size of the fragments, ca < 300 Da, solving the structures of the protein-fragment complexes is particularly challenging. Here, we present the expected performances of NMR2 when applied to protein-fragment complexes. The NMR2 approach has been benchmarked with the SERAPhic fragment library to identify the technical challenges in protein-fragment NMR structure calculation. A straightforward strategy is proposed to increase the method's success rate further. The presented work confirms that NMR2 is an alternative method to X-ray crystallography for solving protein-fragment complex structures.
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Affiliation(s)
- Felix Torres
- Institute of Molecular Physical Science, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland (G.S.); (W.K.)
| | - Gabriela Stadler
- Institute of Molecular Physical Science, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland (G.S.); (W.K.)
| | - Witek Kwiatkowski
- Institute of Molecular Physical Science, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland (G.S.); (W.K.)
| | - Julien Orts
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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3
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Xue Y, Ucieklak K, Gohil S, Niedziela T, Nestor G, Sandström C. Metabolic labeling of hyaluronan: Biosynthesis and quantitative analysis of 13C, 15N-enriched hyaluronan by NMR and MS-based methods. Carbohydr Res 2023; 531:108888. [PMID: 37390793 DOI: 10.1016/j.carres.2023.108888] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Hyaluronan (HA), a member of the GAG family of glycans, has many diverse biological functions that vary a lot depending on the length of the HA chain and its concentration. A better understanding of the structure of different-sized HA at the atomic level is therefore crucial to decipher these biological functions. NMR is a method of choice for conformational studies of biomolecules, but there are limitations due to the low natural abundance of the NMR active nuclei 13C and 15N. We describe here the metabolic labeling of HA using the bacterium Streptococcus equi subsp. Zooepidemicus and the subsequent analysis by NMR and mass spectrometry. The level of 13C and 15N isotope enrichment at each position was determined quantitatively by NMR spectroscopy and was further confirmed by high-resolution mass spectrometry analysis. This study provides a valid methodological approach that can be applied to the quantitative assessment of isotopically labeled glycans and will help improve detection capabilities and facilitate future structure-function relationship analysis of complex glycans.
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Affiliation(s)
- Yan Xue
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.
| | - Karolina Ucieklak
- Hirszfeld Institute of Immunology and Experimental Therapy, 53-114, Wroclaw, Poland.
| | - Suresh Gohil
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.
| | - Tomasz Niedziela
- Hirszfeld Institute of Immunology and Experimental Therapy, 53-114, Wroclaw, Poland.
| | - Gustav Nestor
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.
| | - Corine Sandström
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07, Uppsala, Sweden.
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4
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Zhang W, Xiang Y, Xu W. Probing protein higher-order structures by native capillary electrophoresis-mass spectrometry. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5
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Methyl probes in proteins for determining ligand binding mode in weak protein-ligand complexes. Sci Rep 2022; 12:11231. [PMID: 35789157 PMCID: PMC9253027 DOI: 10.1038/s41598-022-13561-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/25/2022] [Indexed: 11/11/2022] Open
Abstract
Structures of protein–ligand complexes provide critical information for drug design. Most protein–ligand complex structures are determined using X-ray crystallography, but where crystallography is not able to generate a structure for a complex, NMR is often the best alternative. However, the available tools to enable rapid and robust structure determination of protein–ligand complexes by NMR are currently limited. This leads to situations where projects are either discontinued or pursued without structural data, rendering the task more difficult. We previously reported the NMR Molecular Replacement (NMR2) approach that allows the structure of a protein–ligand complex to be determined without requiring the cumbersome task of protein resonance assignment. Herein, we describe the NMR2 approach to determine the binding pose of a small molecule in a weak protein–ligand complex by collecting sparse protein methyl-to-ligand NOEs from a selectively labeled protein sample and an unlabeled ligand. In the selective labeling scheme all methyl containing residues of the protein are protonated in an otherwise deuterated background. This allows measurement of intermolecular NOEs with greater sensitivity using standard NOESY pulse sequences instead of isotope-filtered NMR experiments. This labelling approach is well suited to the NMR2 approach and extends its utility to include larger protein–ligand complexes.
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6
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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7
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Lin Y, Gross ML. Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies. Biomolecules 2022; 12:135. [PMID: 35053283 PMCID: PMC8773722 DOI: 10.3390/biom12010135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 01/01/2023] Open
Abstract
Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), "fast photochemical oxidation of proteins" (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including "protein-ligand interactions by mass spectrometry, titration and HD exchange" (PLIMSTEX) and "ligand titration, fast photochemical oxidation of proteins and mass spectrometry" (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.
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Affiliation(s)
- Yanchun Lin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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8
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Bourafai-Aziez A, Benabderrahmane M, Paysant H, Weiswald LB, Poulain L, Carlier L, Ravault D, Jouanne M, Coadou G, Oulyadi H, Voisin-Chiret AS, Sopková-de Oliveira Santos J, Sebban M. Drug Repurposing: Deferasirox Inhibits the Anti-Apoptotic Activity of Mcl-1. Drug Des Devel Ther 2021; 15:5035-5059. [PMID: 34949914 PMCID: PMC8688747 DOI: 10.2147/dddt.s323077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/27/2021] [Indexed: 11/30/2022] Open
Abstract
Introduction With the aim of repositioning commercially available drugs for the inhibition of the anti-apoptotic myeloid cell leukemia protein, Mcl-1, implied in various cancers, five molecules, highlighted from a published theoretical screening, were selected to experimentally validate their affinity toward Mcl-1. Results A detailed NMR study revealed that only two of the five tested drugs, Torsemide and Deferasirox, interacted with Mcl-1. NMR data analysis allowed the complete characterization of the binding mode of both drugs to Mcl-1, including the estimation of their affinity for Mcl-1. Biological assays evidenced that the biological activity of Torsemide was lower as compared to the Deferasirox, which was able to efficiently and selectively inhibit the anti-apoptotic activity of Mcl-1. Finally, docking and molecular dynamics led to a 3D model for the Deferasirox:Mcl-1 complex and revealed the positioning of the drug in the Mcl-1 P2/P3 pockets as well as almost all synthetic Mcl-1 inhibitors. Interestingly, contrary to known synthetic Mcl-1 inhibitors which interact through Arg263, Deferasirox, establishes a salt bridge with Lys234. Conclusion Deferasirox could be a potential candidate for drug repositioning as Mcl-1 inhibitor.
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Affiliation(s)
- Asma Bourafai-Aziez
- Normandie Université, UNIROUEN, INSA de Rouen, CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Rouen, 76000, France
| | | | - Hippolyte Paysant
- Normandie Université, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, Caen, 14076, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, Caen, 14076, France
| | - Louis-Bastien Weiswald
- Normandie Université, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, Caen, 14076, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, Caen, 14076, France
| | - Laurent Poulain
- Normandie Université, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, Caen, 14076, France.,UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, Caen, 14076, France
| | - Ludovic Carlier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, Paris, France
| | - Delphine Ravault
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, Paris, France
| | | | - Gaël Coadou
- Normandie Université, UNIROUEN, INSA de Rouen, CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Rouen, 76000, France
| | - Hassan Oulyadi
- Normandie Université, UNIROUEN, INSA de Rouen, CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Rouen, 76000, France
| | | | | | - Muriel Sebban
- Normandie Université, UNIROUEN, INSA de Rouen, CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Rouen, 76000, France
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9
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Yong JRJ, Hansen AL, Kupče Ē, Claridge TDW. Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 329:107027. [PMID: 34246882 DOI: 10.1016/j.jmr.2021.107027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 05/22/2023]
Abstract
The sensitivity-enhanced HSQC, as well as HSQC-TOCSY, experiments have been modified for incorporation into NOAH (NMR by Ordered Acquisition using 1H detection) supersequences, adding diversity for 13C and 15N modules. Importantly, these heteronuclear modules have been specifically tailored to preserve the magnetisation required for subsequent acquisition of other heteronuclear or homonuclear modules in a supersequence. In addition, we present protocols for optimally combining HSQC and HSQC-TOCSY elements within the same supersequences, yielding high-quality 2D spectra suitable for structure characterisation but with greatly reduced experiment durations. We further demonstrate that these time savings can translate to increased detection sensitivity per unit time.
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Affiliation(s)
- Jonathan R J Yong
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH 43210, USA
| | - Ēriks Kupče
- Bruker UK Ltd., Banner Lane, Coventry CV4 9GH, UK
| | - Tim D W Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.
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10
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Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
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11
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Orts J, Riek R. Protein-ligand structure determination with the NMR molecular replacement tool, NMR 2. JOURNAL OF BIOMOLECULAR NMR 2020; 74:633-642. [PMID: 32621003 DOI: 10.1007/s10858-020-00324-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.
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Affiliation(s)
- Julien Orts
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Wolgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
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12
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Li Q, Kang C. A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery. Molecules 2020; 25:molecules25132974. [PMID: 32605297 PMCID: PMC7411973 DOI: 10.3390/molecules25132974] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/21/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that 19F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
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13
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Fragments: where are we now? Biochem Soc Trans 2020; 48:271-280. [PMID: 31985743 DOI: 10.1042/bst20190694] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/30/2022]
Abstract
Fragment-based drug discovery (FBDD) has become a mainstream technology for the identification of chemical hit matter in drug discovery programs. To date, the food and drug administration has approved four drugs, and over forty compounds are in clinical studies that can trace their origins to a fragment-based screen. The challenges associated with implementing an FBDD approach are many and diverse, ranging from the library design to developing methods for identifying weak affinity compounds. In this article, we give an overview of current progress in fragment library design, fragment to lead optimisation and on the advancement in techniques used for screening. Finally, we will comment on the future opportunities and challenges in this field.
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14
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Wiegand T. A solid-state NMR tool box for the investigation of ATP-fueled protein engines. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 117:1-32. [PMID: 32471533 DOI: 10.1016/j.pnmrs.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
Motor proteins are involved in a variety of cellular processes. Their main purpose is to convert the chemical energy released during adenosine triphosphate (ATP) hydrolysis into mechanical work. In this review, solid-state Nuclear Magnetic Resonance (NMR) approaches are discussed allowing studies of structures, conformational events and dynamic features of motor proteins during a variety of enzymatic reactions. Solid-state NMR benefits from straightforward sample preparation based on sedimentation of the proteins directly into the Magic-Angle Spinning (MAS) rotor. Protein resonance assignment is the crucial and often time-limiting step in interpreting the wealth of information encoded in the NMR spectra. Herein, potentials, challenges and limitations in resonance assignment for large motor proteins are presented, focussing on both biochemical and spectroscopic approaches. This work highlights NMR tools available to study the action of the motor domain and its coupling to functional processes, as well as to identify protein-nucleotide interactions during events such as DNA replication. Arrested protein states of reaction coordinates such as ATP hydrolysis can be trapped for NMR studies by using stable, non-hydrolysable ATP analogues that mimic the physiological relevant states as accurately as possible. Recent advances in solid-state NMR techniques ranging from Dynamic Nuclear Polarization (DNP), 31P-based heteronuclear correlation experiments, 1H-detected spectra at fast MAS frequencies >100 kHz to paramagnetic NMR are summarized and their applications to the bacterial DnaB helicase from Helicobacter pylori are discussed.
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Affiliation(s)
- Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
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15
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Bourafai-Aziez A, Sebban M, Benabderrahmane M, Marekha B, Denis C, Paysant H, Weiswald LB, Carlier L, Bureau R, Coadou G, Ravault D, Voisin-Chiret AS, Sopková-de Oliveira Santos J, Oulyadi H. Binding mode of Pyridoclax to myeloid cell leukemia-1 (Mcl-1) revealed by nuclear magnetic resonance spectroscopy, docking and molecular dynamics approaches. J Biomol Struct Dyn 2019; 38:4162-4178. [PMID: 31612791 DOI: 10.1080/07391102.2019.1680434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Myeloid cell leukemia-1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 family proteins. Its amplification is one of the most frequent genetic aberrations found in human cancers. Pyridoclax, a promising BH3 mimetic inhibitor, interacts directly with Mcl-1 and induces massive apoptosis at a concentration of 15 µM in combination with anti-Bcl-xL strategies in chemo-resistant ovarian cancer cell lines. In this study, a combined experimental and theoretical approach was used to investigate the binding mode of Pyridoclax to Mcl-1. The representative poses generated from dynamics simulations compared with NMR data revealed: (i) Pyridoclax bound to P1 and P2 pockets of Mcl-1 BH3 binding groove through its styryl and methyl groups establishing mainly hydrophobic contacts, (ii) one of the ending pyridines interacts through electrostatic interaction with K234 side chain, a negatively charged residue present only in this position in Mcl-1. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A Bourafai-Aziez
- CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Normandie Université, UNIROUEN, INSA de Rouen, Rouen, France.,Normandie Université, UniCaen, CERMN, F-14000 Caen, France
| | - M Sebban
- CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Normandie Université, UNIROUEN, INSA de Rouen, Rouen, France
| | | | - B Marekha
- Normandie Université, UniCaen, CERMN, F-14000 Caen, France
| | - C Denis
- Normandie Université, UniCaen, CERMN, F-14000 Caen, France
| | - H Paysant
- Normandie Université, UNICAEN, Inserm U1086 ANTICIPE « Interdisciplinary Research Unit for Cancer Prevention and Treatment », Biologie et Thérapies Innovantes des Cancers de l'ovaire (BioTICLA), Caen, France.,Centre de Lutte Contre le Cancer F. Baclesse, Unicancer, Caen, France
| | - L B Weiswald
- Normandie Université, UNICAEN, Inserm U1086 ANTICIPE « Interdisciplinary Research Unit for Cancer Prevention and Treatment », Biologie et Thérapies Innovantes des Cancers de l'ovaire (BioTICLA), Caen, France.,Centre de Lutte Contre le Cancer F. Baclesse, Unicancer, Caen, France
| | - L Carlier
- Laboratoire Des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Paris, France
| | - R Bureau
- Normandie Université, UniCaen, CERMN, F-14000 Caen, France
| | - G Coadou
- CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Normandie Université, UNIROUEN, INSA de Rouen, Rouen, France
| | - D Ravault
- Laboratoire Des Biomolécules, LBM, Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Paris, France
| | | | | | - H Oulyadi
- CNRS Laboratoire COBRA (UMR 6014 & FR 3038), Normandie Université, UNIROUEN, INSA de Rouen, Rouen, France
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Sánchez-Murcia PA, Mills A, Cortés-Cabrera Á, Gago F. Unravelling the covalent binding of zampanolide and taccalonolide AJ to a minimalist representation of a human microtubule. J Comput Aided Mol Des 2019; 33:627-644. [DOI: 10.1007/s10822-019-00208-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/24/2019] [Indexed: 01/27/2023]
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Assessing molecular interactions with biophysical methods using the validation cross. Biochem Soc Trans 2018; 47:63-76. [DOI: 10.1042/bst20180271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 11/17/2022]
Abstract
Abstract
There are numerous methods for studying molecular interactions. However, each method gives rise to false negative- or false positive binding results, stemming from artifacts of the scientific equipment or from shortcomings of the experimental format. To validate an initial positive binding result, additional methods need to be applied to cover the shortcomings of the primary experiment. The aim of such a validation procedure is to exclude as many artifacts as possible to confirm that there is a true molecular interaction that meets the standards for publishing or is worth investing considerable resources for follow-up activities in a drug discovery project. To simplify this validation process, a graphical scheme — the validation cross — can be used. This simple graphic is a powerful tool for identifying blind spots of a binding hypothesis, for selecting the most informative combination of methods to reveal artifacts and, in general, for understanding more thoroughly the nature of a validation process. The concept of the validation cross was originally introduced for the validation of protein–ligand interactions by NMR in drug discovery. Here, an attempt is made to expand the concept to further biophysical methods and to generalize it for binary molecular interactions.
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NMR Methods of Characterizing Biomolecular Structural Dynamics and Conformational Ensembles. Methods 2018; 148:1-3. [DOI: 10.1016/j.ymeth.2018.08.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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New Methods in Biomolecular Nuclear Magnetic Resonance Spectroscopy. Methods 2018; 138-139:1-2. [DOI: 10.1016/j.ymeth.2018.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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