1
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Cheng K, Wu Q, Yao C, Chai Z, Jiang L, Liu M, Li C. Distinct Inhibition Modes of New Delhi Metallo-β-lactamase-1 Revealed by NMR Spectroscopy. JACS AU 2023; 3:849-859. [PMID: 37006760 PMCID: PMC10052233 DOI: 10.1021/jacsau.2c00651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
The wide spread of antibiotic-resistant "superbugs" containing New Delhi metallo-β-lactamase-1 (NDM-1) has become a threat to human health. However, clinically valid antibiotics to treat the superbugs' infection are not available now. Quick, simple, and reliable methods to assess the ligand-binding mode are key to developing and improving inhibitors against NDM-1. Herein, we report a straightforward NMR method to distinguish the NDM-1 ligand-binding mode using distinct NMR spectroscopy patterns of apo- and di-Zn-NDM-1 titrations with various inhibitors. Elucidating the inhibition mechanism will aid the development of efficient inhibitors for NDM-1.
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Affiliation(s)
- Kai Cheng
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qiong Wu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chendie Yao
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhaofei Chai
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ling Jiang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
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2
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He S, Lim GE. The Application of High-Throughput Approaches in Identifying Novel Therapeutic Targets and Agents to Treat Diabetes. Adv Biol (Weinh) 2023; 7:e2200151. [PMID: 36398493 DOI: 10.1002/adbi.202200151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Indexed: 11/19/2022]
Abstract
During the past decades, unprecedented progress in technologies has revolutionized traditional research methodologies. Among these, advances in high-throughput drug screening approaches have permitted the rapid identification of potential therapeutic agents from drug libraries that contain thousands or millions of molecules. Moreover, high-throughput-based therapeutic target discovery strategies can comprehensively interrogate relationships between biomolecules (e.g., gene, RNA, and protein) and diseases and significantly increase the authors' knowledge of disease mechanisms. Diabetes is a chronic disease primarily characterized by the incapacity of the body to maintain normoglycemia. The prevalence of diabetes in modern society has become a severe public health issue that threatens the well-being of millions of patients. Although a number of pharmacological treatments are available, there is no permanent cure for diabetes, and discovering novel therapeutic targets and agents continues to be an urgent need. The present review discusses the technical details of high-throughput screening approaches in drug discovery, followed by introducing the applications of such approaches to diabetes research. This review aims to provide an example of the applicability of high-throughput technologies in facilitating different aspects of disease research.
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Affiliation(s)
- Siyi He
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
| | - Gareth E Lim
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
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3
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Mandal R, Pham P, Hilty C. Screening of Protein-Ligand Binding Using a SABRE Hyperpolarized Reporter. Anal Chem 2022; 94:11375-11381. [PMID: 35921650 DOI: 10.1021/acs.analchem.2c02250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hyperpolarization through signal amplification by reversible exchange (SABRE) provides a facile means to enhance nuclear magnetic resonance (NMR) signals of small molecules containing an N-heterocycle or other binding site for a polarization transfer catalyst. A purpose-designed reporter ligand, which is capable of binding both to a target protein and to the catalyst, makes the sensitivity enhancement by this technique compatible with the measurement of a range of biomolecular interactions. The 1H polarization of the reporter ligand 4-amidinopyridine, which is targeting trypsin, is used to screen ligands that are not themselves hyperpolarizable by SABRE. The respective protein-ligand dissociation constants (KD) are determined by an observed change in the R2 relaxation rate of the reporter. A calculation of expected signal changes indicates that the accessible ligand KD values extend over several orders of magnitude, while the concentrations of target proteins and ligands can be reduced considering the sensitivity gains from hyperpolarization. In general, the design of a single, weakly binding ligand for a target protein enables the use of SABRE hyperpolarization for ligand screening or other biophysical studies involving macromolecular interactions.
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Affiliation(s)
- Ratnamala Mandal
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Pierce Pham
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Christian Hilty
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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4
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Torres F, Walser R, Kaderli J, Rossi E, Bobby R, Packer MJ, Sarda S, Walker G, Hitchin JR, Milbradt AG, Orts J. NMR Molecular Replacement Provides New Insights into Binding Modes to Bromodomains of BRD4 and TRIM24. J Med Chem 2022; 65:5565-5574. [PMID: 35357834 PMCID: PMC9017284 DOI: 10.1021/acs.jmedchem.1c01703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-based drug discovery (SBDD) largely relies on structural information from X-ray crystallography because traditional NMR structure calculation methods are too time consuming to be aligned with typical drug discovery timelines. The recently developed NMR molecular replacement (NMR2) method dramatically reduces the time needed to generate ligand-protein complex structures using published structures (apo or holo) of the target protein and treating all observed NOEs as ambiguous restraints, bypassing the laborious process of obtaining sequence-specific resonance assignments for the protein target. We apply this method to two therapeutic targets, the bromodomain of TRIM24 and the second bromodomain of BRD4. We show that the NMR2 methodology can guide SBDD by rationalizing the observed SAR. We also demonstrate that new types of restraints and selective methyl labeling have the potential to dramatically reduce "time to structure" and extend the method to targets beyond the reach of traditional NMR structure elucidation.
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Affiliation(s)
- Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Reto Walser
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Emanuele Rossi
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Romel Bobby
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Martin J Packer
- Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Sunil Sarda
- BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Graeme Walker
- Drug Discovery Unit, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - James R Hitchin
- Drug Discovery Unit, Cancer Research UK Manchester Institute, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, HCI F217, Eidgenossische Technische Hochschule Zurich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.,Department of Pharmaceutical Sciences, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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5
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McCoy M, Fradera X, Reutershan MH, Machacek M, Trotter BW. NMR Data-Driven Docking of HDM2-Inhibitor Complexes. Chembiochem 2022; 23:e202100570. [PMID: 35104390 DOI: 10.1002/cbic.202100570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/22/2021] [Indexed: 11/05/2022]
Abstract
We present an automated NMR-guided docking workflow that can be used to generate models of protein-ligand complexes based on data from NOE NMR experiments. The first step is to generate a number of intermolecular distance constraints from experimental NOE data. Then, the ligand is docked on an ensemble of receptor structures to account for protein flexibility, and multiple poses are generated. Finally, we use the NOE-based constraints to filter and score docking poses based on the percentage of NOE constraints that are consistent with protein-ligand interatomic distances. This workflow was successfully used during a Lead Optimization project to generate models of synthetic PPI inhibitors bound to the HDM2 protein.
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Affiliation(s)
- Mark McCoy
- Merck and Co Inc, Merck Research Laboratories, 2000 Galloping Hill Road, 07033, Kenilworth, UNITED STATES
| | - Xavier Fradera
- Merck: Merck & Co Inc, Merck Research Laboratories, UNITED STATES
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6
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Qi C, Wang Y, Hilty C. Application of Relaxation Dispersion of Hyperpolarized 13 C Spins to Protein-Ligand Binding. Angew Chem Int Ed Engl 2021; 60:24018-24021. [PMID: 34468077 DOI: 10.1002/anie.202109430] [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: 07/15/2021] [Indexed: 11/11/2022]
Abstract
Nuclear spin relaxation dispersion parameters are proposed as indicators of the binding mode of a ligand to a protein. Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) provided a 13 C signal enhancement between 3000-6000 for the ligand 4-(trifluoromethyl) benzene-1-carboximidamide binding to trypsin. The measurement of 13 C R2 relaxation dispersion was enabled without isotope enrichment, using a series of single-scan Carr-Purcell-Meiboom-Gill experiments with variable refocusing delays. The magnitude in dispersion for the spins of the ligand is correlated to the position with respect to the salt bridge between protein and the amidine group of the ligand, indicating the ligand binding orientation. Hyperpolarized relaxation dispersion is an alternative to chemical shift or NOE measurements for determining ligand binding modes.
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Affiliation(s)
- Chang Qi
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX, USA
| | - Yunyi Wang
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX, USA
| | - Christian Hilty
- Chemistry Department, Texas A&M University, 3255 TAMU, College Station, TX, USA
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7
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Qi C, Wang Y, Hilty C. Application of Relaxation Dispersion of Hyperpolarized
13
C Spins to Protein–Ligand Binding. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Chang Qi
- Chemistry Department Texas A&M University 3255 TAMU College Station TX USA
| | - Yunyi Wang
- Chemistry Department Texas A&M University 3255 TAMU College Station TX USA
| | - Christian Hilty
- Chemistry Department Texas A&M University 3255 TAMU College Station TX USA
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8
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Anaraki MT, Lysak DH, Downey K, Kock FVC, You X, Majumdar RD, Barison A, Lião LM, Ferreira AG, Decker V, Goerling B, Spraul M, Godejohann M, Helm PA, Kleywegt S, Jobst K, Soong R, Simpson MJ, Simpson AJ. NMR spectroscopy of wastewater: A review, case study, and future potential. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 126-127:121-180. [PMID: 34852923 DOI: 10.1016/j.pnmrs.2021.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
NMR spectroscopy is arguably the most powerful tool for the study of molecular structures and interactions, and is increasingly being applied to environmental research, such as the study of wastewater. With over 97% of the planet's water being saltwater, and two thirds of freshwater being frozen in the ice caps and glaciers, there is a significant need to maintain and reuse the remaining 1%, which is a precious resource, critical to the sustainability of most life on Earth. Sanitation and reutilization of wastewater is an important method of water conservation, especially in arid regions, making the understanding of wastewater itself, and of its treatment processes, a highly relevant area of environmental research. Here, the benefits, challenges and subtleties of using NMR spectroscopy for the analysis of wastewater are considered. First, the techniques available to overcome the specific challenges arising from the nature of wastewater (which is a complex and dilute matrix), including an examination of sample preparation and NMR techniques (such as solvent suppression), in both the solid and solution states, are discussed. Then, the arsenal of available NMR techniques for both structure elucidation (e.g., heteronuclear, multidimensional NMR, homonuclear scalar coupling-based experiments) and the study of intermolecular interactions (e.g., diffusion, nuclear Overhauser and saturation transfer-based techniques) in wastewater are examined. Examples of wastewater NMR studies from the literature are reviewed and potential areas for future research are identified. Organized by nucleus, this review includes the common heteronuclei (13C, 15N, 19F, 31P, 29Si) as well as other environmentally relevant nuclei and metals such as 27Al, 51V, 207Pb and 113Cd, among others. Further, the potential of additional NMR methods such as comprehensive multiphase NMR, NMR microscopy and hyphenated techniques (for example, LC-SPE-NMR-MS) for advancing the current understanding of wastewater are discussed. In addition, a case study that combines natural abundance (i.e. non-concentrated), targeted and non-targeted NMR to characterize wastewater, along with in vivo based NMR to understand its toxicity, is included. The study demonstrates that, when applied comprehensively, NMR can provide unique insights into not just the structure, but also potential impacts, of wastewater and wastewater treatment processes. Finally, low-field NMR, which holds considerable future potential for on-site wastewater monitoring, is briefly discussed. In summary, NMR spectroscopy is one of the most versatile tools in modern science, with abilities to study all phases (gases, liquids, gels and solids), chemical structures, interactions, interfaces, toxicity and much more. The authors hope this review will inspire more scientists to embrace NMR, given its huge potential for both wastewater analysis in particular and environmental research in general.
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Affiliation(s)
- Maryam Tabatabaei Anaraki
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Daniel H Lysak
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Katelyn Downey
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Flávio Vinicius Crizóstomo Kock
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada; Department of Chemistry, Federal University of São Carlos-SP (UFSCar), São Carlos, SP, Brazil
| | - Xiang You
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Rudraksha D Majumdar
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada; Synex Medical, 2 Bloor Street E, Suite 310, Toronto, ON M4W 1A8, Canada
| | - Andersson Barison
- NMR Center, Federal University of Paraná, CP 19081, 81530-900 Curitiba, PR, Brazil
| | - Luciano Morais Lião
- NMR Center, Institute of Chemistry, Universidade Federal de Goiás, Goiânia 74690-900, Brazil
| | | | - Venita Decker
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | | | - Manfred Spraul
- Bruker Biospin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | | | - Paul A Helm
- Environmental Monitoring & Reporting Branch, Ontario Ministry of the Environment, Toronto M9P 3V6, Canada
| | - Sonya Kleywegt
- Technical Assessment and Standards Development Branch, Ontario Ministry of the Environment, Conservation and Parks, Toronto, ON M4V 1M2, Canada
| | - Karl Jobst
- Memorial University of Newfoundland, St. John's, NL A1C 5S7, Canada
| | - Ronald Soong
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Myrna J Simpson
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada
| | - Andre J Simpson
- Environmental NMR Center, University of Toronto Scarborough, 1265 Military Trail, Toronto M1C1A4, Canada.
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9
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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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10
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Wang Y, Kim J, Hilty C. Determination of protein-ligand binding modes using fast multi-dimensional NMR with hyperpolarization. Chem Sci 2020; 11:5935-5943. [PMID: 32874513 PMCID: PMC7441707 DOI: 10.1039/d0sc00266f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/05/2020] [Indexed: 11/21/2022] Open
Abstract
Elucidation of small molecule-protein interactions provides essential information for understanding biological processes such as cellular signaling, as well as for rational drug development. Here, multi-dimensional NMR with sensitivity enhancement by dissolution dynamic nuclear polarization (D-DNP) is shown to allow the determination of the binding epitope of folic acid when complexed with the target dihydrofolate reductase. Protein signals are selectively enhanced by polarization transfer from the hyperpolarized ligand. A pseudo three-dimensional data acquisition with ligand-side Hadamard encoding results in protein-side [13C, 1H] chemical shift correlations that contain intermolecular nuclear Overhauser effect (NOE) information. A scoring function based on this data is used to select pre-docked ligand poses. The top five poses are within 0.76 Å root-mean-square deviation from a reference structure for the encoded five protons, showing improvements compared with the poses selected by an energy-based scoring function without experimental inputs. The sensitivity enhancement provided by the D-DNP combined with multi-dimensional NMR increases the speed and potentially the selectivity of structure elucidation of ligand binding epitopes.
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Affiliation(s)
- Yunyi Wang
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Jihyun Kim
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
| | - Christian Hilty
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , TX 77843 , USA .
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11
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Wang Y, Hilty C. Determination of Ligand Binding Epitope Structures Using Polarization Transfer from Hyperpolarized Ligands. J Med Chem 2019; 62:2419-2427. [PMID: 30715877 DOI: 10.1021/acs.jmedchem.8b01711] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Drug discovery processes require the determination of the protein binding site structure, which can be achieved via nuclear magnetic resonance (NMR) spectroscopy. While traditional NMR spectroscopy suffers from low sensitivity, NMR signals can be significantly enhanced through hyperpolarization of nuclear spins. Here, folic acid is hyperpolarized by dissolution dynamic nuclear polarization (D-DNP). Polarization transfer to dihydrofolate reductase is compared to signal evolution predicted for docking-derived structures. The results demonstrate that a scoring function derived from the experimental data improves the ranking of structures. With data from six methyl groups, Spearman's correlation coefficient of the experimental scoring function to the root-mean-square deviation from a reference structure is 0.88 for five individually addressed ligand protons and 0.59 for the entire ligand, while the same correlation coefficient of the energy calculated from docking alone is 0.49. D-DNP NMR-derived ranking, therefore, is capable of determining the ligand structure with a small number of individually addressed source spins.
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Affiliation(s)
- Yunyi Wang
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , Texas 77843 , United States
| | - Christian Hilty
- Department of Chemistry , Texas A&M University , 3255 TAMU , College Station , Texas 77843 , United States
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12
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Robson-Tull J. Biophysical screening in fragment-based drug design: a brief overview. ACTA ACUST UNITED AC 2019. [DOI: 10.1093/biohorizons/hzy015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jacob Robson-Tull
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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13
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14
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Fu DY, Meiler J. Predictive Power of Different Types of Experimental Restraints in Small Molecule Docking: A Review. J Chem Inf Model 2018; 58:225-233. [PMID: 29286651 DOI: 10.1021/acs.jcim.7b00418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Incorporating experimental restraints is a powerful method of increasing accuracy in computational protein small molecule docking simulations. Different algorithms integrate distinct forms of biochemical data during the docking and/or scoring stages. These so-called hybrid methods make use of receptor-based information such as nuclear magnetic resonance (NMR) restraints or small molecule-based information such as structure-activity relationships (SARs). A third class of methods directly interrogates contacts between the protein receptor and the small molecule. This work reviews the current state of using such restraints in docking simulations, evaluates their feasibility across broad systems, and identifies potential areas of algorithm development.
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Affiliation(s)
- Darwin Y Fu
- Department of Chemistry Vanderbilt University Nashville, Tennessee 37235, United States
| | - Jens Meiler
- Department of Chemistry Vanderbilt University Nashville, Tennessee 37235, United States
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15
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The NMR2 Method to Determine Rapidly the Structure of the Binding Pocket of a Protein–Ligand Complex with High Accuracy. MAGNETOCHEMISTRY 2018. [DOI: 10.3390/magnetochemistry4010012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Structural characterization of complexes is crucial for a better understanding of biological processes and structure-based drug design. However, many protein–ligand structures are not solvable by X-ray crystallography, for example those with low affinity binders or dynamic binding sites. Such complexes are usually targeted by solution-state NMR spectroscopy. Unfortunately, structure calculation by NMR is very time consuming since all atoms in the complex need to be assigned to their respective chemical shifts. To circumvent this problem, we recently developed the Nuclear Magnetic Resonance Molecular Replacement (NMR2) method. NMR2 very quickly provides the complex structure of a binding pocket as measured by solution-state NMR. NMR2 circumvents the assignment of the protein by using previously determined structures and therefore speeds up the whole process from a couple of months to a couple of days. Here, we recall the main aspects of the method, show how to apply it, discuss its advantages over other methods and outline its limitations and future directions.
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16
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Harner MJ, Mueller L, Robbins KJ, Reily MD. NMR in drug design. Arch Biochem Biophys 2017; 628:132-147. [DOI: 10.1016/j.abb.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 02/09/2023]
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17
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18
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Orts J, Wälti MA, Marsh M, Vera L, Gossert AD, Güntert P, Riek R. NMR-Based Determination of the 3D Structure of the Ligand-Protein Interaction Site without Protein Resonance Assignment. J Am Chem Soc 2016; 138:4393-400. [PMID: 26943491 DOI: 10.1021/jacs.5b12391] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular replacement in X-ray crystallography is the prime method for establishing structure-activity relationships of pharmaceutically relevant molecules. Such an approach is not available for NMR. Here, we establish a comparable method, called NMR molecular replacement (NMR(2)). The method requires experimentally measured ligand intramolecular NOEs and ligand-protein intermolecular NOEs as well as a previously known receptor structure or model. Our findings demonstrate that NMR(2) may open a new avenue for the fast and robust determination of the interaction site of ligand-protein complexes at atomic resolution.
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Affiliation(s)
- Julien Orts
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Marielle Aulikki Wälti
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - May Marsh
- Swiss Light Source, Paul Scherrer Institute , CH-5232 Villigen, Switzerland
| | - Laura Vera
- Swiss Light Source, Paul Scherrer Institute , CH-5232 Villigen, Switzerland
| | - Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis AG , CH-4002 Basel, Switzerland
| | - Peter Güntert
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main , Frankfurt am Main 60323, Germany
| | - Roland Riek
- ETH Zürich , Laboratory of Physical Chemistry, HCI F217, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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19
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Dias DM, Ciulli A. NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:101-12. [PMID: 25175337 PMCID: PMC4261069 DOI: 10.1016/j.pbiomolbio.2014.08.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/06/2014] [Accepted: 08/19/2014] [Indexed: 01/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a pivotal method for structure-based and fragment-based lead discovery because it is one of the most robust techniques to provide information on protein structure, dynamics and interaction at an atomic level in solution. Nowadays, in most ligand screening cascades, NMR-based methods are applied to identify and structurally validate small molecule binding. These can be high-throughput and are often used synergistically with other biophysical assays. Here, we describe current state-of-the-art in the portfolio of available NMR-based experiments that are used to aid early-stage lead discovery. We then focus on multi-protein complexes as targets and how NMR spectroscopy allows studying of interactions within the high molecular weight assemblies that make up a vast fraction of the yet untargeted proteome. Finally, we give our perspective on how currently available methods could build an improved strategy for drug discovery against such challenging targets.
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Affiliation(s)
- David M Dias
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alessio Ciulli
- College of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, DD1 5EH, Dundee, UK.
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20
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Aguirre C, Brink TT, Guichou JF, Cala O, Krimm I. Comparing binding modes of analogous fragments using NMR in fragment-based drug design: application to PRDX5. PLoS One 2014; 9:e102300. [PMID: 25025339 PMCID: PMC4099364 DOI: 10.1371/journal.pone.0102300] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 06/16/2014] [Indexed: 02/02/2023] Open
Abstract
Fragment-based drug design is one of the most promising approaches for discovering novel and potent inhibitors against therapeutic targets. The first step of the process consists of identifying fragments that bind the protein target. The determination of the fragment binding mode plays a major role in the selection of the fragment hits that will be processed into drug-like compounds. Comparing the binding modes of analogous fragments is a critical task, not only to identify specific interactions between the protein target and the fragment, but also to verify whether the binding mode is conserved or differs according to the fragment modification. While X-ray crystallography is the technique of choice, NMR methods are helpful when this fails. We show here how the ligand-observed saturation transfer difference (STD) experiment and the protein-observed 15N-HSQC experiment, two popular NMR screening experiments, can be used to compare the binding modes of analogous fragments. We discuss the application and limitations of these approaches based on STD-epitope mapping, chemical shift perturbation (CSP) calculation and comparative CSP sign analysis, using the human peroxiredoxin 5 as a protein model.
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Affiliation(s)
- Clémentine Aguirre
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
| | - Tim ten Brink
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
| | - Jean-François Guichou
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR5048, Université Montpellier 1 et 2, Montpellier, France
| | - Olivier Cala
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
| | - Isabelle Krimm
- Institut des Sciences Analytiques, CNRS UMR 5280, Université de Lyon, Villeurbanne, France
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21
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Harner MJ, Frank AO, Fesik SW. Fragment-based drug discovery using NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2013; 56:65-75. [PMID: 23686385 PMCID: PMC3699969 DOI: 10.1007/s10858-013-9740-z] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/03/2013] [Indexed: 05/04/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable identification of small molecules that bind to proteins and for hit-to-lead optimization. Here, we describe the use of NMR spectroscopy as a method for fragment-based drug discovery and how to most effectively utilize this approach for discovering novel therapeutics based on our experience.
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Affiliation(s)
- Mary J Harner
- Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Ave, 607 Light Hall, Nashville, TN 37232-0146, USA
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22
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Aguirre C, ten Brink T, Walker O, Guillière F, Davesne D, Krimm I. BcL-xL conformational changes upon fragment binding revealed by NMR. PLoS One 2013; 8:e64400. [PMID: 23717610 PMCID: PMC3662666 DOI: 10.1371/journal.pone.0064400] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/12/2013] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4′-fluoro-[1,1′-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices 2, 3 and the very beginning of 5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach.
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Affiliation(s)
- Clémentine Aguirre
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Tim ten Brink
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Olivier Walker
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Florence Guillière
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
| | - Dany Davesne
- UMR5822/IN2P3/F-69622 Lyon, Université de Lyon, IPNL, Villeurbanne, France
| | - Isabelle Krimm
- UMR5280/Université de Lyon/Université Lyon 1, Institut des Sciences Analytiques, Villeurbanne, France
- * E-mail:
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23
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Skjærven L, Codutti L, Angelini A, Grimaldi M, Latek D, Monecke P, Dreyer MK, Carlomagno T. Accounting for Conformational Variability in Protein–Ligand Docking with NMR-Guided Rescoring. J Am Chem Soc 2013; 135:5819-27. [DOI: 10.1021/ja4007468] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lars Skjærven
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Luca Codutti
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Andrea Angelini
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Manuela Grimaldi
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
- Department of Biomedical and
Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo 8, 84024 Fisciano (SA), Italy
| | - Dorota Latek
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
| | - Peter Monecke
- Sanofi-Aventis Deutschland GmbH R&D LGCR/Structure, Design & Informatics, Industriepark Höchst, Bldg. G838, D-65926 Frankfurt am Main, Germany
| | - Matthias K. Dreyer
- Sanofi-Aventis Deutschland GmbH R&D LGCR/Structure, Design & Informatics, Industriepark Höchst, Bldg. G838, D-65926 Frankfurt am Main, Germany
| | - Teresa Carlomagno
- EMBL, Structural and Computational Biology
Unit, Meyerhofstraße
1, D-69117 Heidelberg, Germany
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24
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Abstract
Nuclear magnetic resonance (NMR) is well suited to probing the interactions between ligands and macromolecular receptors. It is a truly label-free technique, requiring only the presence of atoms (usually (1)H or (19)F) which give rise to observable resonances on either the ligand or the receptor. A number of parameters associated with these resonances can be used to distinguish rapidly tumbling compounds from ligands which bind to a macromolecular receptor. As such, NMR reports directly on the molecular components involved in the binding interaction whilst avoiding artifacts arising from the addition of an observable label. NMR is also unique amongst biophysical techniques in giving information on the chemical nature of almost all of the constituents present in the sample, thus allowing ready identification of sample, contaminants, degraded material and buffers. Solution phase NMR is also free of artifacts introduced by the presence of a solid support or matrix, although some interesting NMR techniques have been developed to identify ligand-receptor interactions in both solid and heterogeneous phase systems.NMR can readily report on molecular interactions across a wide range of affinities and timescales. Although NMR is not an inherently sensitive technique, the development of cryogenic probeheads over the past decade has dramatically increased the range of applicability of the technique and reduced the stringent sample requirements that used to be regarded as an "Achilles' heel" of NMR. The last, but by no means the least, NMR has the ability to determine structural information at atomic resolution; this has proved to be particularly useful when applied to those protein-ligand systems which cannot be readily crystallized.
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Affiliation(s)
- Ben Davis
- Vernalis Ltd (R&D), Great Abington, Cambridge, UK
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25
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Shah DM, AB E, Diercks T, Hass MAS, van Nuland NAJ, Siegal G. Rapid Protein–Ligand Costructures from Sparse NOE Data. J Med Chem 2012; 55:10786-90. [DOI: 10.1021/jm301396d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dipen M. Shah
- Leiden Institute of Chemistry,
Leiden University, Leiden 2300RA, The Netherlands
- ZoBio BV, Leiden 2300RA, The
Netherlands
| | - Eiso AB
- ZoBio BV, Leiden 2300RA, The
Netherlands
| | - Tammo Diercks
- Centre for Co-operative
Research
in Biosciences, Derio 48160, Spain
| | - Mathias A. S. Hass
- Leiden Institute of Chemistry,
Leiden University, Leiden 2300RA, The Netherlands
| | - Nico A. J. van Nuland
- Jean Jeener NMR Centre, Structural
Biology, Vrije Universiteit Brussel and Molecular Recognition Unit,
VIB Department of Structural Biology, Brussels 1050, Belgium
| | - Gregg Siegal
- Leiden Institute of Chemistry,
Leiden University, Leiden 2300RA, The Netherlands
- ZoBio BV, Leiden 2300RA, The
Netherlands
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26
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Liu S, Meng L, Moremen KW, Prestegard JH. Nuclear magnetic resonance structural characterization of substrates bound to the alpha-2,6-sialyltransferase, ST6Gal-I. Biochemistry 2009; 48:11211-9. [PMID: 19845399 DOI: 10.1021/bi9015154] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The alpha-2,6-sialyltransferase (ST6Gal-I) is a key enzyme that regulates the distribution of sialic acid-containing molecules on mammalian cell surfaces. However, the fact that its native form is membrane-bound and glycosylated has made structural characterization by X-ray crystallography of this eukaryotic protein difficult. Its large size ( approximately 40 kDa for just the catalytic domain) also poses a challenge for complete structure determination by nuclear magnetic resonance (NMR). However, even without complete structure determination, there are NMR strategies that can return targeted information about select regions of the protein, including information about the active site as seen from the perspective of its bound ligands. Here, in a continuation of a previous study, a spin-labeled mimic of a glycan acceptor ligand is used to identify additional amino acids located in the protein active site. In addition, the spin-labeled donor is used to characterize the relative placement of the two bound ligands. The ligand conformation and protein-ligand contact surfaces are studied by transferred nuclear Overhauser effects (trNOEs) and saturation transfer difference (STD) experiments. The data afforded by the methods mentioned above lead to a geometric model of the bound substrates that in many ways carries an imprint of the ST6Gal-I binding site.
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Affiliation(s)
- Shan Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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27
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Skinner AL, Laurence JS. High-field solution NMR spectroscopy as a tool for assessing protein interactions with small molecule ligands. J Pharm Sci 2009; 97:4670-95. [PMID: 18351634 DOI: 10.1002/jps.21378] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The ability of a small molecule to bind and modify the activity of a protein target at a specific site greatly impacts the success of drugs in the pharmaceutical industry. One of the most important tools for evaluating these interactions has been high-field solution nuclear magnetic resonance (NMR) because of its unique ability to examine even weak protein-drug interactions at high resolution. NMR can be used to evaluate the structural, thermodynamic and kinetic aspects of a binding reaction. The basis of NMR screening experiments is that binding causes a perturbation in the physical properties of both molecules. Unique properties of small and macromolecules allow selective detection of either the protein target or ligand, even in a mixture of compounds. This review outlines current methodologies for assessing protein-ligand interactions from the perspectives of the protein target and ligand and delineates the fundamental principles for understanding NMR approaches in drug research. Advances in instrumentation, pulse sequences, isotopic labeling strategies, and the development of competition experiments support the study of higher molecular weight protein targets, facilitate higher-throughput and expand the range of binding affinities that can be evaluated, enhancing the utility of NMR for identifying and characterizing potential therapeutics to druggable protein targets.
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Affiliation(s)
- Andria L Skinner
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, USA
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28
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Riedinger C, Endicott JA, Kemp SJ, Smyth LA, Watson A, Valeur E, Golding BT, Griffin RJ, Hardcastle IR, Noble ME, McDonnell JM. Analysis of Chemical Shift Changes Reveals the Binding Modes of Isoindolinone Inhibitors of the MDM2-p53 Interaction. J Am Chem Soc 2008; 130:16038-44. [DOI: 10.1021/ja8062088] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christiane Riedinger
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Jane A. Endicott
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Stuart J. Kemp
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Lynette A. Smyth
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Anna Watson
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Eric Valeur
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Bernard T. Golding
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Roger J. Griffin
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Ian R. Hardcastle
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Martin E. Noble
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - James M. McDonnell
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
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29
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Mueller L. Alternate HMQC experiments for recording HN and HC-correlation spectra in proteins at high throughput. JOURNAL OF BIOMOLECULAR NMR 2008; 42:129-137. [PMID: 18820839 DOI: 10.1007/s10858-008-9270-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 08/13/2008] [Indexed: 05/26/2023]
Abstract
Alternate implementations of the SOFAST-HMQC experiment are described. In these alternate SOFAST-HMQC experiments (ALSOFAST-HMQC) excitation of the magnetization of interest is achieved by non-selective rf pulses while preserving the equilibrium polarization of passive spins. This alternate excitation scheme also allows the incorporation of a novel sensitivity enhancement protocol which has been most recently developed by Brutscher and coworkers and which permits simultaneous detection of both the x- and y-components of the indirectly detected t(1)-interferograms without the need to introduce additional rf pulses and delays. We show that the ALSOFAST HC-HMQC experiment, which implements an alternate means of frequency selection, enables the detection of methyl resonances with large secondary proton chemical shifts. This is achieved by selecting coherences of interest via a frequency selective carbon inversion pulse. Detailed comparisons between SOFAST- and the presented ALSOFAST-HMQC experiment reveals a considerable degree of mutual complementarity.
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Affiliation(s)
- Luciano Mueller
- Bristol-Myers Squibb, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA.
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30
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Constantine KL, Mueller L, Metzler WJ, McDonnell PA, Todderud G, Goldfarb V, Fan Y, Newitt JA, Kiefer SE, Gao M, Tortolani D, Vaccaro W, Tokarski J. Multiple and Single Binding Modes of Fragment-Like Kinase Inhibitors Revealed by Molecular Modeling, Residue Type-Selective Protonation, and Nuclear Overhauser Effects. J Med Chem 2008; 51:6225-9. [DOI: 10.1021/jm800747w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Keith L. Constantine
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Luciano Mueller
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - William J. Metzler
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Patricia A. McDonnell
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Gordon Todderud
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Valentina Goldfarb
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Yi Fan
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - John A. Newitt
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Susan E. Kiefer
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Mian Gao
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - David Tortolani
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - Wayne Vaccaro
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
| | - John Tokarski
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543
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31
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Bermejo GA, Llinás M. Deuterated protein folds obtained directly from unassigned nuclear overhauser effect data. J Am Chem Soc 2008; 130:3797-805. [PMID: 18318535 DOI: 10.1021/ja074836e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the feasibility of determining the global fold of a highly deuterated protein from unassigned experimental NMR nuclear Overhauser effect (NOE) data only. The method relies on the calculation of a spatial configuration of covalently unconnected protons-a "cloud"-directly from unassigned distance restraints derived from 13C- and 15N-edited NOESY spectra. Each proton in the cloud, labeled by its chemical shift and that of the directly bound 13C or 15N, is subsequently mapped to specific atoms in the protein. This is achieved via graph-theoretical protocols that search for connectivities in graphs that encode the structural information within the cloud. The peptidyl HN chain is traced by seeking for all possible routes and selecting the one that yields the minimal sum of sequential distances. Complete proton identification in the cloud is achieved by linking the side-chain protons to proximal main-chain HNs via bipartite graph matching. The identified protons automatically yield the NOE assignments, which in turn are used for structure calculation with RosettaNMR, a protocol that incorporates structural bias derived from protein databases. The method, named Sparse-Constraint CLOUDS, was applied to experimental NOESY data on the 58-residue Z domain of staphylococcal protein A. The generated structures are of similar accuracy to those previously reported, which were derived via a conventional approach involving a larger NMR data set. Additional tests were performed on seven reported protein structures of various folds, using restraint lists simulated from the known atomic coordinates.
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Affiliation(s)
- Guillermo A Bermejo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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32
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Jhoti H, Cleasby A, Verdonk M, Williams G. Fragment-based screening using X-ray crystallography and NMR spectroscopy. Curr Opin Chem Biol 2007; 11:485-93. [PMID: 17851109 DOI: 10.1016/j.cbpa.2007.07.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 07/25/2007] [Accepted: 07/27/2007] [Indexed: 11/17/2022]
Abstract
Approaches which start from a study of the interaction of very simple molecules (fragments) with the protein target are proving to be valuable additions to drug design. Fragment-based screening allows the complementarity between a protein active site and drug-like molecules to be rapidly and effectively explored, using structural methods. Recent improvements in the intensities of laboratory X-ray sources permits the collection of greater amounts of high-quality diffraction data and have been matched by developments in automation, crystallisation and data analysis. Developments in NMR screening, including the use of cryogenically cooled NMR probes and (19)F-containing reporter molecules have expanded the scope of this technique, while increasing the availability of binding site and quantitative affinity data for the fragments. Application of these methods has led to a greater knowledge of the chemical variety, structural features and energetics of protein-fragment interactions. While fragment-based screening has already been shown to reduce the timescales of the drug discovery process, a more detailed characterisation of fragment screening hits can reveal unexpected similarities between fragment chemotypes and protein active sites leading to improved understanding of the pharmacophores and the re-use of this information against other protein targets.
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Affiliation(s)
- Harren Jhoti
- Astex Therapeutics, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
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Wang B, Westerhoff LM, Merz KM. A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J Med Chem 2007; 50:5128-34. [PMID: 17867664 PMCID: PMC2525740 DOI: 10.1021/jm070484a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have generated docking poses for the FKBP-GPI complex using eight docking programs, and compared their scoring functions with scoring based on NMR chemical shift perturbations (NMRScore). Because the chemical shift perturbation (CSP) is exquisitely sensitive on the orientation of the ligand inside the binding pocket, NMRScore offers an accurate and straightforward approach to score different poses. All scoring functions were inspected by their abilities to highly rank the native-like structures and separate them from decoy poses generated for a protein-ligand complex. The overall performance of NMRScore is much better than that of energy-based scoring functions associated with docking programs in both aspects. In summary, we find that the combination of docking programs with NMRScore results in an approach that can robustly determine the binding site structure for a protein-ligand complex, thereby providing a new tool facilitating the structure-based drug discovery process.
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Affiliation(s)
- Bing Wang
- Department of Chemistry, Quantum Theory Project, University of Florida, P.O. Box 118435 Gainesville, Florida 32611-8435, USA
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Assfalg M, Bertini I, Del Conte R, Giachetti A, Turano P. Cytochrome c and Organic Molecules: Solution Structure of the p-Aminophenol Adduct†,‡. Biochemistry 2007; 46:6232-8. [PMID: 17488096 DOI: 10.1021/bi7002857] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-protein interactions are driven by specific properties of the molecular surfaces. Cytochrome c, a small electron transfer protein, is involved in a number of biologically relevant interactions with macromolecular partners. Small molecules may interfere with such interactions by binding to the surface of cytochrome c. Here we investigated the possibility of weak intermolecular interactions between reduced cytochrome c and a library of 325 small molecules, using WaterLOGSY NMR spectroscopy. Specific binding was found for p-aminophenol. The solution structure of the p-aminophenol-cytochrome c adduct was determined using a combination of in silico tools and NMR-based restraints. The ligand interacts in a specific binding site on the protein surface through a combination of stacking and H-bond interactions. Small but meaningful rearrangements of the solvent-exposed side chains are observed upon ligand binding and contribute to the stabilization of the complex.
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Affiliation(s)
- Michael Assfalg
- ProtEra srl, viale delle idee 22, 50019 Sesto Fiorentino, Italy
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