1
|
Jiang H, Liu Y, Guo J. NMR-based screening for natural product subfraction to precisely identify ligand of target protein. PHYTOCHEMICAL ANALYSIS : PCA 2021; 32:621-628. [PMID: 33137850 DOI: 10.1002/pca.3010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
INTRODUCTION The inherent diversity of natural product extracts has not only made their value for biological activity attractive, but has also presented significant challenges for separation and detection techniques to enable rapid characterisation of the biologically active component present in the complicated mixture. OBJECTIVE Nuclear magnetic resonance (NMR) is routinely valued for its ability to shed light on molecular structure, when NMR is used as a promising tool in drug screening, it can detect and quantify molecular interactions, and at the same time provide detailed structural information with atomic level resolution. Here, we introduced an accurate and efficient strategy for discovering ligands from natural product extracts, by taking the advantage of NMR-based drug screening. METHODOLOGY The characteristic pre-purified subfraction libraries were brought into screening, and combinatorial ligand-observed NMR interaction detection experiments were performed, once hits were found from one subfraction, the repository of the subfraction would be subject to separation and preparation, and the structure of the hits would be easily identified. RESULTS Screening procedure of Radix Polygoni Multiflori water extract against human serum albumin (HSA) was used as an example, to discuss and verify the detailed methodology. Furthermore, human fatty acid binding protein 4 (FABP4 ) was presented as an example target protein, to illustrate the utility of this method for discovering biologically active component. CONCLUSIONS It is proved that suitable subfraction library and well-combined ligand-detected NMR experiments will make the screening streamline more accurate and efficient. NMR is a promising tool to integrate natural product extracts into modern drug screening.
Collapse
Affiliation(s)
- Haipeng Jiang
- Synergy Innovation Centre of Biological Peptide Antidiabetics of Hubei Province, School of Life Science, Wuchang University of Technology, Wuhan, P. R. China
- Engineering Technology Research Centre of Biological Peptide Antidiabetics of Hubei Province, Wuchang University of Technology, Wuhan, P. R. China
| | - Yang Liu
- Synergy Innovation Centre of Biological Peptide Antidiabetics of Hubei Province, School of Life Science, Wuchang University of Technology, Wuhan, P. R. China
- Engineering Technology Research Centre of Biological Peptide Antidiabetics of Hubei Province, Wuchang University of Technology, Wuhan, P. R. China
| | - Jian Guo
- Synergy Innovation Centre of Biological Peptide Antidiabetics of Hubei Province, School of Life Science, Wuchang University of Technology, Wuhan, P. R. China
| |
Collapse
|
2
|
Rüdisser SH, Goldberg N, Ebert MO, Kovacs H, Gossert AD. Efficient affinity ranking of fluorinated ligands by 19F NMR: CSAR and FastCSAR. JOURNAL OF BIOMOLECULAR NMR 2020; 74:579-594. [PMID: 32556806 DOI: 10.1007/s10858-020-00325-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Fluorine NMR has recently gained high popularity in drug discovery as it allows efficient and sensitive screening of large numbers of ligands. However, the positive hits found in screening must subsequently be ranked according to their affinity in order to prioritize them for follow-up chemistry. Unfortunately, the primary read-out from the screening experiments, namely the increased relaxation rate upon binding, is not proportional to the affinity of the ligand, as it is polluted by effects such as exchange broadening. Here we present the method CSAR (Chemical Shift-anisotropy-based Affinity Ranking) for reliable ranking of fluorinated ligands by NMR, without the need of isotope labeled protein, titrations or setting up a reporter format. Our strategy is to produce relaxation data that is directly proportional to the binding affinity. This is achieved by removing all other contributions to relaxation as follows: (i) exchange effects are efficiently suppressed by using high power spin lock pulses, (ii) dipolar relaxation effects are approximately subtracted by measuring at two different magnetic fields and (iii) differences in chemical shift anisotropy are normalized using calculated values. A similar ranking can be obtained with the simplified approach FastCSAR that relies on a measurement of a single relaxation experiment at high field (preferably > 600 MHz). An affinity ranking obtained in this simple way will enable prioritizing ligands and thus improve the efficiency of fragment-based drug design.
Collapse
Affiliation(s)
- Simon H Rüdisser
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland
| | - Nils Goldberg
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland
| | - Marc-Olivier Ebert
- Laboratorium für Organische Chemie, ETH Zürich, 8093, Zürich, Switzerland
| | | | - Alvar D Gossert
- Institute for Molecular Biology and Biophysics, ETH Zürich, 8093, Zürich, Switzerland.
- Biomolecular NMR Spectroscopy Platform, ETH Zürich, 8093, Zürich, Switzerland.
| |
Collapse
|
3
|
Hanzawa H, Shimada T, Takahashi M, Takahashi H. Revisiting biomolecular NMR spectroscopy for promoting small-molecule drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:501-508. [PMID: 32306215 DOI: 10.1007/s10858-020-00314-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Recently, there has been increasing interest in new modalities such as therapeutic antibodies and gene therapy at a number of pharmaceutical companies. Moreover, in small-molecule drug discovery at such companies, efforts have focused on hard-to-drug targets such as inhibiting protein-protein interactions. Biomolecular NMR spectroscopy has been used in drug discovery in a variety of ways, such as for the reliable detection of binding and providing three-dimensional structural information for structure-based drug design. The advantages of using NMR spectroscopy have been known for decades (Jahnke in J Biomol NMR 39:87-90, (2007); Gossert and Jahnke in Prog Nucl Magn Reson Spectrosc 97:82-125, (2016)). For tackling hard-to-drug targets and increasing the success in discovering drug molecules, in-depth analysis of drug-target protein interactions performed by biophysical methods will be more and more essential. Here, we review the advantages of NMR spectroscopy as a key technology of biophysical methods and also discuss issues such as using cutting-edge NMR spectrometers and increasing the demand of utilizing conformational dynamics information for promoting small-molecule drug discovery.
Collapse
Affiliation(s)
- Hiroyuki Hanzawa
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan.
| | - Takashi Shimada
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Mizuki Takahashi
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| |
Collapse
|
4
|
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.
Collapse
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.)
| |
Collapse
|
5
|
Wan H, Tian Y, Jiang H, Zhang X, Ju X. A NMR-based drug screening strategy for discovering active substances from herbal medicines: Using Radix Polygoni Multiflori as example. JOURNAL OF ETHNOPHARMACOLOGY 2020; 254:112712. [PMID: 32105747 DOI: 10.1016/j.jep.2020.112712] [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: 11/06/2019] [Revised: 01/29/2020] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Herbal medicines have always been important sources for new drugs. And developing new drugs from traditional herbal medicine is currently still an effective way. However, screening for active substances from herbal medicines extracts has ever been a challenging topic, due to their intrinsic complexity. The herb Radix Polygoni Multiflori has been used as a tonic and an antiaging herb in Traditional Chinese Medicine. In clinical studies, the extract of Radix Polygoni Multiflori can improve hypercholesterolemia, atherosclerotic, diabetes and other diseases commonly associated with glycolipid metabolism, however, the molecular mechanisms of these actions are unknown. AIM OF THE STUDY We devised a NMR-based drug screening strategy for discovering active substances from herbal medicines, using Radix Polygoni Multiflori as example to address such challenging topic, meanwhile, to explore molecular target of Radix Polygoni Multiflori's glycolipid metabolism benefit. MATERIALS AND METHODS Herbal medicines extracts were subjected to moderate separation to generate libraries of pre-purified subfractions, target protein was then added to each subfraction, and ligand-observed NMR experiments (line-broadening experiment, chemical shift perturbations measurements and saturation transfer difference spectrum) were performed, active substances identification and structural optimization were then accomplished using signals provided by ligand-observed NMR interaction detection and HPLC-SPE-NMR. The strategy was demonstrated by discovering an active component from extract of herb Radix Polygoni Multiflori, using human fatty acid binding protein 4 (FABP4) as target protein. RESULTS 2,4-dihydroxy-6-[(1E)-2-(4-hydroxyphenyl)ethenyl]phenyl-ß-D-glucopyranoside(TSG), the hit from one subfraction, has obvious interaction with target protein FABP4, due to FABP4 is a potential therapeutic target for metabolic diseases such as diabetes and atherosclerosis, the screening result will give clue to the active component and molecular target of Radix Polygoni Multiflori's glycolipid metabolism benefit. Besides, interaction information at atom level offered by ligand-observed NMR experiment would be valuable in the further stage of lead optimization. CONCLUSIONS The devised NMR-based drug screening strategy can discover active substances from herbal medicines efficiently and precisely, meanwhile, can shed light on molecular mechanism of traditional usage of the herb.
Collapse
Affiliation(s)
- Hong Wan
- School of Life Science, Wuchang University of Technology, Hubei Collaborative Innovation Center for Bioactive Polypeptide Diabetes Drugs, Wuhan, 430223, PR China
| | - Yafeng Tian
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| | - Haipeng Jiang
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China.
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China.
| | - Xiulian Ju
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| |
Collapse
|
6
|
Zloh M. NMR spectroscopy in drug discovery and development: Evaluation of physico-chemical properties. ADMET AND DMPK 2019; 7:242-251. [PMID: 35359618 PMCID: PMC8963582 DOI: 10.5599/admet.737] [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: 10/18/2019] [Revised: 11/19/2019] [Indexed: 11/18/2022] Open
Abstract
Determination of physico-chemical properties of compounds is one of the corner-stones in selection of hit molecules for further progression into lead development in the modern drug discovery process. The speed of traditional analyses and limited quantities of hit molecules are obstacles for efficient acquisition of experimental data. Herein, the range of applications of quantitative nuclear magnetic resonance (NMR) spectroscopy as a fast technique used to evaluate solubility, log P and pKa are discussed.
Collapse
Affiliation(s)
- Mire Zloh
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK.,Faculty of Pharmacy, University Business Academy, Trg mladenaca 5, 21000, Novi Sad, Serbia
| |
Collapse
|
7
|
Cerofolini L, Giuntini S, Louka A, Ravera E, Fragai M, Luchinat C. High-Resolution Solid-State NMR Characterization of Ligand Binding to a Protein Immobilized in a Silica Matrix. J Phys Chem B 2017; 121:8094-8101. [PMID: 28762736 DOI: 10.1021/acs.jpcb.7b05679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Solid-state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to (or trapped in) solid systems that lack long-range three-dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid-state NMR all of the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands. This work provides a proof of concept that also immobilized enzymes can be used for protein-based NMR protein-ligand interactions for drug discovery.
Collapse
Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.,GiottoBiotech S.R.L. , Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| |
Collapse
|
8
|
Gossert AD, Jahnke W. NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:82-125. [PMID: 27888841 DOI: 10.1016/j.pnmrs.2016.09.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 05/12/2023]
Abstract
Protein-ligand interactions are at the heart of drug discovery research. NMR spectroscopy is an excellent technology to identify and validate protein-ligand interactions. A plethora of NMR methods are available which are powerful, robust and information-rich, but also have pitfalls and limitations. In this review, we will focus on how to choose between different experiments, and assess their strengths and liabilities. We introduce the concept of the validation cross, which helps to categorize experiments according to their information content and to simplify the choice of the right experiment in order to address a specific question. Additionally, we will provide the framework for drawing correct conclusions from experimental results in order to accurately evaluate such interactions. Out of scope for this review are methods for subsequent characterization of the interaction such as quantitative KD determination, binding mode analysis, or structure determination.
Collapse
Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland.
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Abstract
Nuclear Magnetic Resonance (NMR) techniques are widely used in the drug discovery process. The primary feature exploited in these investigations is the large difference in mass between drugs and receptors (usually proteins) and the effect this has on the rotational or translational correlation times for drugs bound to their targets. Many NMR parameters, such as the diffusion coefficient, spin diffusion, nuclear Overhauser enhancement, and transverse and longitudinal relaxation times, are strong functions of either the overall tumbling or translation of molecules in solution. This has led to the development of a wide variety of NMR techniques applicable to the elucidation of protein and nucleic acid structure in solution, the screening of drug candidates for binding to a target of choice, and the study of the conformational changes which occur in a target upon drug binding. High-throughput screening by NMR methods has recently received a boost from the introduction of sophisticated computational techniques for reducing the time needed for the acquisition of the primary NMR data for multidimensional studies.
Collapse
Affiliation(s)
- Laurel O Sillerud
- Department of Biochemistry and Molecular Biology, UNM HDC, University of New Mexico, Albuquerque, NM, USA.
| | | |
Collapse
|
11
|
Saio T, Ogura K, Shimizu K, Yokochi M, Burke TR, Inagaki F. An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe. JOURNAL OF BIOMOLECULAR NMR 2011; 51:395-408. [PMID: 21927934 PMCID: PMC3193990 DOI: 10.1007/s10858-011-9566-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 08/29/2011] [Indexed: 05/04/2023]
Abstract
A nuclear magnetic resonance-based ligand screening strategy utilizing a paramagnetic lanthanide probe is presented. By fixing a paramagnetic lanthanide ion to a target protein, a pseudo-contact shift (PCS) and a paramagnetic relaxation enhancement (PRE) can be observed for both the target protein and its bound ligand. Based on PRE and PCS information, the bound ligand is then screened from the compound library and the structure of the ligand-protein complex is determined. PRE is an isotropic paramagnetic effect observed within 30 Å from the lanthanide ion, and is utilized for the ligand screening in the present study. PCS is an anisotropic paramagnetic effect providing long-range (~40 Å) distance and angular information on the observed nuclei relative to the paramagnetic lanthanide ion, and utilized for the structure determination of the ligand-protein complex. Since a two-point anchored lanthanide-binding peptide tag is utilized for fixing the lanthanide ion to the target protein, this screening method can be generally applied to non-metal-binding proteins. The usefulness of this strategy was demonstrated in the case of the growth factor receptor-bound protein 2 (Grb2) Src homology 2 (SH2) domain and its low- and high-affinity ligands.
Collapse
Affiliation(s)
- Tomohide Saio
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Kenji Ogura
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Kazumi Shimizu
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Masashi Yokochi
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Terrence R. Burke
- National Cancer Institute at Frederick, Laboratory of Medicinal Chemistry, Center for Cancer Research, P. O. Box B, Frederick, MD 21702-1201 USA
| | - Fuyuhiko Inagaki
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| |
Collapse
|
12
|
Vega-Vázquez M, Cobas JC, Oliveira de Sousa FF, Martin-Pastor M. A NMR reverse diffusion filter for the simplification of spectra of complex mixtures and the study of drug receptor interactions. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49:464-468. [PMID: 21751249 DOI: 10.1002/mrc.2786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 05/29/2011] [Accepted: 05/31/2011] [Indexed: 05/31/2023]
Abstract
A reverse diffusion filter NMR experiment (Drev) is proposed for the study of small molecules in binding with macromolecules. The filtering efficiency of Drev to eliminate the signals of the macromolecule is shown to be superior to conventional transverse relaxation filters at least for macromolecules containing a significant fraction of flexible residues. The Drev filter was also a useful complement for ligand-based NMR screening in combination with saturation transfer difference experiments.
Collapse
Affiliation(s)
- M Vega-Vázquez
- Unidade de Resonancia Magnética, Edif. CACTUS, RIAIDT, Campus Vida, University of Santiago de Compostela, A Coruña 15706, Spain
| | | | | | | |
Collapse
|
13
|
Combining biophysical screening and X-ray crystallography for fragment-based drug discovery. Top Curr Chem (Cham) 2011; 317:115-43. [PMID: 21837555 DOI: 10.1007/128_2011_225] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Over the past decade, fragment-based drug discovery (FBDD) has gained importance for the generation of novel ideas to inspire synthetic chemistry. In order to identify small molecules that bind to a target protein, multiple approaches have been utilized by various groups in the pharmaceutical industry and by academic groups. The combination of fragment screening by biophysical methods and in particular with surface plasmon resonance technologies (SPR) together with the visualization of the binding properties by X-ray crystallography offers a number of benefits. Screening by SPR identifies ligands for a target protein as well as provides an assessment of the binding properties with respect to affinity, stoichiometry, and specificity of the interaction. Despite the huge technology advances of the past years, X-ray crystallography is still a resource-intensive technology, and SPR binding data provides excellent measures to prioritize X-ray experiments and consequently enable a better success rate in obtaining structural information. Information on the chemical structures of fragments binding to a protein can be used to perform similarity searches in compound libraries in order to establish structure-activity relationships as well as to explore particular scaffolds. At Roche we have applied this workflow for a number of targets and the experiences will be outlined in this review.
Collapse
|
14
|
Jahnke W, Grotzfeld RM, Pellé X, Strauss A, Fendrich G, Cowan-Jacob SW, Cotesta S, Fabbro D, Furet P, Mestan J, Marzinzik AL. Binding or Bending: Distinction of Allosteric Abl Kinase Agonists from Antagonists by an NMR-Based Conformational Assay. J Am Chem Soc 2010; 132:7043-8. [DOI: 10.1021/ja101837n] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | | | - Xavier Pellé
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - André Strauss
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Gabriele Fendrich
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | | | - Simona Cotesta
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Doriano Fabbro
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Pascal Furet
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Jürgen Mestan
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | | |
Collapse
|
15
|
Jahnke W, Henry C. An in vitro Assay to Measure Targeted Drug Delivery to Bone Mineral. ChemMedChem 2010; 5:770-6. [DOI: 10.1002/cmdc.201000016] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
16
|
NMR methods in fragment screening: theory and a comparison with other biophysical techniques. Drug Discov Today 2009; 14:1051-7. [DOI: 10.1016/j.drudis.2009.07.013] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 07/23/2009] [Accepted: 07/27/2009] [Indexed: 11/19/2022]
|
17
|
González-Ruiz D, Gohlke H. Steering Protein−Ligand Docking with Quantitative NMR Chemical Shift Perturbations. J Chem Inf Model 2009; 49:2260-71. [DOI: 10.1021/ci900188r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Domingo González-Ruiz
- Fachbereich Biowissenschaften, Molekulare Bioinformatik, Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany, and Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität, Universitätstrasse 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Fachbereich Biowissenschaften, Molekulare Bioinformatik, Goethe-Universität, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany, and Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität, Universitätstrasse 1, 40225 Düsseldorf, Germany
| |
Collapse
|
18
|
Abstract
BACKGROUND: Drug discovery is a complex and unpredictable endeavor with a high failure rate. Current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. The industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. Recent advances in nuclear magnetic resonance are responding to these self-imposed limitations and are providing opportunities to increase the success rate of drug discovery. OBJECTIVE/METHOD: A review of recent advancements in NMR technology that have the potential of significantly impacting and benefiting the drug discovery process will be presented. These include fast NMR data collection protocols and high-throughput protein structure determination, rapid protein-ligand co-structure determination, lead discovery using fragment-based NMR affinity screens, NMR metabolomics to monitor in vivo efficacy and toxicity for lead compounds, and the identification of new therapeutic targets through the functional annotation of proteins by FAST-NMR. CONCLUSION: NMR is a critical component of the drug discovery process, where the versatility of the technique enables it to continually expand and evolve its role. NMR is expected to maintain this growth over the next decade with advancements in automation, speed of structure calculation, in-cell imaging techniques, and the expansion of NMR amenable targets.
Collapse
Affiliation(s)
- Robert Powers
- Department of Chemistry, University of Nebraska Lincoln, Lincoln, NE 68588
| |
Collapse
|
19
|
Zhang X, Sänger A, Hemmig R, Jahnke W. Ranking of High-Affinity Ligands by NMR Spectroscopy. Angew Chem Int Ed Engl 2009; 48:6691-4. [DOI: 10.1002/anie.200902591] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
20
|
Zhang X, Sänger A, Hemmig R, Jahnke W. Ranking of High-Affinity Ligands by NMR Spectroscopy. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
21
|
Williamson MP, Craven CJ. Automated protein structure calculation from NMR data. JOURNAL OF BIOMOLECULAR NMR 2009; 43:131-143. [PMID: 19137264 DOI: 10.1007/s10858-008-9295-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Accepted: 12/10/2008] [Indexed: 05/27/2023]
Abstract
Current software is almost at the stage to permit completely automatic structure determination of small proteins of <15 kDa, from NMR spectra to structure validation with minimal user interaction. This goal is welcome, as it makes structure calculation more objective and therefore more easily validated, without any loss in the quality of the structures generated. Moreover, it releases expert spectroscopists to carry out research that cannot be automated. It should not take much further effort to extend automation to ca 20 kDa. However, there are technological barriers to further automation, of which the biggest are identified as: routines for peak picking; adoption and sharing of a common framework for structure calculation, including the assembly of an automated and trusted package for structure validation; and sample preparation, particularly for larger proteins. These barriers should be the main target for development of methodology for protein structure determination, particularly by structural genomics consortia.
Collapse
Affiliation(s)
- Mike P Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | | |
Collapse
|
22
|
Abstract
In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility.
Collapse
|
23
|
Moriaud F, Doppelt-Azeroual O, Martin L, Oguievetskaia K, Koch K, Vorotyntsev A, Adcock SA, Delfaud F. Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity. J Chem Inf Model 2009; 49:280-94. [DOI: 10.1021/ci8003094] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabrice Moriaud
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| | - Olivia Doppelt-Azeroual
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| | - Laetitia Martin
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| | - Ksenia Oguievetskaia
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| | - Kerstin Koch
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| | - Artem Vorotyntsev
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| | - Stewart A. Adcock
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| | - François Delfaud
- MEDIT SA, 2 rue du Belvédère, 91120 Palaiseau, France, and IBBMC, Université Paris Sud CNRS UMR-8619, Orsay 91405, France
| |
Collapse
|
24
|
Fehér K, Groves P, Batta G, Jiménez-Barbero J, Muhle-Goll C, Kövér KE. Competition Saturation Transfer Difference Experiments Improved with Isotope Editing and Filtering Schemes in NMR-Based Screening. J Am Chem Soc 2008; 130:17148-53. [DOI: 10.1021/ja804468k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Krisztina Fehér
- MPI for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany, and EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Instituto de Tecnologia Química e Biológica, Av. da República (EAN) 2781-901 Oeiras, Portugal, Department of Protein Science, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary, and Department of Inorganic and Analytical Chemistry, University of Debrecen,
| | - Patrick Groves
- MPI for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany, and EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Instituto de Tecnologia Química e Biológica, Av. da República (EAN) 2781-901 Oeiras, Portugal, Department of Protein Science, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary, and Department of Inorganic and Analytical Chemistry, University of Debrecen,
| | - Gyula Batta
- MPI for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany, and EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Instituto de Tecnologia Química e Biológica, Av. da República (EAN) 2781-901 Oeiras, Portugal, Department of Protein Science, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary, and Department of Inorganic and Analytical Chemistry, University of Debrecen,
| | - Jesús Jiménez-Barbero
- MPI for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany, and EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Instituto de Tecnologia Química e Biológica, Av. da República (EAN) 2781-901 Oeiras, Portugal, Department of Protein Science, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary, and Department of Inorganic and Analytical Chemistry, University of Debrecen,
| | - Claudia Muhle-Goll
- MPI for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany, and EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Instituto de Tecnologia Química e Biológica, Av. da República (EAN) 2781-901 Oeiras, Portugal, Department of Protein Science, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary, and Department of Inorganic and Analytical Chemistry, University of Debrecen,
| | - Katalin E. Kövér
- MPI for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany, and EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Instituto de Tecnologia Química e Biológica, Av. da República (EAN) 2781-901 Oeiras, Portugal, Department of Protein Science, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain, Department of Biochemistry, University of Debrecen, Egyetem tér 1, H-4010 Debrecen, Hungary, and Department of Inorganic and Analytical Chemistry, University of Debrecen,
| |
Collapse
|
25
|
Bertini I, Fragai M, Luchinat C, Talluri E. Water-Based Ligand Screening for Paramagnetic Metalloproteins. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
26
|
Bertini I, Fragai M, Luchinat C, Talluri E. Water-Based Ligand Screening for Paramagnetic Metalloproteins. Angew Chem Int Ed Engl 2008; 47:4533-7. [DOI: 10.1002/anie.200800327] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
27
|
Manzenrieder F, Frank A, Kessler H. Phosphor-NMR-Spektroskopie als vielseitiges Werkzeug für das Screening von Substanzbibliotheken. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
28
|
Manzenrieder F, Frank A, Kessler H. Phosphorus NMR Spectroscopy as a Versatile Tool for Compound Library Screening. Angew Chem Int Ed Engl 2008; 47:2608-11. [DOI: 10.1002/anie.200705256] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|