1
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Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020; 16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
Abstract
Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.
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Affiliation(s)
- Benjamin Diethelm-Varela
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD 21201, USA
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2
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Khattri RB, Morris DL, Bilinovich SM, Manandhar E, Napper KR, Sweet JW, Modarelli DA, Leeper TC. Identifying Ortholog Selective Fragment Molecules for Bacterial Glutaredoxins by NMR and Affinity Enhancement by Modification with an Acrylamide Warhead. Molecules 2019; 25:E147. [PMID: 31905878 PMCID: PMC6983068 DOI: 10.3390/molecules25010147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/30/2022] Open
Abstract
Illustrated here is the development of a new class of antibiotic lead molecules targeted at Pseudomonas aeruginosa glutaredoxin (PaGRX). This lead was produced to (a) circumvent efflux-mediated resistance mechanisms via covalent inhibition while (b) taking advantage of species selectivity to target a fundamental metabolic pathway. This work involved four components: a novel workflow for generating protein specific fragment hits via independent nuclear magnetic resonance (NMR) measurements, NMR-based modeling of the target protein structure, NMR guided docking of hits, and synthetic modification of the fragment hit with a vinyl cysteine trap moiety, i.e., acrylamide warhead, to generate the chimeric lead. Reactivity of the top warhead-fragment lead suggests that the ortholog selectivity observed for a fragment hit can translate into a substantial kinetic advantage in the mature warhead lead, which bodes well for future work to identify potent, species specific drug molecules targeted against proteins heretofore deemed undruggable.
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Affiliation(s)
- Ram B. Khattri
- Department of Physiology and Functional genomics, University of Florida, Gainesville, FL 32610, USA;
| | - Daniel L. Morris
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Stephanie M. Bilinovich
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Kahlilah R. Napper
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Jacob W. Sweet
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - David A. Modarelli
- Department of Chemistry and Biochemistry, The University of Akron, Akron, OH 44325, USA; (D.L.M.); (K.R.N.); (J.W.S.); (D.A.M.)
| | - Thomas C. Leeper
- Department of Chemistry and Biochemistry, Kennesaw State University, GA 30144, USA
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3
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Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Unexpected change in NOE with increasing temperature: Crosstalk between chemical exchange and cross relaxation in a NiN2S2 complex. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2018.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Assessing molecular interactions with biophysical methods using the validation cross. Biochem Soc Trans 2018; 47:63-76. [DOI: 10.1042/bst20180271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 11/17/2022]
Abstract
Abstract
There are numerous methods for studying molecular interactions. However, each method gives rise to false negative- or false positive binding results, stemming from artifacts of the scientific equipment or from shortcomings of the experimental format. To validate an initial positive binding result, additional methods need to be applied to cover the shortcomings of the primary experiment. The aim of such a validation procedure is to exclude as many artifacts as possible to confirm that there is a true molecular interaction that meets the standards for publishing or is worth investing considerable resources for follow-up activities in a drug discovery project. To simplify this validation process, a graphical scheme — the validation cross — can be used. This simple graphic is a powerful tool for identifying blind spots of a binding hypothesis, for selecting the most informative combination of methods to reveal artifacts and, in general, for understanding more thoroughly the nature of a validation process. The concept of the validation cross was originally introduced for the validation of protein–ligand interactions by NMR in drug discovery. Here, an attempt is made to expand the concept to further biophysical methods and to generalize it for binary molecular interactions.
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6
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Erlanson DA, Davis BJ, Jahnke W. Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures. Cell Chem Biol 2018; 26:9-15. [PMID: 30482678 DOI: 10.1016/j.chembiol.2018.10.001] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Accepted: 09/28/2018] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery typically requires an interplay between screening methods, structural methods, and medicinal chemistry. X-ray crystallography is generally the method of choice to obtain three-dimensional structures of the bound ligand/protein complex, but this can sometimes be difficult, particularly for early, low-affinity fragment hits. In this Perspective, we discuss strategies to advance and evolve fragments in the absence of crystal structures of protein-fragment complexes, although the structure of the unliganded protein may be available. The strategies can involve other structural techniques, such as NMR spectroscopy, molecular modeling, or a variety of chemical approaches. Often, these strategies are aimed at guiding evolution of initial fragment hits to a stage where crystal structures can be obtained for further structure-based optimization.
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Affiliation(s)
- Daniel A Erlanson
- Carmot Therapeutics, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA.
| | - Ben J Davis
- Vernalis (R&D) Ltd, Granta Park, Cambridge, UK.
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Novartis Campus, Basel, Switzerland.
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7
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Gabel SA, Duff MR, Pedersen LC, DeRose EF, Krahn JM, Howell EE, London RE. A Structural Basis for Biguanide Activity. Biochemistry 2017; 56:4786-4798. [PMID: 28766937 PMCID: PMC5740485 DOI: 10.1021/acs.biochem.7b00619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metformin is the most commonly prescribed treatment for type II diabetes and related disorders; however, molecular insights into its mode(s) of action have been limited by an absence of structural data. Structural considerations along with a growing body of literature demonstrating its effects on one-carbon metabolism suggest the possibility of folate mimicry and anti-folate activity. Motivated by the growing recognition that anti-diabetic biguanides may act directly upon the gut microbiome, we have determined structures of the complexes formed between the anti-diabetic biguanides (phenformin, buformin, and metformin) and Escherichia coli dihydrofolate reductase (ecDHFR) based on nuclear magnetic resonance, crystallographic, and molecular modeling studies. Interligand Overhauser effects indicate that metformin can form ternary complexes with p-aminobenzoyl-l-glutamate (pABG) as well as other ligands that occupy the region of the folate-binding site that interacts with pABG; however, DHFR inhibition is not cooperative. The biguanides competitively inhibit the activity of ecDHFR, with the phenformin inhibition constant being 100-fold lower than that of metformin. This inhibition may be significant at concentrations present in the gut of treated individuals, and inhibition of DHFR in intestinal mucosal cells may also occur if accumulation levels are sufficient. Perturbation of folate homeostasis can alter the pyridine nucleotide redox ratios that are important regulators of cellular metabolism.
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Affiliation(s)
- Scott A. Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Michael R. Duff
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Lars C. Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | - Eugene F. DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
| | | | - Elizabeth E. Howell
- Department of Biochemistry, Cellular & Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Robert E. London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, 111 T. W. Alexander Dr. Research Triangle Park, NC 27709
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8
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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.
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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
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9
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Wätzig H, Oltmann-Norden I, Steinicke F, Alhazmi HA, Nachbar M, El-Hady DA, Albishri HM, Baumann K, Exner T, Böckler FM, El Deeb S. Data quality in drug discovery: the role of analytical performance in ligand binding assays. J Comput Aided Mol Des 2015; 29:847-65. [DOI: 10.1007/s10822-015-9851-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/02/2015] [Indexed: 01/24/2023]
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10
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Pilger J, Mazur A, Monecke P, Schreuder H, Elshorst B, Bartoschek S, Langer T, Schiffer A, Krimm I, Wegstroth M, Lee D, Hessler G, Wendt KU, Becker S, Griesinger C. A Combination of Spin Diffusion Methods for the Determination of Protein-Ligand Complex Structural Ensembles. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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11
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Pilger J, Mazur A, Monecke P, Schreuder H, Elshorst B, Bartoschek S, Langer T, Schiffer A, Krimm I, Wegstroth M, Lee D, Hessler G, Wendt KU, Becker S, Griesinger C. A Combination of Spin Diffusion Methods for the Determination of Protein-Ligand Complex Structural Ensembles. Angew Chem Int Ed Engl 2015; 54:6511-5. [DOI: 10.1002/anie.201500671] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Indexed: 01/22/2023]
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12
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Vögeli B. The nuclear Overhauser effect from a quantitative perspective. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 78:1-46. [PMID: 24534087 DOI: 10.1016/j.pnmrs.2013.11.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/13/2013] [Indexed: 05/26/2023]
Abstract
The nuclear Overhauser enhancement or effect (NOE) is the most important measure in liquid-state NMR with macromolecules. Thus, the NOE is the subject of numerous reviews and books. Here, the NOE is revisited in light of our recently introduced measurements of exact nuclear Overhauser enhancements (eNOEs), which enabled the determination of multiple-state 3D protein structures. This review encompasses all relevant facets from the theoretical considerations to the use of eNOEs in multiple-state structure calculation. Important aspects include a detailed presentation of the relaxation theory relevant for the nuclear Overhauser effect, the estimation of the correction for spin diffusion, the experimental determination of the eNOEs, the conversion of eNOE rates into distances and validation of their quality, the distance-restraint classification and the protocols for calculation of structures and ensembles.
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Affiliation(s)
- Beat Vögeli
- Laboratory of Physical Chemistry, HCI F217, Wolfgang-Pauli-Str. 10, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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13
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Stauch B, Orts J, Carlomagno T. The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method. JOURNAL OF BIOMOLECULAR NMR 2012; 54:245-256. [PMID: 23001323 PMCID: PMC3483107 DOI: 10.1007/s10858-012-9662-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/13/2012] [Indexed: 05/31/2023]
Abstract
Protein internal motions influence observables of NMR experiments. The effect of internal motions occurring at the sub-nanosecond timescale can be described by NMR order parameters. Here, we report that the use of order parameters derived from Molecular Dynamics (MD) simulations of two holo-structures of Protein Kinase A increase the discrimination power of INPHARMA, an NMR based methodology that selects docked ligand orientations by maximizing the correlation of back-calculated to experimental data. By including internal motion in the back-calculation of the INPHARMA transfer, we obtain a more realistic description of the system, which better represents the experimental data. Furthermore, we propose a set of generic order parameters, derived from MD simulations of globular proteins, which can be used in the back-calculation of INPHARMA NOEs for any protein-ligand complex, thus by-passing the need of obtaining system-specific order parameters for new protein-ligand complexes.
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Affiliation(s)
- Benjamin Stauch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Present Address: European Bioinformatics Institute (EBI), Hinxton, UK
| | - Julien Orts
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Present Address: Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland
| | - Teresa Carlomagno
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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14
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Carlomagno T. NMR in natural products: understanding conformation, configuration and receptor interactions. Nat Prod Rep 2012; 29:536-54. [PMID: 22456471 DOI: 10.1039/c2np00098a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.
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Affiliation(s)
- Teresa Carlomagno
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg
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15
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Jordan JB, Poppe L, Xia X, Cheng AC, Sun Y, Michelsen K, Eastwood H, Schnier PD, Nixey T, Zhong W. Fragment Based Drug Discovery: Practical Implementation Based on 19F NMR Spectroscopy. J Med Chem 2012; 55:678-87. [DOI: 10.1021/jm201441k] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John B. Jordan
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Leszek Poppe
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Xiaoyang Xia
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Alan C. Cheng
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Yax Sun
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Klaus Michelsen
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Heather Eastwood
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Paul D. Schnier
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Thomas Nixey
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Wenge Zhong
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
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16
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Rademacher C, Guiard J, Kitov PI, Fiege B, Dalton KP, Parra F, Bundle DR, Peters T. Targeting norovirus infection-multivalent entry inhibitor design based on NMR experiments. Chemistry 2011; 17:7442-53. [PMID: 21567493 DOI: 10.1002/chem.201003432] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Indexed: 01/17/2023]
Abstract
Noroviruses attach to their host cells through histo blood group antigens (HBGAs), and compounds that interfere with this interaction are likely to be of therapeutic or diagnostic interest. It is shown that NMR binding studies can simultaneously identify and differentiate the site for binding HBGA ligands and complementary ligands from a large compound library, thereby facilitating the design of potent heterobifunctional ligands. Saturation transfer difference (STD) NMR experiments, spin-lock filtered NMR experiments, and interligand NOE (ILOE) experiments in the presence of virus-like particles (VLPs), identified compounds that bind to the HBGA binding site of human norovirus. Based on these data two multivalent prototype entry-inhibitors against norovirus infection were synthesized. A surface plasmon resonance based inhibition assay showed avidity gains of 1000 and one million fold over a millimolar univalent ligand. This suggests that further rational design of multivalent inhibitors based on our strategy will identify potent entry-inhibitors against norovirus infections.
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Affiliation(s)
- Christoph Rademacher
- Center of Structural and Cell Biology in Medicine, Institute of Chemistry, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
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17
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Sledz P, Silvestre HL, Hung AW, Ciulli A, Blundell TL, Abell C. Optimization of the interligand Overhauser effect for fragment linking: application to inhibitor discovery against Mycobacterium tuberculosis pantothenate synthetase. J Am Chem Soc 2010; 132:4544-5. [PMID: 20232910 DOI: 10.1021/ja100595u] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fragment-based methods are a new and emerging approach for the discovery of protein binders that are potential new therapeutic agents. Several ways of utilizing structural information to guide the inhibitor assembly have been explored to date. One of the approaches, application of interligand Overhauser effect (ILOE) observations, is of particular interest, as it does not require the availability of a three-dimensional protein structure and is an NMR-based method that can be applied to targets that cannot be observed directly because of their size. Fragments, as small and often hydrophobic molecules, suffer from problems including compound aggregation in an aqueous environment and nonspecific binding contributions, especially when screened at higher concentrations suitable for ILOE observations. Here we report how this problem can be overcome by applying a step-by-step iterative procedure that includes the application of optimized probe molecules with known binding modes to elucidate the unknown binding modes of fragments. An enzyme substrate with well-characterized binding was used as a starting point, and the relative binding modes of modified fragments derived from ILOE observations were used to guide the fragment linking, leading to a potent inhibitor of our model system, Mycobacterium tuberculosis pantothenate synthetase, a potential drug target. We have supported our NMR data with crystal structures, thus establishing the guidelines for optimizing the ILOE observations. This model study should expand the application of the technique in drug discovery.
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Affiliation(s)
- Pawel Sledz
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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18
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Leung IKH, Flashman E, Yeoh KK, Schofield CJ, Claridge TDW. Using NMR solvent water relaxation to investigate metalloenzyme-ligand binding interactions. J Med Chem 2010; 53:867-75. [PMID: 20025281 DOI: 10.1021/jm901537q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This report demonstrates that solvent water relaxation measurements can be used for quantitative screening of ligand binding and for mechanistic investigations of enzymes containing paramagnetic metal centers by using conventional NMR instrumentation at high field. The method was exemplified using prolyl hydroxylase domain containing enzyme 2 (PHD2), a human enzyme involved in hypoxic sensing, with Mn(II) substituting for Fe(II) at the active site. K(D) values were determined for inhibitors that hinder access of water to the paramagnetic center. This technique is also useful for investigating the mechanism of suitable metalloenzymes, including order of ligand binding and modes of inhibition.
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Affiliation(s)
- Ivanhoe K H Leung
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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19
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Ludwig C, Michiels PJA, Lodi A, Ride J, Bunce C, Günther UL. Evaluation of solvent accessibility epitopes for different dehydrogenase inhibitors. ChemMedChem 2008; 3:1371-6. [PMID: 18576452 DOI: 10.1002/cmdc.200800110] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Knowledge about the orientation of ligands or inhibitors bound to a protein is vital for the development of new drugs. It was recently shown that solvent accessibility epitopes for protein ligands can be mapped by transferring magnetization from water molecules to the ligand to derive the ligand orientation. This is based on the fact that NMR signals of ligands arising from magnetization transferred from solvent molecules via the protein have a different sign from those arising from direct magnetization transfer from bulk water. Herein we critically evaluate the applicability of solvent accessibility mapping to derive binding orientations for ligands of two dehydrogenases (AKR1C3 and HSD17beta1) with very different binding pockets, including complexes in which the ligand is buried more deeply inside the protein. We also evaluate the possibility of using co-solvents, such as DMSO, for magnetization transfer.
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Affiliation(s)
- Christian Ludwig
- University of Birmingham, Vincent Drive, Edgbaston, Birmingham B152TT, UK
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20
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The Tubulin Binding Mode of MT Stabilizing and Destabilizing Agents Studied by NMR. Top Curr Chem (Cham) 2008; 286:151-208. [DOI: 10.1007/128_2008_22] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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21
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Orts J, Tuma J, Reese M, Grimm S, Monecke P, Bartoschek S, Schiffer A, Wendt K, Griesinger C, Carlomagno T. Crystallography-Independent Determination of Ligand Binding Modes. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801792] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Orts J, Tuma J, Reese M, Grimm S, Monecke P, Bartoschek S, Schiffer A, Wendt K, Griesinger C, Carlomagno T. Crystallography-Independent Determination of Ligand Binding Modes. Angew Chem Int Ed Engl 2008; 47:7736-40. [DOI: 10.1002/anie.200801792] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Orts J, Grimm SK, Griesinger C, Wendt KU, Bartoschek S, Carlomagno T. Specific Methyl Group Protonation for the Measurement of Pharmacophore-Specific Interligand NOE Interactions. Chemistry 2008; 14:7517-20. [DOI: 10.1002/chem.200800880] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Hajduk PJ, Greer J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat Rev Drug Discov 2007; 6:211-9. [PMID: 17290284 DOI: 10.1038/nrd2220] [Citation(s) in RCA: 753] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since the early 1990s, several technological and scientific advances - such as combinatorial chemistry, high-throughput screening and the sequencing of the human genome - have been heralded as remedies to the problems facing the pharmaceutical industry. The use of these technologies in some form is now well established at most pharmaceutical companies; however, the return on investment in terms of marketed products has not met expectations. Fragment-based drug design is another tool for drug discovery that has emerged in the past decade. Here, we describe the development and evolution of fragment-based drug design, analyse the role that this approach can have in combination with other discovery technologies and highlight the impact that fragment-based methods have made in progressing new medicines into the clinic.
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Affiliation(s)
- Philip J Hajduk
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
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25
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Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. The INPHARMA method: protein-mediated interligand NOEs for pharmacophore mapping. Angew Chem Int Ed Engl 2006; 44:4172-5. [PMID: 15929149 DOI: 10.1002/anie.200500503] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Martín-Pastor M, Vega-Vázquez M, De Capua A, Canales A, André S, Gabius HJ, Jiménez-Barbero J. Enhanced signal dispersion in saturation transfer difference experiments by conversion to a 1D-STD-homodecoupled spectrum. JOURNAL OF BIOMOLECULAR NMR 2006; 36:103-9. [PMID: 17013681 DOI: 10.1007/s10858-006-9055-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 07/07/2006] [Indexed: 05/12/2023]
Abstract
The saturation transfer difference (STD) experiment is a rich source of information on topological aspects of ligand binding to a receptor. The epitope mapping is based on a magnetization transfer after signal saturation from the receptor to the ligand, where interproton distances permit this process. Signal overlap in the STD spectrum can cause difficulties to correctly assign and/or quantitate the measured enhancements. To address this issue we report here a modified version of the routine experiment and a processing scheme that provides a 1D-STD homodecoupled spectrum (i.e. an experiment in which all STD signals appear as singlets) with line widths similar to those in original STD spectrum. These refinements contribute to alleviate problems of signal overlap. The experiment is based on 2D-J-resolved spectroscopy, one of the fastest 2D experiments under conventional data sampling in the indirect dimension, and provides excellent sensitivity, a key factor for the difference experiments.
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Affiliation(s)
- Manuel Martín-Pastor
- Laboratorio Integral de Dinámica e Estructura de Biomoléculas José R. Carracido, Unidade de Resonancia Magnética, Edificio CACTUS, RIAIDT, Universidade de Santiago de Compostela, 15706, Santiago de Compostela, Spain
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Abstract
Reverse chemical genetics is an emerging technique that makes use of small molecule inhibitors to characterize how a protein functions. In this regard, we have developed an NMR-based approach (SAR by ILOEs) that enables the identification of high affinity ligands for a given protein target without the need of a specific assay. Our approach is of general applicability and could result very powerful in reverse chemical-genetics studies, target validation, and lead discovery. We report a recent application on the design and synthesis of compounds that inhibit protein-membrane interactions.
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Affiliation(s)
- Barbara Becattini
- The Burnham Institute, 10901 North Torrey Pines Rd. La Jolla, CA 92037, USA
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Ruan KH, Wu J, Wang LH. Solution structure of a common substrate mimetic of cyclooxygenase-downstream synthases bound to an engineered thromboxane A2 synthase using a high-resolution NMR technique. Arch Biochem Biophys 2005; 444:165-73. [PMID: 16297851 DOI: 10.1016/j.abb.2005.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Revised: 10/04/2005] [Accepted: 10/05/2005] [Indexed: 11/15/2022]
Abstract
Understanding the docking mechanism of the common substrate, prostaglandin H(2) (PGH(2)), into the active sites of different cyclooxygenase(COX)-downstream synthases is a key step toward uncovering the molecular basis of the isomerization of PGH(2) to different prostanoids. A high-resolution NMR spectroscopy was used to determine the conformational changes and solution 3D structure of U44069, a PGH(2) analogue, bound to one of the COX-downstream synthases-an engineered thromboxane A(2) synthase (TXAS). The dynamic binding was clearly observed by (1)D NMR titration. The detailed conformational change and 3D structure of U44069 bound to the TXAS were demonstrated by 2D (1)H NMR experiments using transferred NOEs. Through the assignments for the 2D (1)H NMR spectra, TOCSY, DQF-COSY, NOESY, and the structural calculations based on the NOE constraints, they demonstrated that the widely open conformation with a triangle shape of the free U44069 changed to a compact structure with an oval shape when bound to the TXAS. The putative substrate-binding pocket of the TXAS model fits the conformation of the TXAS-bound U44069 appropriately, but could not fit the free form of U44069. It was the first to provide structural information for the dynamic docking of the PGH(2) mimic of the TXAS in solution, and to imply that PGH(2) undergoes conformational changes when bound to different COX-downstream synthases, which may play important roles in the isomerization of PGH(2) to different prostanoids. The NMR technique can be used as a powerful tool to determine the conformations of PGH(2) bound to other COX-downstream synthases.
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Affiliation(s)
- Ke-He Ruan
- Vascular Biology Research Center, Division of Hematology, Department of Internal Medicine, The University of Texas Health Science Center, Houston, 77030, USA.
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29
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Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T. The INPHARMA Method: Protein-Mediated Interligand NOEs for Pharmacophore Mapping. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500503] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Abstract
The advent of large-scale NMR-based screening has enabled new strategies for the design of novel, potent inhibitors of therapeutic targets. In particular, fragment-based strategies, in which molecular portions of the final high-affinity ligand are experimentally identified prior to chemical synthesis, have found widespread utility. This chapter will discuss some of the practical considerations for identifying and utilizing these fragment leads in drug design, with special emphasis on some of the lessons learned from more than a decade of industry experience.
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31
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Abstract
The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.
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Affiliation(s)
- Teresa Carlomagno
- Max Planck Institute for Biophysical Chemistry, Department of NMR Based Structural Biology, Am Fassberg, 11-D 37077 Göttingen, Germany.
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Lucas LH, Price KE, Larive CK. Epitope Mapping and Competitive Binding of HSA Drug Site II Ligands by NMR Diffusion Measurements. J Am Chem Soc 2004; 126:14258-66. [PMID: 15506793 DOI: 10.1021/ja0479538] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is important to characterize drug-albumin binding during drug discovery and lead optimization as strong binding may reduce bioavailability and/or increase the drug's in vivo half-life. Despite knowing about the location of human serum albumin (HSA) drug binding sites and the residues important for binding, less is understood about the binding dynamics between exogenous drugs and endogenous fatty acids. In contrast to highly specific antibody-antigen interactions, the conformational flexibility of albumin allows the protein to adopt multiple conformations of approximately equal energy in order to accommodate a variety of ligands. Nuclear magnetic resonance (NMR) diffusion measurements are a simple way to quantitatively describe ligand-protein interactions without prior knowledge of the number of binding sites or the binding stoichiometry. This method can also provide information about ligand orientation at the binding site due to buildup of exchange-transferred NOE (trNOE) on the diffusion time scale of the experiment. The results of NMR diffusion and NOE experiments reveal multiple binding interactions of HSA with dansylglycine, a drug site II probe, and caprylate, a medium-chain fatty acid that also has primary affinity for HSA's drug site II. Interligand NOE (ilNOE) detected in the diffusion analysis of a protein solution containing both ligands provides insight into the conformations adopted by these ligands while bound in common HSA binding pockets. The results demonstrate the ability of NMR diffusion experiments to identify ternary complex formation and show the potential of this method for characterizing other biologically important ternary structures, such as enzyme-cofactor-inhibitor complexes.
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Affiliation(s)
- Laura H Lucas
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
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Yan J, Kline AD, Mo H, Shapiro MJ, Zartler ER. The effect of relaxation on the epitope mapping by saturation transfer difference NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 163:270-276. [PMID: 12914842 DOI: 10.1016/s1090-7807(03)00106-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The effect of longitudinal relaxation of ligand protons on saturation transfer difference (STD) was investigated by using a known binding system, dihydrofolate reductase and trimethoprim. The results indicate that T1 relaxation of ligand protons has a severe interference on the epitope map derived from a STD measurement. When the T1s of individual ligand protons are distinctly different, STD experiments may not give an accurate epitope map for the ligand-target interactions. Measuring the relaxation times prior to mapping is strongly advised. A saturation time shorter than T1s is suggested for improving the potential epitope map. Reduction in temperature was seen to enhance the saturation efficiency in small to medium size targets.
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Affiliation(s)
- Jiangli Yan
- Discovery Chemistry Research and Technologies, Lilly Research Labs, Lilly Corporate Center, Eli Lilly & Co, Indianapolis, IN 46285, USA
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Abstract
NMR spectroscopy has evolved into an important technique in support of structure-based drug design. Here, we survey the principles that enable NMR to provide information on the nature of molecular interactions and, on this basis, we discuss current NMR-based strategies that can identify weak-binding compounds and aid their development into potent, drug-like inhibitors for use as lead compounds in drug discovery.
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Affiliation(s)
- Maurizio Pellecchia
- TRIAD Therapeutics, Inc., 9381 Judicial Drive, San Diego, California 92121, USA
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35
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Li D, Levy LA, Gabel SA, Lebetkin MS, DeRose EF, Wall MJ, Howell EE, London RE. Interligand Overhauser effects in type II dihydrofolate reductase. Biochemistry 2001; 40:4242-52. [PMID: 11284680 DOI: 10.1021/bi0026425] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
R67 dihydrofolate reductase (DHFR) is a type II DHFR produced by bacteria as a resistance mechanism to the increased clinical use of the antibacterial drug trimethoprim. Type II DHFRs are not homologous in either sequence or structure with chromosomal DHFRs. The type II enzymes contain four identical subunits which form a homotetramer containing a single active site pore accessible from either end. Although the crystal structure of the complex of R67 DHFR with folate has been reported [Narayana et al. (1995) Nat. Struct. Biol. 2, 1018], the nature of the ternary complex which must form with substrate and cofactor is unclear. We have performed transferred NOE and interligand NOE (ILOE) studies to analyze the ternary complexes formed from NADP(+) and folate in order to probe the structure of the ternary complex. Consistent with previous studies of the binary complex formed from another type II DHFR, the ribonicotinamide bond of NADP(+) was found to adopt a syn conformation, while the adenosine moiety adopts an anti conformation. Large ILOE peaks connecting NADP(+) H4 and H5 with folate H9 protons are observed, while the absence of a large ILOE connecting NADP(+) H4 and H5 with folate H7 indicates that the relative orientation of the two ligands differs significantly from the orientation in the chromosomal enzyme. To obtain more detailed insight, we prepared and studied the folate analogue 2-deamino-2-methyl-5,8-dideazafolate (DMDDF) which contains additional protons in order to provide additional NOEs. For this analogue, the exchange characteristics of the corresponding ternary complex were considerably poorer, and it was necessary to utilize higher enzyme concentrations and higher temperature in order to obtain ILOE information. The results support a structure in which the NADP(+) and folate/DMDDF molecules extend in opposite directions parallel to the long axis of the pore, with the nicotinamide and pterin ring systems approximately stacked at the center. Such a structure leads to a ternary complex which is in many respects similar to the gas-phase theoretical calculations of the dihydrofolate-NADPH transition state by Andres et al. [(1996) Bioorg. Chem. 24, 10-18]. Analogous NMR studies performed on folate, DMDDF, and R67 DHFR indicate formation of a ternary complex in which two symmetry-related binding sites are occupied by folate and DMDDF.
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Affiliation(s)
- D Li
- Laboratory of Structural Biology, MR-01, National Institute of Environmental and Health Sciences, Box 12233, Research Triangle Park, North Carolina 27709, USA
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36
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Affiliation(s)
- M Shapiro
- Novartis Institute for Biomedical Research, Summit, NJ 07901, USA
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