1
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Martin MP, Noble MEM. Exiting the tunnel of uncertainty: crystal soak to validated hit. Acta Crystallogr D Struct Biol 2022; 78:1294-1302. [PMID: 36322414 PMCID: PMC9629488 DOI: 10.1107/s2059798322009986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/12/2022] [Indexed: 11/28/2022] Open
Abstract
Crystallographic fragment screens provide an efficient and effective way to identify small-molecule ligands of a crystallized protein. Due to their low molecular weight, such hits tend to have low, often unquantifiable, affinity for their target, complicating the twin challenges of validating the hits as authentic solution-phase ligands of the target and identifying the `best' hit(s) for further elaboration. In this article, approaches that address these challenges are assessed. Using retrospective analysis of a recent ATAD2 hit-identification campaign, alongside other examples of successful fragment-screening campaigns, it is suggested that hit validation and prioritization are best achieved by a `triangulation' approach in which the results of multiple available biochemical and biophysical techniques are correlated to develop qualitative structure-activity relationships (SARs). Such qualitative SARs may indeed be the only means by which to navigate a project through the tunnel of uncertainty that prevails before on-scale biophysical, biochemical and/or biological measurements become possible.
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Affiliation(s)
- Mathew P. Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Martin E. M. Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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2
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Applications of Solution NMR in Drug Discovery. Molecules 2021; 26:molecules26030576. [PMID: 33499337 PMCID: PMC7865596 DOI: 10.3390/molecules26030576] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/13/2023] Open
Abstract
During the past decades, solution nuclear magnetic resonance (NMR) spectroscopy has demonstrated itself as a promising tool in drug discovery. Especially, fragment-based drug discovery (FBDD) has benefited a lot from the NMR development. Multiple candidate compounds and FDA-approved drugs derived from FBDD have been developed with the assistance of NMR techniques. NMR has broad applications in different stages of the FBDD process, which includes fragment library construction, hit generation and validation, hit-to-lead optimization and working mechanism elucidation, etc. In this manuscript, we reviewed the current progresses of NMR applications in fragment-based drug discovery, which were illustrated by multiple reported cases. Moreover, the NMR applications in protein-protein interaction (PPI) modulators development and the progress of in-cell NMR for drug discovery were also briefly summarized.
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3
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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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4
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Ángeles Canales M, Félix Espinosa J. Ligand-detected NMR Methods in Drug Discovery. BIOPHYSICAL TECHNIQUES IN DRUG DISCOVERY 2017. [DOI: 10.1039/9781788010016-00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This book chapter describes the basic principles of NMR-based techniques for detecting ligand binding and uses examples of the application of these techniques in drug discovery programs for screening, hit validation and optimization to illustrate their utility in characterizing ligand–protein interactions. The binding of small molecules to biological receptors can be observed directly by detecting changes in a particular NMR parameter when the protein is added to a sample containing the ligand, or indirectly, using a “spy” molecule in competitive NMR experiments. Combinations of different NMR experiments can be used to confirm binding and also to obtain structural information that can be used to guide medicinal chemistry decisions. Ligand-observed NMR methods are able to identify weak affinity ligands that cannot be detected by other biophysical techniques, which means that NMR-based methods are extremely valuable tools for fragment-based drug discovery approaches.
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Affiliation(s)
- María Ángeles Canales
- Department of Química Orgánica I, Universidad Complutense de Madrid Avd. Complutense s/n 28040 Madrid Spain
| | - Juan Félix Espinosa
- Centro de Investigación Lilly Avda. de la Industria 30 28108, Alcobendas, Madrid Spain
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5
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NMR in structure-based drug design. Essays Biochem 2017; 61:485-493. [PMID: 29118095 DOI: 10.1042/ebc20170037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 12/13/2022]
Abstract
NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed.
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6
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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.
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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
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7
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Genick CC, Wright SK. Biophysics: for HTS hit validation, chemical lead optimization, and beyond. Expert Opin Drug Discov 2017; 12:897-907. [DOI: 10.1080/17460441.2017.1349096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christine C. Genick
- Novartis Pharma AG, Novartis Institutes for BioMedical Research, Chemical Biology and Therapeutics, Protein Sciences, Basel, Switzerland
- Protein Sciences, Research Parkway Meriden, Cambridge, MA, USA
| | - S. Kirk Wright
- Protein Sciences, Research Parkway Meriden, Cambridge, MA, USA
- Protein Sciences, Novartis Pharma AG, Novartis Institutes for BioMedical Research, Chemical Biology and Therapeutics, Cambridge, MA, USA
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8
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Huber S, Casagrande F, Hug MN, Wang L, Heine P, Kummer L, Plückthun A, Hennig M. SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands. PLoS One 2017; 12:e0175842. [PMID: 28510609 PMCID: PMC5433701 DOI: 10.1371/journal.pone.0175842] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 04/01/2017] [Indexed: 12/22/2022] Open
Abstract
The neurotensin receptor 1 represents an important drug target involved in various diseases of the central nervous system. So far, the full exploitation of potential therapeutic activities has been compromised by the lack of compounds with favorable physicochemical and pharmacokinetic properties which efficiently penetrate the blood-brain barrier. Recent progress in the generation of stabilized variants of solubilized neurotensin receptor 1 and its subsequent purification and successful structure determination presents a solid starting point to apply the approach of fragment-based screening to extend the chemical space of known neurotensin receptor 1 ligands. In this report, surface plasmon resonance was used as primary method to screen 6369 compounds. Thereby 44 hits were identified and confirmed in competition as well as dose-response experiments. Furthermore, 4 out of 8 selected hits were validated using nuclear magnetic resonance spectroscopy as orthogonal biophysical method. Computational analysis of the compound structures, taking the known crystal structure of the endogenous peptide agonist into consideration, gave insight into the potential fragment-binding location and interactions and inspires chemistry efforts for further exploration of the fragments.
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Affiliation(s)
- Sylwia Huber
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
- * E-mail: (SH); (MH)
| | - Fabio Casagrande
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Melanie N. Hug
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Lisha Wang
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Philipp Heine
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lutz Kummer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Michael Hennig
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
- * E-mail: (SH); (MH)
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9
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Hetényi A, Hegedűs Z, Fajka-Boja R, Monostori É, Kövér KE, Martinek TA. Target-specific NMR detection of protein-ligand interactions with antibody-relayed 15N-group selective STD. JOURNAL OF BIOMOLECULAR NMR 2016; 66:227-232. [PMID: 27885546 DOI: 10.1007/s10858-016-0076-3] [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: 07/14/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
Fragment-based drug design has been successfully applied to challenging targets where the detection of the weak protein-ligand interactions is a key element. 1H saturation transfer difference (STD) NMR spectroscopy is a powerful technique for this work but it requires pure homogeneous proteins as targets. Monoclonal antibody (mAb)-relayed 15N-GS STD spectroscopy has been developed to resolve the problem of protein mixtures and impure proteins. A 15N-labelled target-specific mAb is selectively irradiated and the saturation is relayed through the target to the ligand. Tests on the anti-Gal-1 mAb/Gal-1/lactose system showed that the approach is experimentally feasible in a reasonable time frame. This method allows detection and identification of binding molecules directly from a protein mixture in a multicomponent system.
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Affiliation(s)
- Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm t. 8., Szeged, 6720, Hungary
| | - Zsófia Hegedűs
- SZTE-MTA Lendület Foldamer Research Group, Institute of Pharmaceutical Analysis Department, University of Szeged, Somogyi u. 4, Szeged, 6720, Hungary
| | - Roberta Fajka-Boja
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Éva Monostori
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1., Debrecen, 4032, Hungary
| | - Tamás A Martinek
- SZTE-MTA Lendület Foldamer Research Group, Institute of Pharmaceutical Analysis Department, University of Szeged, Somogyi u. 4, Szeged, 6720, Hungary.
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10
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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: 121] [Impact Index Per Article: 15.1] [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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11
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19F nuclear magnetic resonance screening of glucokinase activators. Anal Biochem 2015; 477:62-8. [DOI: 10.1016/j.ab.2015.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/29/2015] [Accepted: 02/04/2015] [Indexed: 11/20/2022]
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12
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Yuan G, Gedeon NG, Jankins TC, Jones GB. Novel approaches for targeting the adenosine A2Areceptor. Expert Opin Drug Discov 2014; 10:63-80. [DOI: 10.1517/17460441.2015.971006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Barile E, Pellecchia M. NMR-based approaches for the identification and optimization of inhibitors of protein-protein interactions. Chem Rev 2014; 114:4749-63. [PMID: 24712885 PMCID: PMC4027952 DOI: 10.1021/cr500043b] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Elisa Barile
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maurizio Pellecchia
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
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14
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A new NMR technique to probe protein–ligand interaction. J Pharm Biomed Anal 2014; 89:18-23. [DOI: 10.1016/j.jpba.2013.10.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 11/20/2022]
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15
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Lodge JM, Rettenmaier TJ, Wells JA, Pomerantz WC, Mapp AK. FP Tethering: a screening technique to rapidly identify compounds that disrupt protein-protein interactions. MEDCHEMCOMM 2014; 5:370-375. [PMID: 24795804 DOI: 10.1039/c3md00356f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tethering is a screening technique for discovering small-molecule fragments that bind to pre-determined sites via formation of a disulphide bond. Tethering screens traditionally rely upon mass spectrometry to detect disulphide bind formation, which requires a time-consuming liquid chromatography step. Here we show that Tethering can be performed rapidly and inexpensively using a homogenous fluorescence polarization (FP) assay that detects displacement of a peptide ligand from the protein target as an indirect readout of disulphide formation. We apply this method, termed FP Tethering, to identify fragments that disrupt the protein-protein interaction between the KIX domain of the transcriptional coactivator CBP and the transcriptional activator peptide pKID.
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Affiliation(s)
- Jean M Lodge
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States ; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - T Justin Rettenmaier
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - William C Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States ; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States ; Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
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16
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Regnström K, Yan J, Nguyen L, Callaway K, Yang Y, Diep L, Xing W, Adhikari A, Beroza P, Hom RK, Riley B, Rudolph D, Jobling MF, Baker J, Johnston J, Konradi A, Bova MP, Artis DR. Label free fragment screening using surface plasmon resonance as a tool for fragment finding - analyzing parkin, a difficult CNS target. PLoS One 2013; 8:e66879. [PMID: 23861750 PMCID: PMC3702509 DOI: 10.1371/journal.pone.0066879] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/12/2013] [Indexed: 11/18/2022] Open
Abstract
Surface Plasmon Resonance (SPR) is rarely used as a primary High-throughput Screening (HTS) tool in fragment-based approaches. With SPR instruments becoming increasingly high-throughput it is now possible to use SPR as a primary tool for fragment finding. SPR becomes, therefore, a valuable tool in the screening of difficult targets such as the ubiquitin E3 ligase Parkin. As a prerequisite for the screen, a large number of SPR tests were performed to characterize and validate the active form of Parkin. A set of compounds was designed and used to define optimal SPR assay conditions for this fragment screen. Using these conditions, more than 5000 pre-selected fragments from our in-house library were screened for binding to Parkin. Additionally, all fragments were simultaneously screened for binding to two off target proteins to exclude promiscuous binding compounds. A low hit rate was observed that is in line with hit rates usually obtained by other HTS screening assays. All hits were further tested in dose responses on the target protein by SPR for confirmation before channeling the hits into Nuclear Magnetic Resonance (NMR) and other hit-confirmation assays.
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17
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Taylor SJ, Padyana AK, Abeywardane A, Liang S, Hao MH, De Lombaert S, Proudfoot J, Farmer BS, Li X, Collins B, Martin L, Albaugh DR, Hill-Drzewi M, Pullen SS, Takahashi H. Discovery of Potent, Selective Chymase Inhibitors via Fragment Linking Strategies. J Med Chem 2013; 56:4465-81. [DOI: 10.1021/jm400138z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
| | | | | | | | - Ming-Hong Hao
- H3 Biomedicine, 300 Technology Square,
Cambridge, Massachusetts 02139, United States
| | - Stéphane De Lombaert
- Karos Pharmaceuticals, 5 Science Park, 401 Winchester Avenue, New Haven, Connecticut 06511,
United States
| | | | | | | | | | | | | | - Melissa Hill-Drzewi
- Lead Evaluation
Department, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford,
Connecticut 06492, United States
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18
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Visegrády A, Keserű GM. Fragment-based lead discovery on G-protein-coupled receptors. Expert Opin Drug Discov 2013; 8:811-20. [PMID: 23621346 DOI: 10.1517/17460441.2013.794135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION G-protein-coupled receptors (GPCRs) form one of the largest groups of potential targets for novel medications. Low druggability of many GPCR targets and inefficient sampling of chemical space in high-throughput screening expertise however often hinder discovery of drug discovery leads for GPCRs. Fragment-based drug discovery is an alternative approach to the conventional strategy and has proven its efficiency on several enzyme targets. Based on developments in biophysical screening techniques, receptor stabilization and in vitro assays, virtual and experimental fragment screening and fragment-based lead discovery recently became applicable for GPCR targets. AREAS COVERED This article provides a review of the biophysical as well as biological detection techniques suitable to study GPCRs together with their applications to screen fragment libraries and identify fragment-size ligands of cell surface receptors. The article presents several recent examples including both virtual and experimental protocols for fragment hit discovery and early hit to lead progress. EXPERT OPINION With the recent progress in biophysical detection techniques, the advantages of fragment-based drug discovery could be exploited for GPCR targets. Structural information on GPCRs will be more abundantly available for early stages of drug discovery projects, providing information on the binding process and efficiently supporting the progression of fragment hit to lead. In silico approaches in combination with biological assays can be used to address structurally challenging GPCRs and confirm biological relevance of interaction early in the drug discovery project.
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19
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Duong-Thi MD, Bergström M, Fex T, Isaksson R, Ohlson S. High-Throughput Fragment Screening by Affinity LC-MS. ACTA ACUST UNITED AC 2012; 18:160-71. [DOI: 10.1177/1087057112459271] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fragment screening, an emerging approach for hit finding in drug discovery, has recently been proven effective by its first approved drug, vemurafenib, for cancer treatment. Techniques such as nuclear magnetic resonance, surface plasmon resonance, and isothemal titration calorimetry, with their own pros and cons, have been employed for screening fragment libraries. As an alternative approach, screening based on high-performance liquid chromatography separation has been developed. In this work, we present weak affinity LC/MS as a method to screen fragments under high-throughput conditions. Affinity-based capillary columns with immobilized thrombin were used to screen a collection of 590 compounds from a fragment library. The collection was divided into 11 mixtures (each containing 35 to 65 fragments) and screened by MS detection. The primary screening was performed in <4 h (corresponding to >3500 fragments per day). Thirty hits were defined, which subsequently entered a secondary screening using an active site-blocked thrombin column for confirmation of specificity. One hit showed selective binding to thrombin with an estimated dissociation constant ( KD) in the 0.1 mM range. This study shows that affinity LC/MS is characterized by high throughput, ease of operation, and low consumption of target and fragments, and therefore it promises to be a valuable method for fragment screening.
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Affiliation(s)
| | | | - Tomas Fex
- Astra&Zeneca R&D Mölndal, Mölndal, Sweden
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20
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Biophysical and computational fragment-based approaches to targeting protein-protein interactions: applications in structure-guided drug discovery. Q Rev Biophys 2012; 45:383-426. [PMID: 22971516 DOI: 10.1017/s0033583512000108] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Drug discovery has classically targeted the active sites of enzymes or ligand-binding sites of receptors and ion channels. In an attempt to improve selectivity of drug candidates, modulation of protein-protein interfaces (PPIs) of multiprotein complexes that mediate conformation or colocation of components of cell-regulatory pathways has become a focus of interest. However, PPIs in multiprotein systems continue to pose significant challenges, as they are generally large, flat and poor in distinguishing features, making the design of small molecule antagonists a difficult task. Nevertheless, encouragement has come from the recognition that a few amino acids - so-called hotspots - may contribute the majority of interaction-free energy. The challenges posed by protein-protein interactions have led to a wellspring of creative approaches, including proteomimetics, stapled α-helical peptides and a plethora of antibody inspired molecular designs. Here, we review a more generic approach: fragment-based drug discovery. Fragments allow novel areas of chemical space to be explored more efficiently, but the initial hits have low affinity. This means that they will not normally disrupt PPIs, unless they are tethered, an approach that has been pioneered by Wells and co-workers. An alternative fragment-based approach is to stabilise the uncomplexed components of the multiprotein system in solution and employ conventional fragment-based screening. Here, we describe the current knowledge of the structures and properties of protein-protein interactions and the small molecules that can modulate them. We then describe the use of sensitive biophysical methods - nuclear magnetic resonance, X-ray crystallography, surface plasmon resonance, differential scanning fluorimetry or isothermal calorimetry - to screen and validate fragment binding. Fragment hits can subsequently be evolved into larger molecules with higher affinity and potency. These may provide new leads for drug candidates that target protein-protein interactions and have therapeutic value.
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Zeder-Lutz G, Choulier L, Besse M, Cousido-Siah A, Figueras FXR, Didier B, Jung ML, Podjarny A, Altschuh D. Validation of surface plasmon resonance screening of a diverse chemical library for the discovery of protein tyrosine phosphatase 1b binders. Anal Biochem 2012; 421:417-27. [DOI: 10.1016/j.ab.2011.09.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 01/07/2023]
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Emerging role of surface plasmon resonance in fragment-based drug discovery. Future Med Chem 2012; 3:1809-20. [PMID: 22004086 DOI: 10.4155/fmc.11.128] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Surface plasmon resonance (SPR) offers a method of biophysical fragment screening that is fast, efficient, cost effective and accurate. SPR is increasingly being adopted as a secondary assay to validate fragment hits. Recently, technical advances have resulted in the emergence of SPR as a primary screening methodology for fragment-based drug discovery. Moreover, SPR biosensor assays can be developed for a wide range of proteins, including membrane proteins, such as G-protein-coupled receptors. In this review, we discuss the advantages and limitations of SPR fragment screening including experimental consideration of reducing false positive and false negative rates to a minimum. We discuss how ligand efficiency can be used both as a method to eliminate false positives and to understand which fragments in a library may be a source of false negatives.
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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.
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Affiliation(s)
- Laurel O Sillerud
- Department of Biochemistry and Molecular Biology, UNM HDC, University of New Mexico, Albuquerque, NM, USA.
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Kemp MM, Weïwer M, Koehler AN. Unbiased binding assays for discovering small-molecule probes and drugs. Bioorg Med Chem 2011; 20:1979-89. [PMID: 22230199 DOI: 10.1016/j.bmc.2011.11.071] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/22/2011] [Accepted: 11/30/2011] [Indexed: 11/28/2022]
Abstract
2011 marks the 10-year anniversary of milestone manuscripts describing drafts of the human genome sequence. Over the past decade, a number of new proteins have been linked to disease-many of which fall into classes that have been historically considered challenging from the perspective of drug discovery. Several of these newly associated proteins lack structural information or strong annotation with regard to function, making development of conventional in vitro functional assays difficult. A recent resurgence in the popularity of simple small molecule binding assays has led to new approaches that do not require knowledge of protein structure or function in advance. Here we briefly review selected methods for executing binding assays that have been used successfully to discover small-molecule probes or drug candidates.
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Affiliation(s)
- Melissa M Kemp
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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Bamborough P, Brown MJ, Christopher JA, Chung CW, Mellor GW. Selectivity of kinase inhibitor fragments. J Med Chem 2011; 54:5131-43. [PMID: 21699136 DOI: 10.1021/jm200349b] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A kinase-focused screening set of fragments has been assembled and has proved successful for the discovery of ligand-efficient hits against many targets. Here we present some of our general conclusions from this exercise. Notably, we present the first profiling results for literature fragments that have previously been used as starting points for optimization against individual kinases. We consider the importance of screening format and the extent to which selectivity is helpful in selecting fragments for progression. Results are also outlined for fragments targeting the DFG-out conformation and for atypical kinases such as PIM1 and lipid kinases.
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Affiliation(s)
- Paul Bamborough
- GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
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Abstract
Fragment-based drug discovery (FBDD) has emerged in the past decade as a powerful tool for discovering drug leads. The approach first identifies starting points: very small molecules (fragments) that are about half the size of typical drugs. These fragments are then expanded or linked together to generate drug leads. Although the origins of the technique date back some 30 years, it was only in the mid-1990s that experimental techniques became sufficiently sensitive and rapid for the concept to be become practical. Since that time, the field has exploded: FBDD has played a role in discovery of at least 18 drugs that have entered the clinic, and practitioners of FBDD can be found throughout the world in both academia and industry. Literally dozens of reviews have been published on various aspects of FBDD or on the field as a whole, as have three books (Jahnke and Erlanson, Fragment-based approaches in drug discovery, 2006; Zartler and Shapiro, Fragment-based drug discovery: a practical approach, 2008; Kuo, Fragment based drug design: tools, practical approaches, and examples, 2011). However, this chapter will assume that the reader is approaching the field with little prior knowledge. It will introduce some of the key concepts, set the stage for the chapters to follow, and demonstrate how X-ray crystallography plays a central role in fragment identification and advancement.
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