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FitzGerald EA, Vagrys D, Opassi G, Klein HF, Hamilton DJ, Talibov VO, Abramsson M, Moberg A, Lindgren MT, Holmgren C, Davis B, O'Brien P, Wijtmans M, Hubbard RE, de Esch IJP, Danielson UH. Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:40-51. [PMID: 37714432 DOI: 10.1016/j.slasd.2023.09.001] [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: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Beactica Therapeutics AB, Virdings allé 2, Uppsala, Sweden
| | - Darius Vagrys
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Giulia Opassi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Hanna F Klein
- Department of Chemistry, University of York, York, United Kingdom
| | - David J Hamilton
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | | | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Ben Davis
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom
| | - Peter O'Brien
- Department of Chemistry, University of York, York, United Kingdom
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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2
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Ai Y, Hwang L, MacKerell AD, Melnick A, Xue F. Progress toward B-Cell Lymphoma 6 BTB Domain Inhibitors for the Treatment of Diffuse Large B-Cell Lymphoma and Beyond. J Med Chem 2021; 64:4333-4358. [PMID: 33844535 DOI: 10.1021/acs.jmedchem.0c01686] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
B-cell lymphoma 6 (BCL6) is a master regulator of germinal center formation that produce antibody-secreting plasma cells and memory B-cells for sustained immune responses. The BTB domain of BCL6 (BCL6BTB) forms a homodimer that mediates transcriptional repression by recruiting its corepressor proteins to form a biologically functional transcriptional complex. The protein-protein interaction (PPI) between the BCL6BTB and its corepressors has emerged as a therapeutic target for the treatment of DLBCL and a number of other human cancers. This Perspective provides an overview of recent advances in the development of BCL6BTB inhibitors from reversible inhibitors, irreversible inhibitors, to BCL6 degraders. Inhibitor design and medicinal chemistry strategies for the development of novel compounds will be provided. The binding mode of new inhibitors to BCL6BTB are highlighted. Also, the in vitro and in vivo assays used for the evaluation of new compounds will be discussed.
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Affiliation(s)
- Yong Ai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Lucia Hwang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Ari Melnick
- Department of Hematology and Oncology, Weill Cornell Medical College, New York, New York 10021, United States.,Department of Pharmacology, Weill Cornell Medical College, New York, New York 10021, United States
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
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3
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Coyle J, Walser R. Applied Biophysical Methods in Fragment-Based Drug Discovery. SLAS DISCOVERY 2020; 25:471-490. [PMID: 32345095 DOI: 10.1177/2472555220916168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fragment-based drug discovery (FBDD) has come of age in the last decade with the FDA approval of four fragment-derived drugs. Biophysical methods are at the heart of hit discovery and validation in FBDD campaigns. The three most commonly used methods, thermal shift, surface plasmon resonance, and nuclear magnetic resonance, can be daunting for the novice user. We aim here to provide the nonexpert user of these methods with a summary of problems and challenges that might be faced, but also highlight the potential gains that each method can contribute to an FBDD project. While our view on FBDD is slightly biased toward enabling structure-guided drug discovery, most of the points we address in this review are also valid for non-structure-focused FBDD.
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Affiliation(s)
- Joe Coyle
- Astex Pharmaceuticals, Cambridge, UK
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4
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Zhi Y, Dai Y, Yang J, Tan S, Lin D, Lin K. Lead compounds and key residues of ribosomal protein S1 in drug-resistant Mycobacterium tuberculosis. Bioorg Chem 2018; 82:58-67. [PMID: 30268974 DOI: 10.1016/j.bioorg.2018.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/16/2022]
Abstract
Ribosomal protein S1 (RpsA) has been identified as a novel target of pyrazinoic acid (POA), which is the active form of pyrazinamide (PZA), in vivo. RpsA plays a crucial role in trans-translation, which is widespread in microbes. In our investigation, we first described the discovery of promising RpsA antagonists for drug-resistant mycobacterium (MtRpsAd438A) and M. smegmatis, as well as wild-type M. tuberculosis. These antagonists were discovered via structure/ligand-based virtual screening approaches. A total of 21 targeted compounds were selected by virtual screening, combined scores, affinity, similarities and rules for potential as drugs. Next, the affinities of these compounds for three targeted proteins were tested in vitro by applying various technologies, including fluorescence quenching titration (FQT), saturation transfer difference (STD), and chemical shift perturbation (CSP) assays. The results showed that seven compounds had a high affinity for the targeted proteins. Our discovery set the stage for discovering new chemical entities (NCEs) for PZA-resistant tuberculosis and providing key residues for rational drug design to target RpsA.
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Affiliation(s)
- Yunbao Zhi
- China Pharmaceutical University, Nanjing 210009, China; Shandong New Time Pharmaceutical Company, Lunan Pharmaceutical Group, Linyi 273400, China
| | - Yazhuang Dai
- China Pharmaceutical University, Nanjing 210009, China; Hangzhou Ipharmacare Information Technology Co., Ltd, Hangzhou 310000, China
| | - Juanjuan Yang
- College of Biological Science and Biotechnology, Fuzhou University, Fuzhou 350000, China
| | - Shuhua Tan
- China Pharmaceutical University, Nanjing 210009, China
| | | | - Kejiang Lin
- China Pharmaceutical University, Nanjing 210009, China.
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5
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Kenny PW. Comment on The Ecstasy and Agony of Assay Interference Compounds. J Chem Inf Model 2017; 57:2640-2645. [DOI: 10.1021/acs.jcim.7b00313] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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6
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Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach. J Med Chem 2017; 60:4358-4368. [PMID: 28471657 DOI: 10.1021/acs.jmedchem.7b00313] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
B-cell lymphoma 6 (BCL6) is a transcriptional factor that expresses in lymphocytes and regulates the differentiation and proliferation of lymphocytes. Therefore, BCL6 is a therapeutic target for autoimmune diseases and cancer treatment. This report presents the discovery of BCL6-corepressor interaction inhibitors by using a biophysics-driven fragment-based approach. Using the surface plasmon resonance (SPR)-based fragment screening, we successfully identified fragment 1 (SPR KD = 1200 μM, ligand efficiency (LE) = 0.28), a competitive binder to the natural ligand BCoR peptide. Moreover, we elaborated 1 into the more potent compound 7 (SPR KD = 0.078 μM, LE = 0.37, cell-free protein-protein interaction (PPI) IC50 = 0.48 μM (ELISA), cellular PPI IC50 = 8.6 μM (M2H)) by a structure-based design and structural integration with a second high-throughput screening hit.
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7
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Rogez-Florent T, Goossens L, Drucbert AS, Duban-Deweer S, Six P, Depreux P, Danzé PM, Goossens JF, Foulon C. Amine coupling versus biotin capture for the assessment of sulfonamide as ligands of hCA isoforms. Anal Biochem 2016; 511:42-51. [DOI: 10.1016/j.ab.2016.07.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/08/2016] [Accepted: 07/29/2016] [Indexed: 12/11/2022]
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8
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Hoagland DT, Liu J, Lee RB, Lee RE. New agents for the treatment of drug-resistant Mycobacterium tuberculosis. Adv Drug Deliv Rev 2016; 102:55-72. [PMID: 27151308 PMCID: PMC4903924 DOI: 10.1016/j.addr.2016.04.026] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 02/06/2023]
Abstract
Inadequate dosing and incomplete treatment regimens, coupled with the ability of the tuberculosis bacilli to cause latent infections that are tolerant of currently used drugs, have fueled the rise of multidrug-resistant tuberculosis (MDR-TB). Treatment of MDR-TB infections is a major clinical challenge that has few viable or effective solutions; therefore patients face a poor prognosis and years of treatment. This review focuses on emerging drug classes that have the potential for treating MDR-TB and highlights their particular strengths as leads including their mode of action, in vivo efficacy, and key medicinal chemistry properties. Examples include the newly approved drugs bedaquiline and delaminid, and other agents in clinical and late preclinical development pipeline for the treatment of MDR-TB. Herein, we discuss the challenges to developing drugs to treat tuberculosis and how the field has adapted to these difficulties, with an emphasis on drug discovery approaches that might produce more effective agents and treatment regimens.
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Affiliation(s)
- Daniel T Hoagland
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Pharmaceutical Sciences Graduate Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jiuyu Liu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robin B Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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9
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Abstract
INTRODUCTION Fragment-based approaches have played an increasing role alongside high-throughput screening in drug discovery for 15 years. The label-free biosensor technology based on surface plasmon resonance (SPR) is now sensitive and informative enough to serve during primary screens and validation steps. AREAS COVERED In this review, the authors discuss the role of SPR in fragment screening. After a brief description of the underlying principles of the technique and main device developments, they evaluate the advantages and adaptations of SPR for fragment-based drug discovery. SPR can also be applied to challenging targets such as membrane receptors and enzymes. EXPERT OPINION The high-level of immobilization of the protein target and its stability are key points for a relevant screening that can be optimized using oriented immobilized proteins and regenerable sensors. Furthermore, to decrease the rate of false negatives, a selectivity test may be performed in parallel on the main target bearing the binding site mutated or blocked with a low-off-rate ligand. Fragment-based drug design, integrated in a rational workflow led by SPR, will thus have a predominant role for the next wave of drug discovery which could be greatly enhanced by new improvements in SPR devices.
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Affiliation(s)
- Alain Chavanieu
- a Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 , Université de Montpellier, CNRS, ENSCM , Montpellier Cedex 5, France
| | - Martine Pugnière
- b IRCM , Institut de Recherche en Cancérologie de Montpellier , Montpellier , France.,c INSERM, U1194 , Université Montpellier , Montpellier , France.,d ICM , Institut Régional du Cancer , Montpellier , France
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10
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Christopeit T, Carlsen TJO, Helland R, Leiros HKS. Discovery of Novel Inhibitor Scaffolds against the Metallo-β-lactamase VIM-2 by Surface Plasmon Resonance (SPR) Based Fragment Screening. J Med Chem 2015; 58:8671-82. [DOI: 10.1021/acs.jmedchem.5b01289] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tony Christopeit
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Trine Josefine O. Carlsen
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ronny Helland
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hanna-Kirsti S. Leiros
- Department of Chemistry,
Faculty of Science and Technology, The Norwegian Structural Biology
Centre (NorStruct), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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11
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Huang B, Kang D, Zhan P, Liu X. Fragment-based approaches to anti-HIV drug discovery: state of the art and future opportunities. Expert Opin Drug Discov 2015; 10:1271-81. [PMID: 26372893 DOI: 10.1517/17460441.2015.1083007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION The search for additional drugs to treat HIV infection is a continuing effort due to the emergence and spread of HIV strains resistant to nearly all current drugs. The recent literature reveals that fragment-based drug design/discovery (FBDD) has become an effective alternative to conventional high-throughput screening strategies for drug discovery. AREAS COVERED In this critical review, the authors describe the state of the art in FBDD strategies for the discovery of anti-HIV drug-like compounds. The article focuses on fragment screening techniques, direct fragment-based design and early hit-to-lead progress. EXPERT OPINION Rapid progress in biophysical detection and in silico techniques has greatly aided the application of FBDD to discover candidate agents directed at a variety of anti-HIV targets. Growing evidence suggests that structural insights on key proteins in the HIV life cycle can be applied in the early phase of drug discovery campaigns, providing valuable information on the binding modes and efficiently prompting fragment hit-to-lead progression. The combination of structural insights with improved methodologies for FBDD, including the privileged fragment-based reconstruction approach, fragment hybridization based on crystallographic overlays, fragment growth exploiting dynamic combinatorial chemistry, and high-speed fragment assembly via diversity-oriented synthesis followed by in situ screening, offers the possibility of more efficient and rapid discovery of novel drugs for HIV-1 prevention or treatment. Though the use of FBDD in anti-HIV drug discovery is still in its infancy, it is anticipated that anti-HIV agents developed via fragment-based strategies will be introduced into the clinic in the future.
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Affiliation(s)
- Boshi Huang
- a Shandong University, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry , 44 West Culture Road, 250012, Jinan, Shandong, China ,
| | - Dongwei Kang
- a Shandong University, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry , 44 West Culture Road, 250012, Jinan, Shandong, China ,
| | - Peng Zhan
- a Shandong University, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry , 44 West Culture Road, 250012, Jinan, Shandong, China ,
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12
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Kutchukian PS, So SS, Fischer C, Waller CL. Fragment library design: using cheminformatics and expert chemists to fill gaps in existing fragment libraries. Methods Mol Biol 2015; 1289:43-53. [PMID: 25709032 DOI: 10.1007/978-1-4939-2486-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fragment based screening (FBS) has emerged as a mainstream lead discovery strategy in academia, biotechnology start-ups, and large pharma. As a prerequisite of FBS, a structurally diverse library of fragments is desirable in order to identify chemical matter that will interact with the range of diverse target classes that are prosecuted in contemporary screening campaigns. In addition, it is also desirable to offer synthetically amenable starting points to increase the probability of a successful fragment evolution through medicinal chemistry. Herein we describe a method to identify biologically relevant chemical substructures that are missing from an existing fragment library (chemical gaps), and organize these chemical gaps hierarchically so that medicinal chemists can efficiently navigate the prioritized chemical space and subsequently select purchasable fragments for inclusion in an enhanced fragment library.
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Affiliation(s)
- Peter S Kutchukian
- Cheminformatics, Merck Research Laboratories, BMB3-146, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA,
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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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Liu LK, Finzel BC. Fragment-based identification of an inducible binding site on cell surface receptor CD44 for the design of protein-carbohydrate interaction inhibitors. J Med Chem 2014; 57:2714-25. [PMID: 24606063 DOI: 10.1021/jm5000276] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Selective inhibitors of hyaluronan (HA) binding to the cell surface receptor CD44 will have value as probes of CD44-mediated signaling and have potential as therapeutic agents in chronic inflammation, cardiovascular disease, and cancer. Using biophysical binding assays, fragment screening, and crystallographic characterization of complexes with the CD44 HA binding domain, we have discovered an inducible pocket adjacent to the HA binding groove into which small molecules may bind. Iterations of fragment combination and structure-driven design have allowed identification of a series of 1,2,3,4-tetrahydroisoquinolines as the first nonglycosidic inhibitors of the CD44-HA interaction. The affinity of these molecules for the CD44 HA binding domain parallels their ability to interfere with CD44 binding to polymeric HA in vitro. X-ray crystallographic complexes of lead compounds are described and compared to a new complex with a short HA tetrasaccharide, to establish the tetrahydroisoquinoline pharmacophore as an attractive starting point for lead optimization.
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Affiliation(s)
- Li-Kai Liu
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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15
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Abstract
Surface plasmon resonance (SPR) biosensors have become the mainstream method for biomolecular interaction analysis. It offers many advantages over conventional methods by its label-free, real-time monitoring, low sample consumption, high throughput, and remarkable sensitivity. We have examined dengue virus protein interactions in the context of antibody affinity measurement, protein-protein interaction, and in the screening of small molecule inhibitors as well as the characterization of the interactions between the small molecule binders and the relevant dengue protein. Here we describe the basic methods involved in performing SPR assays as well as in data processing and evaluation using some examples of dengue proteins.
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Affiliation(s)
- Yin Hoe Yau
- Division of Chemical Biology and Biotechnology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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16
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Choulier L, Nominé Y, Zeder-Lutz G, Charbonnier S, Didier B, Jung ML, Altschuh D. Chemical Library Screening Using a SPR-Based Inhibition in Solution Assay: Simulations and Experimental Validation. Anal Chem 2013; 85:8787-95. [DOI: 10.1021/ac4019445] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Laurence Choulier
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Yves Nominé
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Gabrielle Zeder-Lutz
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Sebastian Charbonnier
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
| | - Bruno Didier
- Prestwick Chemical, Bd Gonthier d’Andernach, Parc d’Innovation,
67400
Illkirch, France
| | - Marie-Louise Jung
- Prestwick Chemical, Bd Gonthier d’Andernach, Parc d’Innovation,
67400
Illkirch, France
| | - Danièle Altschuh
- Biotechnologie et Signalisation
Cellulaire, Université de Strasbourg, CNRS, ESBS, Boulevard Sébastien Brant BP10413, 67412 Illkirch,
France
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17
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Surface plasmon resonance spectroscopy for characterisation of membrane protein-ligand interactions and its potential for drug discovery. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:43-55. [PMID: 23665295 DOI: 10.1016/j.bbamem.2013.04.028] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/25/2013] [Accepted: 04/29/2013] [Indexed: 11/22/2022]
Abstract
Surface plasmon resonance (SPR) spectroscopy is a rapidly developing technique for the study of ligand binding interactions with membrane proteins, which are the major molecular targets for validated drugs and for current and foreseeable drug discovery. SPR is label-free and capable of measuring real-time quantitative binding affinities and kinetics for membrane proteins interacting with ligand molecules using relatively small quantities of materials and has potential to be medium-throughput. The conventional SPR technique requires one binding component to be immobilised on a sensor chip whilst the other binding component in solution is flowed over the sensor surface; a binding interaction is detected using an optical method that measures small changes in refractive index at the sensor surface. This review first describes the basic SPR experiment and the challenges that have to be considered for performing SPR experiments that measure membrane protein-ligand binding interactions, most importantly having the membrane protein in a lipid or detergent environment that retains its native structure and activity. It then describes a wide-range of membrane protein systems for which ligand binding interactions have been characterised using SPR, including the major drug targets G protein-coupled receptors, and how challenges have been overcome for achieving this. Finally it describes some recent advances in SPR-based technology and future potential of the technique to screen ligand binding in the discovery of drugs. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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18
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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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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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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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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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