1
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Herbst C, Endres S, Würz R, Sotriffer C. Assessment of fragment docking and scoring with the endothiapepsin model system. Arch Pharm (Weinheim) 2024; 357:e2400061. [PMID: 38631672 DOI: 10.1002/ardp.202400061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Fragment-based screening has become indispensable in drug discovery. Yet, the weak binding affinities of these small molecules still represent a challenge for the reliable detection of fragment hits. The extent of this issue was illustrated in the literature for the aspartic protease endothiapepsin: When seven biochemical and biophysical in vitro screening methods were applied to screen a library of 361 fragments, very poor overlap was observed between the hit fragments identified by the individual approaches, resulting in high levels of false positive and/or false negative results depending on the mutually compared methods. Here, the reported in vitro findings are juxtaposed with the results from in silico docking and scoring approaches. The docking programs GOLD and Glide were considered with the scoring functions ASP, ChemScore, ChemPLP, GoldScore, DSXCSD, and GlideScore. First, the ranking power and scoring power were assessed for the named scoring functions. Second, the capability of reproducing the crystallized fragment binding modes was tested in a structure-based redocking approach. The redocking success notably depended on the ligand efficiency of the considered fragments. Third, a blinded virtual screening approach was employed to evaluate whether in silico screening can compete with in vitro methods in the enrichment of fragment databases.
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Affiliation(s)
- Carina Herbst
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Sara Endres
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Rebecca Würz
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität, Würzburg, Germany
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2
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Schmitz B, Frieg B, Homeyer N, Jessen G, Gohlke H. Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin. Arch Pharm (Weinheim) 2024; 357:e2300612. [PMID: 38319801 DOI: 10.1002/ardp.202300612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Fragment-based drug discovery (FBDD) aims to discover a set of small binding fragments that may be subsequently linked together. Therefore, in-depth knowledge of the individual fragments' structural and energetic binding properties is essential. In addition to experimental techniques, the direct simulation of fragment binding by molecular dynamics (MD) simulations became popular to characterize fragment binding. However, former studies showed that long simulation times and high computational demands per fragment are needed, which limits applicability in FBDD. Here, we performed short, unbiased MD simulations of direct fragment binding to endothiapepsin, a well-characterized model system of pepsin-like aspartic proteases. To evaluate the strengths and limitations of short MD simulations for the structural and energetic characterization of fragment binding, we predicted the fragments' absolute free energies and binding poses based on the direct simulations of fragment binding and compared the predictions to experimental data. The predicted absolute free energies are in fair agreement with the experiment. Combining the MD data with binding mode predictions from molecular docking approaches helped to correctly identify the most promising fragments for further chemical optimization. Importantly, all computations and predictions were done within 5 days, suggesting that MD simulations may become a viable tool in FBDD projects.
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Affiliation(s)
- Birte Schmitz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Nadine Homeyer
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Gisela Jessen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
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3
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Gising J, Honarnejad S, Bras M, Baillie GL, McElroy SP, Jones PS, Morrison A, Beveridge J, Hallberg M, Larhed M. The Discovery of New Inhibitors of Insulin-Regulated Aminopeptidase by a High-Throughput Screening of 400,000 Drug-like Compounds. Int J Mol Sci 2024; 25:4084. [PMID: 38612894 PMCID: PMC11012289 DOI: 10.3390/ijms25074084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
With the ambition to identify novel chemical starting points that can be further optimized into small drug-like inhibitors of insulin-regulated aminopeptidase (IRAP) and serve as potential future cognitive enhancers in the clinic, we conducted an ultra-high-throughput screening campaign of a chemically diverse compound library of approximately 400,000 drug-like small molecules. Three biochemical and one biophysical assays were developed to enable large-scale screening and hit triaging. The screening funnel, designed to be compatible with high-density microplates, was established with two enzyme inhibition assays employing either fluorescent or absorbance readouts. As IRAP is a zinc-dependent enzyme, the remaining active compounds were further evaluated in the primary assay, albeit with the addition of zinc ions. Rescreening with zinc confirmed the inhibitory activity for most compounds, emphasizing a zinc-independent mechanism of action. Additionally, target engagement was confirmed using a complementary biophysical thermal shift assay where compounds causing positive/negative thermal shifts were considered genuine binders. Triaging based on biochemical activity, target engagement, and drug-likeness resulted in the selection of 50 qualified hits, of which the IC50 of 32 compounds was below 3.5 µM. Despite hydroxamic acid dominance, diverse chemotypes with biochemical activity and target engagement were discovered, including non-hydroxamic acid compounds. The most potent compound (QHL1) was resynthesized with a confirmed inhibitory IC50 of 320 nM. Amongst these compounds, 20 new compound structure classes were identified, providing many new starting points for the development of unique IRAP inhibitors. Detailed characterization and optimization of lead compounds, considering both hydroxamic acids and other diverse structures, are in progress for further exploration.
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Affiliation(s)
- Johan Gising
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
| | - Saman Honarnejad
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (S.H.); (M.B.)
| | - Maaike Bras
- Pivot Park Screening Centre, Kloosterstraat 9, 5349 AB Oss, The Netherlands; (S.H.); (M.B.)
| | - Gemma L. Baillie
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Stuart P. McElroy
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Philip S. Jones
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Angus Morrison
- BioAscent Discovery Ltd., Bo‘Ness Road, Newhouse, Motherwell ML1 5UH, UK; (G.L.B.); (S.P.M.); (P.S.J.); (A.M.)
| | - Julia Beveridge
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
| | - Mathias Hallberg
- The Beijer Laboratory, Department of Pharmaceutical Biosciences, Neuropharmacology and Addiction Research, Biomedical Centre, Uppsala University, P.O. Box 591, SE-751 24 Uppsala, Sweden;
| | - Mats Larhed
- The Beijer Laboratory, Science for Life Laboratory, Department of Medicinal Chemistry, Biomedical Centre, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden; (J.B.); (M.L.)
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4
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Nandi S, Bhaduri S, Das D, Ghosh P, Mandal M, Mitra P. Deciphering the Lexicon of Protein Targets: A Review on Multifaceted Drug Discovery in the Era of Artificial Intelligence. Mol Pharm 2024; 21:1563-1590. [PMID: 38466810 DOI: 10.1021/acs.molpharmaceut.3c01161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Understanding protein sequence and structure is essential for understanding protein-protein interactions (PPIs), which are essential for many biological processes and diseases. Targeting protein binding hot spots, which regulate signaling and growth, with rational drug design is promising. Rational drug design uses structural data and computational tools to study protein binding sites and protein interfaces to design inhibitors that can change these interactions, thereby potentially leading to therapeutic approaches. Artificial intelligence (AI), such as machine learning (ML) and deep learning (DL), has advanced drug discovery and design by providing computational resources and methods. Quantum chemistry is essential for drug reactivity, toxicology, drug screening, and quantitative structure-activity relationship (QSAR) properties. This review discusses the methodologies and challenges of identifying and characterizing hot spots and binding sites. It also explores the strategies and applications of artificial-intelligence-based rational drug design technologies that target proteins and protein-protein interaction (PPI) binding hot spots. It provides valuable insights for drug design with therapeutic implications. We have also demonstrated the pathological conditions of heat shock protein 27 (HSP27) and matrix metallopoproteinases (MMP2 and MMP9) and designed inhibitors of these proteins using the drug discovery paradigm in a case study on the discovery of drug molecules for cancer treatment. Additionally, the implications of benzothiazole derivatives for anticancer drug design and discovery are deliberated.
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Affiliation(s)
- Suvendu Nandi
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Soumyadeep Bhaduri
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Debraj Das
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Priya Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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5
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Custódio TF, Killer M, Yu D, Puente V, Teufel DP, Pautsch A, Schnapp G, Grundl M, Kosinski J, Löw C. Molecular basis of TASL recruitment by the peptide/histidine transporter 1, PHT1. Nat Commun 2023; 14:5696. [PMID: 37709742 PMCID: PMC10502012 DOI: 10.1038/s41467-023-41420-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
PHT1 is a histidine /oligopeptide transporter with an essential role in Toll-like receptor innate immune responses. It can act as a receptor by recruiting the adaptor protein TASL which leads to type I interferon production via IRF5. Persistent stimulation of this signalling pathway is known to be involved in the pathogenesis of systemic lupus erythematosus (SLE). Understanding how PHT1 recruits TASL at the molecular level, is therefore clinically important for the development of therapeutics against SLE and other autoimmune diseases. Here we present the Cryo-EM structure of PHT1 stabilized in the outward-open conformation. By combining biochemical and structural modeling techniques we propose a model of the PHT1-TASL complex, in which the first 16 N-terminal TASL residues fold into a helical structure that bind in the central cavity of the inward-open conformation of PHT1. This work provides critical insights into the molecular basis of PHT1/TASL mediated type I interferon production.
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Affiliation(s)
- Tânia F Custódio
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607, Hamburg, Germany
| | - Maxime Killer
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607, Hamburg, Germany
- Collaboration for joint PhD degree between EMBL, and Heidelberg University, Faculty of Biosciences, 69120, Heidelberg, Germany
| | - Dingquan Yu
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607, Hamburg, Germany
- Collaboration for joint PhD degree between EMBL, and Heidelberg University, Faculty of Biosciences, 69120, Heidelberg, Germany
| | - Virginia Puente
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607, Hamburg, Germany
| | - Daniel P Teufel
- Boehringer Ingelheim Pharma, Birkendorferstraße 65, 88397, Biberach, Germany
| | - Alexander Pautsch
- Boehringer Ingelheim Pharma, Birkendorferstraße 65, 88397, Biberach, Germany
| | - Gisela Schnapp
- Boehringer Ingelheim Pharma, Birkendorferstraße 65, 88397, Biberach, Germany
| | - Marc Grundl
- Boehringer Ingelheim Pharma, Birkendorferstraße 65, 88397, Biberach, Germany
| | - Jan Kosinski
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607, Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany.
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestraße 85, 22607, Hamburg, Germany.
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6
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Rosdah AA, Abbott BM, Langendorf CG, Deng Y, Truong JQ, Waddell HMM, Ling NXY, Smiles WJ, Delbridge LMD, Liu GS, Oakhill JS, Lim SY, Holien JK. A novel small molecule inhibitor of human Drp1. Sci Rep 2022; 12:21531. [PMID: 36513726 PMCID: PMC9747717 DOI: 10.1038/s41598-022-25464-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial dynamin-related protein 1 (Drp1) is a large GTPase regulator of mitochondrial dynamics and is known to play an important role in numerous pathophysiological processes. Despite being the most widely used Drp1 inhibitor, the specificity of Mdivi-1 towards human Drp1 has not been definitively proven and there have been numerous issues reported with its use including off-target effects. In our hands Mdivi-1 showed varying binding affinities toward human Drp1, potentially impacted by compound aggregation. Herein, we sought to identify a novel small molecule inhibitor of Drp1. From an initial virtual screening, we identified DRP1i27 as a compound which directly bound to the human isoform 3 of Drp1 via surface plasmon resonance and microscale thermophoresis. Importantly, DRP1i27 was found to have a dose-dependent increase in the cellular networks of fused mitochondria but had no effect in Drp1 knock-out cells. Further analogues of this compound were identified and screened, though none displayed greater affinity to human Drp1 isoform 3 than DRP1i27. To date, this is the first small molecule inhibitor shown to directly bind to human Drp1.
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Affiliation(s)
- Ayeshah A. Rosdah
- grid.1073.50000 0004 0626 201XSt Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.108126.c0000 0001 0557 0975Faculty of Medicine, Universitas Sriwijaya, Palembang, Indonesia ,grid.1008.90000 0001 2179 088XDepartment of Surgery and Medicine, University of Melbourne, Melbourne, VIC Australia
| | - Belinda M. Abbott
- grid.1018.80000 0001 2342 0938Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC Australia
| | | | - Yali Deng
- grid.1073.50000 0004 0626 201XSt Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Surgery and Medicine, University of Melbourne, Melbourne, VIC Australia
| | - Jia Q. Truong
- grid.1017.70000 0001 2163 3550School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001 Australia
| | - Helen M. M. Waddell
- grid.1008.90000 0001 2179 088XDepartment of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Naomi X. Y. Ling
- grid.1073.50000 0004 0626 201XSt Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
| | - William J. Smiles
- grid.1073.50000 0004 0626 201XSt Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
| | - Lea M. D. Delbridge
- grid.1008.90000 0001 2179 088XDepartment of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Guei-Sheung Liu
- grid.1008.90000 0001 2179 088XDepartment of Surgery and Medicine, University of Melbourne, Melbourne, VIC Australia ,grid.410670.40000 0004 0625 8539Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC Australia ,grid.1009.80000 0004 1936 826XMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS Australia
| | - Jonathan S. Oakhill
- grid.1073.50000 0004 0626 201XSt Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.411958.00000 0001 2194 1270Australian Catholic University, Fitzroy, VIC Australia
| | - Shiang Y. Lim
- grid.1073.50000 0004 0626 201XSt Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Surgery and Medicine, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Drug Discovery Biology, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, VIC Australia ,grid.419385.20000 0004 0620 9905National Heart Centre, National Heart Research Institute Singapore, Singapore, Singapore
| | - Jessica K. Holien
- grid.1073.50000 0004 0626 201XSt Vincent’s Institute of Medical Research, Fitzroy, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Surgery and Medicine, University of Melbourne, Melbourne, VIC Australia ,grid.1017.70000 0001 2163 3550School of Science, RMIT University, GPO Box 2476, Melbourne, VIC 3001 Australia
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7
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Narayanan D, Tran KT, Pallesen JS, Solbak SMØ, Qin Y, Mukminova E, Luchini M, Vasilyeva KO, González Chichón D, Goutsiou G, Poulsen C, Haapanen N, Popowicz GM, Sattler M, Olagnier D, Gajhede M, Bach A. Development of Noncovalent Small-Molecule Keap1-Nrf2 Inhibitors by Fragment-Based Drug Discovery. J Med Chem 2022; 65:14481-14526. [PMID: 36263945 DOI: 10.1021/acs.jmedchem.2c00830] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting the protein-protein interaction (PPI) between the transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) and its repressor, Kelch-like ECH-associated protein 1 (Keap1), constitutes a promising strategy for treating diseases involving oxidative stress and inflammation. Here, a fragment-based drug discovery (FBDD) campaign resulted in novel, high-affinity (Ki = 280 nM), and cell-active noncovalent small-molecule Keap1-Nrf2 PPI inhibitors. We screened 2500 fragments using orthogonal assays─fluorescence polarization (FP), thermal shift assay (TSA), and surface plasmon resonance (SPR)─and validated the hits by saturation transfer difference (STD) NMR, leading to 28 high-priority hits. Thirteen co-structures showed fragments binding mainly in the P4 and P5 subpockets of Keap1's Kelch domain, and three fluorenone-based fragments featuring a novel binding mode were optimized by structure-based drug discovery. We thereby disclose several fragment hits, including their binding modes, and show how FBDD can be performed to find new small-molecule Keap1-Nrf2 PPI inhibitors.
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Affiliation(s)
- Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kim T Tran
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jakob S Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Yuting Qin
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Elina Mukminova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Martina Luchini
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kristina O Vasilyeva
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Dorleta González Chichón
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Georgia Goutsiou
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Cecilie Poulsen
- Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
| | - Nanna Haapanen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Bavarian NMR Center, Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - David Olagnier
- Department of Biomedicine, Faculty of Health, Aarhus University, 8000 Aarhus C, Denmark
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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8
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Ibrahim MA, Yamasaki T, Furukawa K, Yamasaki K. Fragment-Based Drug Discovery for Trypanosoma brucei Glycosylphosphatidylinositol-Specific Phospholipase C through Biochemical and WaterLOGSY-NMR Methods. J Biochem 2022; 171:619-629. [PMID: 35191956 DOI: 10.1093/jb/mvac020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/16/2022] [Indexed: 11/15/2022] Open
Abstract
Glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC) of Trypanosoma brucei, the causative protozoan parasite of African trypanosomiasis, is a membrane-bound enzyme essential for antigenic variation, because it catalyses the release of the membrane-bound form of variable surface glycoproteins. Here, we performed a fragment-based drug discovery of TbGPI-PLC inhibitors using a combination of enzymatic inhibition assay and water-ligand observed via gradient spectroscopy (WaterLOGSY) NMR experiment. The TbGPI-PLC was cloned and over-expressed using an Escherichia coli expression system followed by purification using three-phase partitioning and gel filtration. Subsequently, the inhibitory activity of 873 fragment compounds against the recombinant TbGPI-PLC led to the identification of 66 primary hits. These primary hits were subjected to the WaterLOGSY NMR experiment where 10 fragment hits were confirmed to directly bind to the TbGPI-PLC. These included benzothiazole, chlorobenzene, imidazole, indole, pyrazol and quinolinone derivatives. Molecular docking simulation indicated that six of them share a common binding site, which corresponds to the catalytic pocket. The present study identified chemically diverse fragment hits that could directly bind and inhibit the TbGPI-PLC activity which constructed a framework for fragment optimisation or linking towards the design of novel drugs for African trypanosomiasis.
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Affiliation(s)
- Mohammed Auwal Ibrahim
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan.,Department of Biochemistry, Ahmadu Bello University, Zaria, Kaduna 800001, Nigeria
| | - Tomoko Yamasaki
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan
| | - Koji Furukawa
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan
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9
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Bartoschik T, Zoephel A, Rumpel K, Ciulli A, Heffern C. MST and TRIC Technology to Reliably Study PROTAC Binary and Ternary Binding in Drug Development. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2365:115-133. [PMID: 34432241 DOI: 10.1007/978-1-0716-1665-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PROTACs have shown promise as a new class of therapy, with a unique mechanism of action orthogonal to traditional small molecules that are used to regulate protein activity. Their novel MOA utilizing the body's natural protein degradation machinery degrades a protein of interest rather than inhibiting its function. This strategy has several advantages over conventional small-molecule inhibitors, e.g., higher sensitivity, less off-target effects, and greater target space. However, unlocking the potential of PROTACs necessitates drug discovery techniques that can support the complexity of the novel MOA. In this chapter, we describe the application of MicroScale Thermophoresis (MST) and Temperature-Related Intensity Change (TRIC) to characterize both the binary and ternary binding of PROTACs with target proteins and ubiquitin ligases along with an efficient determination of the cooperativity of the ternary complex formation. The assay development and experimental procedure to characterize the well-described BET PROTAC MZ1 show how MST and TRIC can be applied as a fast and highly sensitive method for PROTAC discovery.
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Affiliation(s)
| | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Alessio Ciulli
- School of Life Sciences, University of Dundee, Scotland, UK
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10
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Shi Y, El-Deeb IM, Masic V, Hartley-Tassell L, Maggioni A, Itzstein MV, Ve T. Discovery of Cofactor Competitive Inhibitors against the Human Methyltransferase Fibrillarin. Pharmaceuticals (Basel) 2021; 15:26. [PMID: 35056083 PMCID: PMC8779173 DOI: 10.3390/ph15010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 11/21/2022] Open
Abstract
Fibrillarin (FBL) is an essential and evolutionarily highly conserved S-adenosyl methionine (SAM) dependent methyltransferase. It is the catalytic component of a multiprotein complex that facilitates 2'-O-methylation of ribosomal RNAs (rRNAs), a modification essential for accurate and efficient protein synthesis in eukaryotic cells. It was recently established that human FBL (hFBL) is critical for Nipah, Hendra, and respiratory syncytial virus infections. In addition, overexpression of hFBL contributes towards tumorgenesis and is associated with poor survival in patients with breast cancer, suggesting that hFBL is a potential target for the development of both antiviral and anticancer drugs. An attractive strategy to target cofactor-dependent enzymes is the selective inhibition of cofactor binding, which has been successful for the development of inhibitors against several protein methyltransferases including PRMT5, DOT1L, and EZH2. In this work, we solved crystal structures of the methyltransferase domain of hFBL in apo form and in complex with the cofactor SAM. Screening of a fluorinated fragment library, via X-ray crystallography and 19F NMR spectroscopy, yielded seven hit compounds that competed with cofactor binding, two of which resulted in co-crystal structures. One of these structures revealed unexpected conformational variability in the cofactor binding site, which allows it to accommodate a compound significantly different from SAM. Our structural data provide critical information for the design of selective cofactor competitive inhibitors targeting hFBL, and preliminary elaboration of hit compounds has led to additional cofactor site binders.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Ibrahim M El-Deeb
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Andrea Maggioni
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Mark von Itzstein
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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11
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Kaeslin J, Brunner C, Ghiasikhou S, Schneider G, Zenobi R. Bioaffinity Screening with a Rapid and Sample-Efficient Autosampler for Native Electrospray Ionization Mass Spectrometry. Anal Chem 2021; 93:13342-13350. [PMID: 34546705 DOI: 10.1021/acs.analchem.1c03130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fast and efficient handling of ligands and biological targets are required in bioaffinity screening based on native electrospray ionization mass spectrometry (ESI-MS). We use a prototype microfluidic autosampler, called the "gap sampler", to sequentially mix and electrospray individual small molecule ligands together with a target protein and compare the screening results with data from thermal shift assay and surface plasmon resonance. In a first round, all three techniques were used for a screening of 110 ligands against bovine carbonic anhydrase II, which resulted in five mutual hits and some false positives with ESI-MS presumably due to the high ligand concentration or interferences from dimethyl sulfoxide. In a second round, 33 compounds were screened in lower concentrations and in a less complex matrix, resulting in only true positives with ESI-MS. Within a cycle time of 30 s, dissociation constants were determined within an order of magnitude accuracy consuming only 5 pmol of ligand and less than 15 pmol of protein per screened compound. In a third round, dissociation constants of five compounds were accurately determined in a titration experiment. Thus, the gap sampler can rapidly and efficiently be used for high-throughput screening.
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Affiliation(s)
- Jérôme Kaeslin
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Cyrill Brunner
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Sahar Ghiasikhou
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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12
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Veltri L, Amuso R, Vitale P, Chiacchio MA, Benincasa C, Gabriele B. Synthesis of 1,3-oxazine-2,4-diones by DBU-catalyzed incorporation of carbon dioxide into 3-ynamides. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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13
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Wilson DM, Deacon AM, Duncton MAJ, Pellicena P, Georgiadis MM, Yeh AP, Arvai AS, Moiani D, Tainer JA, Das D. Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:130-142. [PMID: 33115610 PMCID: PMC8666131 DOI: 10.1016/j.pbiomolbio.2020.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
Cancer will directly affect the lives of over one-third of the population. The DNA Damage Response (DDR) is an intricate system involving damage recognition, cell cycle regulation, DNA repair, and ultimately cell fate determination, playing a central role in cancer etiology and therapy. Two primary therapeutic approaches involving DDR targeting include: combinatorial treatments employing anticancer genotoxic agents; and synthetic lethality, exploiting a sporadic DDR defect as a mechanism for cancer-specific therapy. Whereas, many DDR proteins have proven "undruggable", Fragment- and Structure-Based Drug Discovery (FBDD, SBDD) have advanced therapeutic agent identification and development. FBDD has led to 4 (with ∼50 more drugs under preclinical and clinical development), while SBDD is estimated to have contributed to the development of >200, FDA-approved medicines. Protein X-ray crystallography-based fragment library screening, especially for elusive or "undruggable" targets, allows for simultaneous generation of hits plus details of protein-ligand interactions and binding sites (orthosteric or allosteric) that inform chemical tractability, downstream biology, and intellectual property. Using a novel high-throughput crystallography-based fragment library screening platform, we screened five diverse proteins, yielding hit rates of ∼2-8% and crystal structures from ∼1.8 to 3.2 Å. We consider current FBDD/SBDD methods and some exemplary results of efforts to design inhibitors against the DDR nucleases meiotic recombination 11 (MRE11, a.k.a., MRE11A), apurinic/apyrimidinic endonuclease 1 (APE1, a.k.a., APEX1), and flap endonuclease 1 (FEN1).
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Affiliation(s)
- David M Wilson
- Hasselt University, Biomedical Research Institute, Diepenbeek, Belgium; Boost Scientific, Heusden-Zolder, Belgium; XPose Therapeutics Inc., San Carlos, CA, USA
| | - Ashley M Deacon
- Accelero Biostructures Inc., San Francisco, CA, USA; XPose Therapeutics Inc., San Carlos, CA, USA
| | | | | | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; XPose Therapeutics Inc., San Carlos, CA, USA
| | - Andrew P Yeh
- Accelero Biostructures Inc., San Francisco, CA, USA
| | - Andrew S Arvai
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Davide Moiani
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - John A Tainer
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Debanu Das
- Accelero Biostructures Inc., San Francisco, CA, USA; XPose Therapeutics Inc., San Carlos, CA, USA.
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14
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Pallesen JS, Narayanan D, Tran KT, Solbak SMØ, Marseglia G, Sørensen LME, Høj LJ, Munafò F, Carmona RMC, Garcia AD, Desu HL, Brambilla R, Johansen TN, Popowicz GM, Sattler M, Gajhede M, Bach A. Deconstructing Noncovalent Kelch-like ECH-Associated Protein 1 (Keap1) Inhibitors into Fragments to Reconstruct New Potent Compounds. J Med Chem 2021; 64:4623-4661. [PMID: 33818106 DOI: 10.1021/acs.jmedchem.0c02094] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Targeting the protein-protein interaction (PPI) between nuclear factor erythroid 2-related factor 2 (Nrf2) and Kelch-like ECH-associated protein 1 (Keap1) is a potential therapeutic strategy to control diseases involving oxidative stress. Here, six classes of known small-molecule Keap1-Nrf2 PPI inhibitors were dissected into 77 fragments in a fragment-based deconstruction reconstruction (FBDR) study and tested in four orthogonal assays. This gave 17 fragment hits of which six were shown by X-ray crystallography to bind in the Keap1 Kelch binding pocket. Two hits were merged into compound 8 with a 220-380-fold stronger affinity (Ki = 16 μM) relative to the parent fragments. Systematic optimization resulted in several novel analogues with Ki values of 0.04-0.5 μM, binding modes determined by X-ray crystallography, and enhanced microsomal stability. This demonstrates how FBDR can be used to find new fragment hits, elucidate important ligand-protein interactions, and identify new potent inhibitors of the Keap1-Nrf2 PPI.
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Affiliation(s)
- Jakob S Pallesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kim T Tran
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Giuseppe Marseglia
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,Food and Drug Department, University of Parma, Parco Area delle Scienze 27/a, 43124 Parma, Italy
| | - Louis M E Sørensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars J Høj
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Federico Munafò
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Rosa M C Carmona
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anthony D Garcia
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,École Nationale Supérieure de Chimie de Rennes, 11 Allée de Beaulieu, CS 50837, Rennes Cedex 7 35708, France
| | - Haritha L Desu
- The Miami Project to Cure Paralysis, Dept. Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida 33136, United States
| | - Roberta Brambilla
- The Miami Project to Cure Paralysis, Dept. Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida 33136, United States.,Department of Neurobiology Research, Institute of Molecular Medicine, and BRIDGE-Brain Research Inter Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Tommy N Johansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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15
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Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery. Sci Rep 2021; 11:1121. [PMID: 33441849 PMCID: PMC7806715 DOI: 10.1038/s41598-020-80588-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 12/18/2020] [Indexed: 01/29/2023] Open
Abstract
Despite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, we use fragment-based ligand discovery to identify novel scaffolds for targeting the isolated UHRF1 tandem Tudor domain (TTD), which recognizes the heterochromatin-associated histone mark H3K9me3 and supports intramolecular contacts with other regions of UHRF1. Using both binding-based and function-based screens of a ~ 2300-fragment library in parallel, we identified 2,4-lutidine as a hit for follow-up NMR and X-ray crystallography studies. Unlike previous reported ligands, 2,4-lutidine binds to two binding pockets that are in close proximity on TTD and so has the potential to be evolved into more potent inhibitors using a fragment-linking strategy. Our study provides a useful starting point for developing potent chemical probes against UHRF1.
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16
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Goossens K, Wroblowski B, Langini C, van Vlijmen H, Caflisch A, De Winter H. Assessment of the Fragment Docking Program SEED. J Chem Inf Model 2020; 60:4881-4893. [PMID: 32820916 DOI: 10.1021/acs.jcim.0c00556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The fragment docking program solvation energy for exhaustive docking (SEED) is evaluated on 15 different protein targets, with a focus on enrichment and the hit rate. It is shown that SEED allows for consistent computational enrichment of fragment libraries, independent of the effective hit rate. Depending on the actual target protein, true positive rates ranging up to 27% are observed at a cutoff value corresponding to the experimental hit rate. The impact of variations in docking protocols and energy filters is discussed in detail. Remaining issues, limitations, and use cases of SEED are also discussed. Our results show that fragment library selection or enhancement for a particular target is likely to benefit from docking with SEED, suggesting that SEED is a useful resource for fragment screening campaigns. A workflow is presented for the use of the program in virtual screening, including filtering and postprocessing to optimize hit rates.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | | | - Cassiano Langini
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Herman van Vlijmen
- Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
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17
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Lecas L, Hartmann L, Caro L, Mohamed-Bouteben S, Raingeval C, Krimm I, Wagner R, Dugas V, Demesmay C. Miniaturized weak affinity chromatography for ligand identification of nanodiscs-embedded G-protein coupled receptors. Anal Chim Acta 2020; 1113:26-35. [DOI: 10.1016/j.aca.2020.03.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
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18
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Messick TE, Tolvinski L, Zartler ER, Moberg A, Frostell Å, Smith GR, Reitz AB, Lieberman PM. Biophysical Screens Identify Fragments That Bind to the Viral DNA-Binding Proteins EBNA1 and LANA. Molecules 2020; 25:molecules25071760. [PMID: 32290261 PMCID: PMC7180839 DOI: 10.3390/molecules25071760] [Citation(s) in RCA: 6] [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: 02/14/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
The human gamma-herpesviruses Epstein-Barr virus (EBV) (HHV-4) and Kaposi's sarcoma-associated herpesvirus (KSHV) (HHV-8) are responsible for a number of diseases, including various types of cancer. Epstein-Barr nuclear antigen 1 (EBNA1) from EBV and latency-associated nuclear antigen (LANA) from KSHV are viral-encoded DNA-binding proteins that are essential for the replication and maintenance of their respective viral genomes during latent, oncogenic infection. As such, EBNA1 and LANA are attractive targets for the development of small-molecule inhibitors. To this end, we performed a biophysical screen of EBNA1 and LANA using a fragment library by saturation transfer difference (STD)-NMR spectroscopy and surface plasmon resonance (SPR). We identified and validated a number of unique fragment hits that bind to EBNA1 or LANA. We also determined the high-resolution crystal structure of one fragment bound to EBNA1. Results from this screening cascade provide new chemical starting points for the further development of potent inhibitors for this class of viral proteins.
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Affiliation(s)
- Troy E. Messick
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA;
- Correspondence: (T.E.M.); (P.M.L.); Tel.: +215-898-3896 (T.E.M.); +215-898-9523 (P.M.L.)
| | - Lois Tolvinski
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA;
| | | | - Anna Moberg
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden; (A.M.); (Å.F.)
| | - Åsa Frostell
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-751 84 Uppsala, Sweden; (A.M.); (Å.F.)
| | - Garry R. Smith
- Fox Chase Chemical Diversity Center, Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA; (G.R.S.); (A.B.R.)
| | - Allen B. Reitz
- Fox Chase Chemical Diversity Center, Inc., 3805 Old Easton Road, Doylestown, PA 18902, USA; (G.R.S.); (A.B.R.)
| | - Paul M. Lieberman
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA;
- Correspondence: (T.E.M.); (P.M.L.); Tel.: +215-898-3896 (T.E.M.); +215-898-9523 (P.M.L.)
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19
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Hassaan E, Eriksson P, Geschwindner S, Heine A, Klebe G. Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies. ChemMedChem 2020; 15:324-337. [PMID: 31808981 PMCID: PMC7687107 DOI: 10.1002/cmdc.201900604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/02/2019] [Indexed: 12/02/2022]
Abstract
Crystallography provides structural information crucial for fragment optimization, however several criteria must be met to screen directly on protein crystals as soakable, well-diffracting specimen must be available. We screened a 96-fragment library against the tRNA-modifying enzyme TGT using crystallography. Eight hits, some with surprising binding poses, were detected. However, the amount of data collection, reduction and refinement is assumed substantial. Therefore, having a reliable cascade of fast and cost-efficient methods available for pre-screening before embarking to elaborate crystallographic screening appears beneficial. This allows filtering of compounds to the most promising hits, available to rapidly progress from hit-to-lead. But how to ensure that this workflow is reliable? To answer this question, we also applied SPR and NMR to the same screening sample to study whether identical hits are retrieved. Upon hit-list comparisons, crystallography shows with NMR and SPR, only one overlapping hit and all three methods shared no common hits. This questions a cascade-type screening protocol at least in the current example. Compared to crystallography, SPR and NMR detected higher percentages of non-active-site binders suggesting the importance of running reporter ligand-based competitive screens in SPR and NMR, a requirement not needed in crystallography. Although not specific, NMR proved a more sensitive method relative to SPR and crystallography, as it picked up the highest numbers of binders.
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Affiliation(s)
- Engi Hassaan
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
| | - Per‐Olof Eriksson
- Structure, Biophysics and Fragment-based Lead GenerationDiscovery Sciences, R&D, AstraZeneca431 83GothenburgSweden
| | - Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead GenerationDiscovery Sciences, R&D, AstraZeneca431 83GothenburgSweden
| | - Andreas Heine
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
| | - Gerhard Klebe
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
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20
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Solbak SMØ, Zang J, Narayanan D, Høj LJ, Bucciarelli S, Softley C, Meier S, Langkilde AE, Gotfredsen CH, Sattler M, Bach A. Developing Inhibitors of the p47phox-p22phox Protein-Protein Interaction by Fragment-Based Drug Discovery. J Med Chem 2020; 63:1156-1177. [PMID: 31922756 DOI: 10.1021/acs.jmedchem.9b01492] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nicotinamide adenine dinucleotide phosphate oxidase isoform 2 is an enzyme complex, which generates reactive oxygen species and contributes to oxidative stress. The p47phox-p22phox interaction is critical for the activation of the catalytical NOX2 domain, and p47phox is a potential target for therapeutic intervention. By screening 2500 fragments using fluorescence polarization and a thermal shift assay and validation by surface plasmon resonance, we found eight hits toward the tandem SH3 domain of p47phox (p47phoxSH3A-B) with KD values of 400-600 μM. Structural studies revealed that fragments 1 and 2 bound two separate binding sites in the elongated conformation of p47phoxSH3A-B and these competed with p22phox for binding to p47phoxSH3A-B. Chemical optimization led to a dimeric compound with the ability to potently inhibit the p47phoxSH3A-B-p22phox interaction (Ki of 20 μM). Thereby, we reveal a new way of targeting p47phox and present the first report of drug-like molecules with the ability to bind p47phox and inhibit its interaction with p22phox.
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Affiliation(s)
- Sara Marie Øie Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Jie Zang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Dilip Narayanan
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Lars Jakobsen Høj
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Saskia Bucciarelli
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Charlotte Softley
- Institute of Structural Biology , Helmholtz Zentrum München , 85764 Neuherberg , Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry , Technical University of Munich , 85747 Garching , Germany
| | - Sebastian Meier
- Department of Chemistry , Technical University of Denmark , Kemitorvet , 2800 Kgs Lyngby , Denmark
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | | | - Michael Sattler
- Institute of Structural Biology , Helmholtz Zentrum München , 85764 Neuherberg , Germany.,Biomolecular NMR and Center for Integrated Protein Science Munich at Department of Chemistry , Technical University of Munich , 85747 Garching , Germany
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
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21
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Rainard JM, Pandarakalam GC, McElroy SP. Using Microscale Thermophoresis to Characterize Hits from High-Throughput Screening: A European Lead Factory Perspective. SLAS DISCOVERY 2019; 23:225-241. [PMID: 29460707 PMCID: PMC5824829 DOI: 10.1177/2472555217744728] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
High-throughput screening (HTS) is a proven method for discovering new lead matter for drug discovery and chemical biology. To maximize the likelihood of identifying genuine binders to a molecular target, and avoid wasting resources following up compounds with unproductive/nonspecific mechanisms of action, it is important to employ a range of assays during an HTS campaign that build confidence of target engagement for hit compounds. Biophysical methods that measure direct target/compound engagement have established themselves as key techniques in generating this confidence, and they are now integral to the latter stages of HTS triage at the European Lead Factory (ELF). One relatively new technique that the ELF is using is microscale thermophoresis (MST), which measures the differences in rate of movement through a temperature gradient that are caused when single molecular species form complexes. Here we provide an overview of the MST assay development workflow that the ELF employs and a perspective of our experience to date of using MST to triage the output of HTS campaigns and how it compares and contrasts with the use of other biophysical techniques.
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Affiliation(s)
- Julie M Rainard
- 1 European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
| | - George C Pandarakalam
- 1 European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
| | - Stuart P McElroy
- 1 European Screening Centre Newhouse, Biocity Scotland, University of Dundee, Newhouse, UK
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22
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Linker SM, Magarkar A, Köfinger J, Hummer G, Seeliger D. Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models. J Chem Theory Comput 2019; 15:4974-4981. [PMID: 31402652 DOI: 10.1021/acs.jctc.9b00069] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Predicting the costructure of small-molecule ligands and their respective target proteins has been a long-standing problem in drug discovery. For weak binding compounds typically identified in fragment-based screening (FBS) campaigns, determination of the correct binding site and correct binding mode is usually done experimentally via X-ray crystallography. For many targets of pharmaceutical interest, however, establishing an X-ray system which allows for sufficient throughput to support a drug discovery project is not possible. In this case, exploration of fragment hits becomes a very laborious and consequently slow process with the generation of protein/ligand cocrystal structures as the bottleneck of the entire process. In this work, we introduce a computational method which is able to reliably predict binding sites and binding modes of fragment-like small molecules using solely the structure of the apoprotein and the ligand's chemical structure as input information. The method is based on molecular dynamics simulations and Markov-state models and can be run as a fully automated protocol requiring minimal human intervention. We describe the application of the method to a representative subset of different target classes and fragments from historical FBS efforts at Boehringer Ingelheim and discuss its potential integration into the overall fragment-based drug discovery workflow.
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Affiliation(s)
- Stephanie Maria Linker
- Department of Medicinal Chemistry , Boehringer Ingelheim Pharma , Birkendorfer Straße 65 , 88397 Biberach an der Riß , Germany.,Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany
| | - Aniket Magarkar
- Department of Medicinal Chemistry , Boehringer Ingelheim Pharma , Birkendorfer Straße 65 , 88397 Biberach an der Riß , Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany.,Institute for Biophysics , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Daniel Seeliger
- Department of Medicinal Chemistry , Boehringer Ingelheim Pharma , Birkendorfer Straße 65 , 88397 Biberach an der Riß , Germany
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23
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Targeting Quorum Sensing: High-Throughput Screening to Identify Novel LsrK Inhibitors. Int J Mol Sci 2019; 20:ijms20123112. [PMID: 31242708 PMCID: PMC6627609 DOI: 10.3390/ijms20123112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 12/22/2022] Open
Abstract
Since quorum sensing (QS) is linked to the establishment of bacterial infection, its inactivation represents one of the newest strategies to fight bacterial pathogens. LsrK is a kinase playing a key role in the processing of autoinducer-2 (AI-2), a quorum-sensing mediator in gut enteric bacteria. Inhibition of LsrK might thus impair the quorum-sensing cascade and consequently reduce bacterial pathogenicity. Aiming for the development of a target-based assay for the discovery of LsrK inhibitors, we evaluated different assay set-ups based on ATP detection and optimized an automation-compatible method for the high-throughput screening of chemical libraries. The assay was then used to perform the screening of a 2000-compound library, which provided 12 active compounds with an IC50 ≤ 10 µM confirming the effectiveness and sensitivity of our assay. Follow-up studies on the positive hits led to the identification of two compounds, harpagoside and rosolic acid, active in a cell-based AI-2 QS interference assay, which are at the moment the most promising candidates for the development of a new class of antivirulence agents based on LsrK inhibition.
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24
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Bai N, Roder H, Dickson A, Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Sci Rep 2019; 9:2650. [PMID: 30804351 PMCID: PMC6389909 DOI: 10.1038/s41598-018-37072-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/30/2018] [Indexed: 01/20/2023] Open
Abstract
Differential scanning fluorimetry (DSF), also known as ThermoFluor or Thermal Shift Assay, has become a commonly-used approach for detecting protein-ligand interactions, particularly in the context of fragment screening. Upon binding to a folded protein, most ligands stabilize the protein; thus, observing an increase in the temperature at which the protein unfolds as a function of ligand concentration can serve as evidence of a direct interaction. While experimental protocols for this assay are well-developed, it is not straightforward to extract binding constants from the resulting data. Because of this, DSF is often used to probe for an interaction, but not to quantify the corresponding binding constant (Kd). Here, we propose a new approach for analyzing DSF data. Using unfolding curves at varying ligand concentrations, our "isothermal" approach collects from these the fraction of protein that is folded at a single temperature (chosen to be temperature near the unfolding transition). This greatly simplifies the subsequent analysis, because it circumvents the complicating temperature dependence of the binding constant; the resulting constant-temperature system can then be described as a pair of coupled equilibria (protein folding/unfolding and ligand binding/unbinding). The temperature at which the binding constants are determined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature. We demonstrate the application of this isothermal analysis using experimental data for maltose binding protein binding to maltose, and for two carbonic anhydrase isoforms binding to each of four inhibitors. To facilitate adoption of this new approach, we provide a free and easy-to-use Python program that analyzes thermal unfolding data and implements the isothermal approach described herein ( https://sourceforge.net/projects/dsf-fitting ).
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Heinrich Roder
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology and Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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25
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Schulze J, Baukmann H, Wawrzinek R, Fuchsberger FF, Specker E, Aretz J, Nazaré M, Rademacher C. CellFy: A Cell-Based Fragment Screen against C-Type Lectins. ACS Chem Biol 2018; 13:3229-3235. [PMID: 30480432 DOI: 10.1021/acschembio.8b00875] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Fragment-based drug discovery is a powerful complement to conventional high-throughput screening, especially for difficult targets. Screening low-molecular-weight fragments usually requires highly sensitive biophysical methods, because of the generally low affinity of the identified ligands. Here, we developed a cell-based fragment screening assay (cellFy) that allows sensitive identification of fragment hits in a physiologically more relevant environment, in contrast to isolated target screenings in solution. For this, a fluorescently labeled multivalent reporter was employed, enabling direct measurement of displacement by low-molecular-weight fragments without requiring enzymatic reactions or receptor activation. We applied this technique to identify hits against two challenging targets of the C-type lectin receptor (CLR) family: Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Nonintegrin (DC-SIGN) and Langerin. Both receptors are involved in pathogen recognition and initiation of an immune response, which renders them attractive targets for immune modulation. Because of their shallow and hydrophilic primary binding site, hit identification for CLRs is challenging and druglike ligands for CLRs are sparse. Screening of a fragment library followed by hit validation identified several promising candidates for further fragment evolution for DC-SIGN. In addition, a multiplexed assay format was developed for simultaneous screening against multiple CLRs, allowing a selectivity counterscreening. Overall, this sensitive cell-based fragment screening assay provides a powerful tool for rapid identification of bioactive fragments, even for difficult targets.
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Affiliation(s)
- Jessica Schulze
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Hannes Baukmann
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Robert Wawrzinek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Felix F. Fuchsberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Edgar Specker
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Jonas Aretz
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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26
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Chingin K, Barylyuk K. Charge-State-Dependent Variation of Signal Intensity Ratio between Unbound Protein and Protein-Ligand Complex in Electrospray Ionization Mass Spectrometry: The Role of Solvent-Accessible Surface Area. Anal Chem 2018; 90:5521-5528. [PMID: 29653057 DOI: 10.1021/acs.analchem.7b05349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Native electrospray ionization mass spectrometry (ESI-MS) is nowadays widely used for the direct and sensitive determination of protein complex stoichiometry and binding affinity constants ( Ka). A common yet poorly understood phenomenon in native ESI-MS is the difference between the charge-state distributions (CSDs) of the bound protein-ligand complex (PL) and unbound protein (P) signals. This phenomenon is typically attributed to experimental artifacts such as nonspecific binding or in-source dissociation and is considered highly undesirable, because the determined Ka values display strong variation with charge state. This situation raises serious concerns regarding the reliability of ESI-MS for the analysis of protein complexes. Here we demonstrate that, contrary to the common belief, the CSD difference between P and PL ions can occur without any loss of complex integrity, simply due to a change in the solvent-accessible surface area (ΔSASA) of the protein upon ligand binding in solution. The experimental CSD shifts for PL and P ions in ESI-MS are explained in relation to the magnitude of ΔSASA for diverse protein-ligand systems using a simple model based on the charged residue mechanism. Our analysis shows that the revealed ΔSASA factor should be considered rather general and be given attention for the correct spectral interpretation of protein complexes.
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Affiliation(s)
- Konstantin Chingin
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation , East China University of Technology , Guanglan Road 418 , Nanchang , Jiangxi , China 330013
| | - Konstantin Barylyuk
- Department of Biochemistry , University of Cambridge , Hopkins Building, Tennis Court Road , Cambridge CB2 1QW , United Kingdom
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27
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W Young D. Using Fragment Based Drug Discovery to Target Epigenetic Regulators in Cancer. ACTA ACUST UNITED AC 2017. [DOI: 10.15406/mojbb.2017.04.00062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Chrysanthopoulos PK, Mujumdar P, Woods LA, Dolezal O, Ren B, Peat TS, Poulsen SA. Identification of a New Zinc Binding Chemotype by Fragment Screening. J Med Chem 2017; 60:7333-7349. [PMID: 28817930 DOI: 10.1021/acs.jmedchem.7b00606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The discovery of a new zinc binding chemotype from screening a nonbiased fragment library is reported. Using the orthogonal fragment screening methods of native state mass spectrometry and surface plasmon resonance a 3-unsubstituted 2,4-oxazolidinedione fragment was found to have low micromolar binding affinity to the zinc metalloenzyme carbonic anhydrase II (CA II). This affinity approached that of fragment sized primary benzenesulfonamides, the classical zinc binding group found in most CA II inhibitors. Protein X-ray crystallography established that 3-unsubstituted 2,4-oxazolidinediones bound to CA II via an interaction of the acidic ring nitrogen with the CA II active site zinc, as well as two hydrogen bonds between the oxazolidinedione ring oxygen and the CA II protein backbone. Furthermore, 3-unsubstituted 2,4-oxazolidinediones appear to be a viable starting point for the development of an alternative class of CA inhibitor, wherein the medicinal chemistry pedigree of primary sulfonamides has dominated for several decades.
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Affiliation(s)
| | - Prashant Mujumdar
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Lucy A Woods
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
| | - Olan Dolezal
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Bin Ren
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Thomas S Peat
- CSIRO , Biomedical Manufacturing Program, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia
| | - Sally-Ann Poulsen
- Griffith University , Griffith Institute for Drug Discovery, Nathan, Brisbane, Queensland 4111, Australia
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29
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Göth M, Badock V, Weiske J, Pagel K, Kuropka B. Critical Evaluation of Native Electrospray Ionization Mass Spectrometry for Fragment-Based Screening. ChemMedChem 2017; 12:1201-1211. [PMID: 28618179 DOI: 10.1002/cmdc.201700177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/19/2017] [Indexed: 12/24/2022]
Abstract
Fragment-based screening presents a promising alternative to high-throughput screening and has gained great attention in recent years. So far, only a few studies have discussed mass spectrometry as a screening technology for fragments. Herein, we report the application of native electrospray ionization mass spectrometry (MS) for screening defined sets of fragments against four different target proteins. Fragments were selected from a primary screening conducted with a thermal shift assay (TSA) and represented different binding categories. Our data indicated that, beside specific complex formation, many fragments show extensive multiple binding and also charge-state shifts. Both of these factors complicate automated data analysis and decrease the attractiveness of native MS as a primary screening tool for fragments. A comparison of the hits identified by native MS and TSA showed good agreement for two of the proteins. Furthermore, we discuss general challenges, including the determination of an optimal fragment concentration and the question of how to rank fragment hits according to their affinity. In conclusion, we consider native MS to be a highly valuable tool for the validation and deeper investigation of promising fragment hits rather than a method for primary screening.
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Affiliation(s)
- Melanie Göth
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Volker Badock
- Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
| | - Jörg Weiske
- Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany.,Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
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30
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Chan DSH, Mendes V, Thomas SE, McConnell BN, Matak-Vinković D, Coyne AG, Blundell TL, Abell C. Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Vitor Mendes
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Sherine E. Thomas
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Brendan N. McConnell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Dijana Matak-Vinković
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G. Coyne
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tom L. Blundell
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Chris Abell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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31
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Chan DSH, Mendes V, Thomas SE, McConnell BN, Matak-Vinković D, Coyne AG, Blundell TL, Abell C. Fragment Screening against the EthR-DNA Interaction by Native Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:7488-7491. [DOI: 10.1002/anie.201702888] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Vitor Mendes
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Sherine E. Thomas
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Brendan N. McConnell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Dijana Matak-Vinković
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G. Coyne
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Tom L. Blundell
- Department of Biochemistry; University of Cambridge; 80 Tennis Court Road CB2 1GA Cambridge UK
| | - Chris Abell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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32
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Cramer J, Schiebel J, Wulsdorf T, Grohe K, Najbauer EE, Ehrmann FR, Radeva N, Zitzer N, Linne U, Linser R, Heine A, Klebe G. Falsch-positiver Treffer im Fragment-basierten Wirkstoffdesign: Lass Dich nicht auf die falsche Fährte locken! Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jonathan Cramer
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Kristof Grohe
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
- Fakultät für Chemie und Pharmazie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13, Haus F 81377 München Deutschland
| | - Eszter Eva Najbauer
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
| | - Frederik R. Ehrmann
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Nedyalka Radeva
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Nina Zitzer
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Uwe Linne
- Fachbereich Chemie; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35043 Marburg Deutschland
| | - Rasmus Linser
- Abteilung für NMR-basierte Strukturbiologie; Max-Planck-Institut für Biophysikalische Chemie; Am Faßberg 11 37077 Göttingen Deutschland
- Fakultät für Chemie und Pharmazie; Ludwig-Maximilians-Universität München; Butenandtstr. 5-13, Haus F 81377 München Deutschland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie; Philipps-Universität Marburg; Marbacher Weg 6 35032 Marburg Deutschland
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33
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Cramer J, Schiebel J, Wulsdorf T, Grohe K, Najbauer EE, Ehrmann FR, Radeva N, Zitzer N, Linne U, Linser R, Heine A, Klebe G. A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring. Angew Chem Int Ed Engl 2017; 56:1908-1913. [PMID: 28097765 DOI: 10.1002/anie.201609824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/24/2016] [Indexed: 01/08/2023]
Abstract
With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false-positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease endothiapepsin (EP) across multiple screening assays. This molecule shows its biological effect mainly after conversion into another entity through a reaction cascade that involves major rearrangements of its heterocyclic scaffold. The formed ligand binds EP through an induced-fit mechanism involving remarkable electrostatic interactions. Structural information in the initial screening proved to be crucial for the identification of this false-positive hit.
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Affiliation(s)
- Jonathan Cramer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Kristof Grohe
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany.,Fakultät für Chemie und Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus F, 81377, München, Germany
| | - Eszter Eva Najbauer
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Nedyalka Radeva
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Nina Zitzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Uwe Linne
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043, Marburg, Germany
| | - Rasmus Linser
- Abteilung für NMR-basierte Strukturbiologie, Max Planck Institut für Biophysikalische Chemie, Am Faßberg 11, 37077, Göttingen, Germany.,Fakultät für Chemie und Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Haus F, 81377, München, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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34
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Urick AK, Calle LP, Espinosa JF, Hu H, Pomerantz WCK. Protein-Observed Fluorine NMR Is a Complementary Ligand Discovery Method to 1H CPMG Ligand-Observed NMR. ACS Chem Biol 2016; 11:3154-3164. [PMID: 27627661 PMCID: PMC8325173 DOI: 10.1021/acschembio.6b00730] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To evaluate its potential as a ligand discovery tool, we compare a newly developed 1D protein-observed fluorine NMR (PrOF NMR) screening method with the well-characterized ligand-observed 1H CPMG NMR screen. We selected the first bromodomain of Brd4 as a model system to benchmark PrOF NMR because of the high ligandability of Brd4 and the need for small molecule inhibitors of related epigenetic regulatory proteins. We compare the two methods' hit sensitivity, triaging ability, experiment speed, material consumption, and the potential for false positives and negatives. To this end, we screened 930 fragment molecules against Brd4 in mixtures of five and followed up these studies with mixture deconvolution and affinity characterization of the top hits. In selected examples, we also compare the environmental responsiveness of the 19F chemical shift to 1H in 1D-protein observed 1H NMR experiments. To address concerns of perturbations from fluorine incorporation, ligand binding trends and affinities were verified via thermal shift assays and isothermal titration calorimetry. We conclude that for the protein understudy here, PrOF NMR and 1H CPMG have similar sensitivity, with both being effective tools for ligand discovery. In cases where an unlabeled protein can be used, 1D protein-observed 1H NMR may also be effective; however, the 19F chemical shift remains significantly more responsive.
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Affiliation(s)
- Andrew K. Urick
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Luis Pablo Calle
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Centro de Investigación Lilly, 28108 Alcobendas, Madrid, Spain
| | - Juan F. Espinosa
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Centro de Investigación Lilly, 28108 Alcobendas, Madrid, Spain
| | - Haitao Hu
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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35
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Doak BC, Norton RS, Scanlon MJ. The ways and means of fragment-based drug design. Pharmacol Ther 2016; 167:28-37. [DOI: 10.1016/j.pharmthera.2016.07.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
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36
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Radeva N, Schiebel J, Wang X, Krimmer SG, Fu K, Stieler M, Ehrmann FR, Metz A, Rickmeyer T, Betz M, Winquist J, Park AY, Huschmann FU, Weiss MS, Mueller U, Heine A, Klebe G. Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures: Versatile Warheads To Address a Catalytic Dyad. J Med Chem 2016; 59:9743-9759. [PMID: 27726357 DOI: 10.1021/acs.jmedchem.6b01195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease endothiapepsin by individual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1' pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S1 and S1' are promising starting points for fragment-growing strategies.
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Affiliation(s)
- Nedyalka Radeva
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G Krimmer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Kan Fu
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Martin Stieler
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Frederik R Ehrmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Thomas Rickmeyer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Michael Betz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johan Winquist
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Ah Young Park
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany.,MAX IV Laboratory, Lund University , Fotongatan 2, 225 94 Lund, Sweden
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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37
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Mendes V, Blundell TL. Targeting tuberculosis using structure-guided fragment-based drug design. Drug Discov Today 2016; 22:546-554. [PMID: 27742535 DOI: 10.1016/j.drudis.2016.10.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/20/2023]
Abstract
Fragment-based drug discovery is now widely used in academia and industry to obtain small molecule inhibitors for a given target and is established for many fields of research including antimicrobials and oncology. Many molecules derived from fragment-based approaches are already in clinical trials and two - vemurafenib and venetoclax - are on the market, but the approach has been used sparsely in the tuberculosis field. Here, we describe the progress of our group and others, and examine the most recent successes and challenges in developing compounds with antimycobacterial activity.
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Affiliation(s)
- Vitor Mendes
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB21GA, UK.
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38
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Renaud JP, Chung CW, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H. Biophysics in drug discovery: impact, challenges and opportunities. Nat Rev Drug Discov 2016; 15:679-98. [PMID: 27516170 DOI: 10.1038/nrd.2016.123] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.
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Affiliation(s)
- Jean-Paul Renaud
- NovAliX, Boulevard Sébastien Brant, 67405 Illkirch Cedex, France.,Institut de Génétique et Biologie Moléculaire et Cellulaire, CNRS UMR7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries - BP10142, 67404 Illkirch Cedex, France.,RiboStruct, 15 rue Neuve, 67540 Ostwald, France
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - U Helena Danielson
- Department of Chemistry - BMC and Science for Life Laboratory, Drug Discovery &Development Platform, Uppsala University, SE-751 05 Uppsala, Sweden.,Beactica AB, Uppsala Business Park, 754 50 Uppsala, Sweden
| | - Ursula Egner
- Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin, Germany
| | - Michael Hennig
- Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland.,leadXpro AG, PARK INNOVAARE, CH-5234 Villigen, Switzerland
| | - Roderick E Hubbard
- University of York, Heslington, York, YO10 5DD, UK.,Vernalis (R&D), Granta Park, Cambridge, CB21 6GB, UK
| | - Herbert Nar
- Boehringer Ingelheim GmbH &Co. KG, Birkendorfer Strasse 65, 88400 Biberach, Germany
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39
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Radeva N, Krimmer SG, Stieler M, Fu K, Wang X, Ehrmann FR, Metz A, Huschmann FU, Weiss MS, Mueller U, Schiebel J, Heine A, Klebe G. Experimental Active-Site Mapping by Fragments: Hot Spots Remote from the Catalytic Center of Endothiapepsin. J Med Chem 2016; 59:7561-75. [PMID: 27463859 DOI: 10.1021/acs.jmedchem.6b00645] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Successful optimization of a given lead scaffold requires thorough binding-site mapping of the target protein particular in regions remote from the catalytic center where high conservation across protein families is given. We screened a 361-entry fragment library for binding to the aspartic protease endothiapepsin by crystallography. This enzyme is frequently used as a surrogate for the design of renin and β-secretase inhibitors. A hit rate of 20% was achieved, providing 71 crystal structures. Here, we discuss 45 binding poses of fragments accommodated in pockets remote from the catalytic dyad. Three major hot spots are discovered in remote binding areas: Asp81, Asp119, and Phe291. Compared to the dyad binders, bulkier fragments occupy these regions. Many of the discovered fragments suggest an optimization concept on how to grow them into larger ligands occupying adjacent binding pockets that will possibly endow them with the desired selectivity for one given member of a protein family.
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Affiliation(s)
- Nedyalka Radeva
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G Krimmer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Martin Stieler
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Kan Fu
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Frederik R Ehrmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, BESSY II , Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, BESSY II , Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, BESSY II , Albert-Einstein-Straße 15, 12489 Berlin, Germany.,MAX IV Laboratory, Lund University , Fotongatan 2, 225 94 Lund, Sweden
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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40
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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41
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Schiebel J, Krimmer SG, Röwer K, Knörlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glöckner S, Weiss MS, Mueller U, Klebe G, Heine A. High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits. Structure 2016; 24:1398-1409. [PMID: 27452405 DOI: 10.1016/j.str.2016.06.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 11/29/2022]
Abstract
Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that ∼25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods.
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Affiliation(s)
- Johannes Schiebel
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G Krimmer
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Karine Röwer
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Anna Knörlein
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Ah Young Park
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Martin Stieler
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Frederik R Ehrmann
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Kan Fu
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Nedyalka Radeva
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Michael Krug
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Franziska U Huschmann
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany; Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Steffen Glöckner
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Gerhard Klebe
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Institute for Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
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42
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Abstract
After 20 years of sometimes quiet growth, fragment-based drug discovery (FBDD) has become mainstream. More than 30 drug candidates derived from fragments have entered the clinic, with two approved and several more in advanced trials. FBDD has been widely applied in both academia and industry, as evidenced by the large number of papers from universities, non-profit research institutions, biotechnology companies and pharmaceutical companies. Moreover, FBDD draws on a diverse range of disciplines, from biochemistry and biophysics to computational and medicinal chemistry. As the promise of FBDD strategies becomes increasingly realized, now is an opportune time to draw lessons and point the way to the future. This Review briefly discusses how to design fragment libraries, how to select screening techniques and how to make the most of information gleaned from them. It also shows how concepts from FBDD have permeated and enhanced drug discovery efforts.
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43
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Schiebel J, Radeva N, Krimmer SG, Wang X, Stieler M, Ehrmann FR, Fu K, Metz A, Huschmann FU, Weiss MS, Mueller U, Heine A, Klebe G. Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study. ACS Chem Biol 2016; 11:1693-701. [PMID: 27028906 DOI: 10.1021/acschembio.5b01034] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fragment-based lead discovery (FBLD) has become a pillar in drug development. Typical applications of this method comprise at least two biophysical screens as prefilter and a follow-up crystallographic experiment on a subset of fragments. Clearly, structural information is pivotal in FBLD, but a key question is whether such a screening cascade strategy will retrieve the majority of fragment-bound structures. We therefore set out to screen 361 fragments for binding to endothiapepsin, a representative of the challenging group of aspartic proteases, employing six screening techniques and crystallography in parallel. Crystallography resulted in the very high number of 71 structures. Yet alarmingly, 44% of these hits were not detected by any biophysical screening approach. Moreover, any screening cascade, building on the results from two or more screening methods, would have failed to predict at least 73% of these hits. We thus conclude that, at least in the present case, the frequently applied biophysical prescreening filters deteriorate the number of possible X-ray hits while only the immediate use of crystallography enables exhaustive retrieval of a maximum of fragment structures, which represent a rich source guiding hit-to-lead-to-drug evolution.
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Affiliation(s)
- Johannes Schiebel
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Nedyalka Radeva
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Stefan G. Krimmer
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Martin Stieler
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Frederik R. Ehrmann
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Kan Fu
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Alexander Metz
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Franziska U. Huschmann
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie,
Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie,
Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, HZB, BESSY II, Abteilung Makromolekulare Kristallographie,
Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Andreas Heine
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut
für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg
6, 35032 Marburg, Germany
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44
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- György M. Keserű
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Daniel A. Erlanson
- Carmot Therapeutics, Inc. 409 Illinois Street, San Francisco, California 94158, United States
| | - György G. Ferenczy
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Michael M. Hann
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Stephen D. Pickett
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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45
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Huschmann FU, Linnik J, Sparta K, Ühlein M, Wang X, Metz A, Schiebel J, Heine A, Klebe G, Weiss MS, Mueller U. Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library. Acta Crystallogr F Struct Biol Commun 2016; 72:346-55. [PMID: 27139825 PMCID: PMC4854561 DOI: 10.1107/s2053230x16004623] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.
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Affiliation(s)
- Franziska U. Huschmann
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Janina Linnik
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Karine Sparta
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Monika Ühlein
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Xiaojie Wang
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Alexander Metz
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Johannes Schiebel
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - Uwe Mueller
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
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46
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Borthwick JA, Ancellin N, Bertrand SM, Bingham RP, Carter PS, Chung CW, Churcher I, Dodic N, Fournier C, Francis PL, Hobbs A, Jamieson C, Pickett SD, Smith SE, Somers DO, Spitzfaden C, Suckling CJ, Young RJ. Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening. J Med Chem 2016; 59:2452-67. [DOI: 10.1021/acs.jmedchem.5b01607] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jennifer A. Borthwick
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Nicolas Ancellin
- Les Ulis, Centre de Recherche, GlaxoSmithKline R&D, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Sophie M. Bertrand
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Ryan P. Bingham
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Paul S. Carter
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Chun-wa Chung
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Ian Churcher
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Nerina Dodic
- Les Ulis, Centre de Recherche, GlaxoSmithKline R&D, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Charlène Fournier
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Peter L. Francis
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Andrew Hobbs
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Craig Jamieson
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Stephen D. Pickett
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Sarah E. Smith
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Donald O’N. Somers
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Claus Spitzfaden
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Colin J. Suckling
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Robert J. Young
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
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47
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Woods LA, Dolezal O, Ren B, Ryan JH, Peat TS, Poulsen SA. Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination. J Med Chem 2016; 59:2192-204. [PMID: 26882437 DOI: 10.1021/acs.jmedchem.5b01940] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.
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Affiliation(s)
- Lucy A Woods
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
| | - Olan Dolezal
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Bin Ren
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - John H Ryan
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Thomas S Peat
- CSIRO Biomedical Manufacturing Program, Melbourne, Victoria Australia
| | - Sally-Ann Poulsen
- Griffith University , Eskitis Institute for Drug Discovery, Brisbane, Queensland Australia
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48
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Schiedel M, Rumpf T, Karaman B, Lehotzky A, Gerhardt S, Ovádi J, Sippl W, Einsle O, Jung M. Structure-Based Development of an Affinity Probe for Sirtuin 2. Angew Chem Int Ed Engl 2016; 55:2252-6. [DOI: 10.1002/anie.201509843] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Matthias Schiedel
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg im Breisgau Germany
| | - Tobias Rumpf
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg im Breisgau Germany
| | - Berin Karaman
- Institute für Pharmazie; Martin-Luther-Universität Halle-Wittenberg; Wolfgang-Langenbeck-Strasse 4 06120 Halle, Saale Germany
| | - Attila Lehotzky
- Institute of Enzymology, Research Centre for Natural Sciences; Hungarian Academy of Sciences; Magyar Tudósok körútja 2 H-1117 Budapest Hungary
| | - Stefan Gerhardt
- Institute für Biochemie und BIOSS Centre for Biological, Signaling Studies; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Judit Ovádi
- Institute of Enzymology, Research Centre for Natural Sciences; Hungarian Academy of Sciences; Magyar Tudósok körútja 2 H-1117 Budapest Hungary
| | - Wolfgang Sippl
- Institute für Pharmazie; Martin-Luther-Universität Halle-Wittenberg; Wolfgang-Langenbeck-Strasse 4 06120 Halle, Saale Germany
| | - Oliver Einsle
- Institute für Biochemie und BIOSS Centre for Biological, Signaling Studies; Albert-Ludwigs-Universität Freiburg; Albertstrasse 21 79104 Freiburg im Breisgau Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstrasse 25 79104 Freiburg im Breisgau Germany
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49
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Aretz J, Kondoh Y, Honda K, Anumala UR, Nazaré M, Watanabe N, Osada H, Rademacher C. Chemical fragment arrays for rapid druggability assessment. Chem Commun (Camb) 2016; 52:9067-70. [DOI: 10.1039/c5cc10457b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Incorporation of early druggability assessment in the drug discovery process provides a means to prioritize target proteins for high-throughput screening.
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Affiliation(s)
- J. Aretz
- Department of Biomolecular Systems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
- Department of Biology
| | - Y. Kondoh
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - K. Honda
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - U. R. Anumala
- Leibniz Institut für Molekulare Pharmakologie (FMP)
- Berlin
- Germany
| | - M. Nazaré
- Leibniz Institut für Molekulare Pharmakologie (FMP)
- Berlin
- Germany
| | - N. Watanabe
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - H. Osada
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - C. Rademacher
- Department of Biomolecular Systems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
- Department of Biology
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50
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Schiedel M, Rumpf T, Karaman B, Lehotzky A, Gerhardt S, Ovádi J, Sippl W, Einsle O, Jung M. Strukturbasierte Entwicklung einer Affinitätssonde für Sirtuin 2. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509843] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Matthias Schiedel
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstraße 25 79104 Freiburg im Breisgau Deutschland
| | - Tobias Rumpf
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstraße 25 79104 Freiburg im Breisgau Deutschland
| | - Berin Karaman
- Institut für Pharmazie; Martin-Luther-Universität Halle-Wittenberg; Wolfgang-Langenbeck-Straße 4 06120 Halle, Saale Deutschland
| | - Attila Lehotzky
- Institute of Enzymology, Research Centre for Natural Sciences; Hungarian Academy of Sciences; Magyar Tudósok körútja 2 H-1117 Budapest Ungarn
| | - Stefan Gerhardt
- Institut für Biochemie und BIOSS Centre for Biological Signaling Studies; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg im Breisgau Deutschland
| | - Judit Ovádi
- Institute of Enzymology, Research Centre for Natural Sciences; Hungarian Academy of Sciences; Magyar Tudósok körútja 2 H-1117 Budapest Ungarn
| | - Wolfgang Sippl
- Institut für Pharmazie; Martin-Luther-Universität Halle-Wittenberg; Wolfgang-Langenbeck-Straße 4 06120 Halle, Saale Deutschland
| | - Oliver Einsle
- Institut für Biochemie und BIOSS Centre for Biological Signaling Studies; Albert-Ludwigs-Universität Freiburg; Albertstraße 21 79104 Freiburg im Breisgau Deutschland
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften; Albert-Ludwigs-Universität Freiburg; Albertstraße 25 79104 Freiburg im Breisgau Deutschland
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