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FitzGerald EA, Vagrys D, Opassi G, Klein HF, Hamilton DJ, Talibov VO, Abramsson M, Moberg A, Lindgren MT, Holmgren C, Davis B, O'Brien P, Wijtmans M, Hubbard RE, de Esch IJP, Danielson UH. Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:40-51. [PMID: 37714432 DOI: 10.1016/j.slasd.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Beactica Therapeutics AB, Virdings allé 2, Uppsala, Sweden
| | - Darius Vagrys
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Giulia Opassi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Hanna F Klein
- Department of Chemistry, University of York, York, United Kingdom
| | - David J Hamilton
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | | | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Ben Davis
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom
| | - Peter O'Brien
- Department of Chemistry, University of York, York, United Kingdom
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Opassi G, Nordström H, Lundin A, Napolitano V, Magari F, Dzus T, Klebe G, Danielson UH. Establishing Trypanosoma cruzi farnesyl pyrophosphate synthase as a viable target for biosensor driven fragment-based lead discovery. Protein Sci 2020; 29:991-1003. [PMID: 31994261 PMCID: PMC7096706 DOI: 10.1002/pro.3834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
Abstract
Procedures for producing and exploring Trypanosoma cruzi farnesyl pyrophosphate synthase (tcFPPS) for surface plasmon resonance (SPR) biosensor‐driven fragment‐based discovery have been established. The method requires functional sensor surfaces with high sensitivity for extended times and appropriate controls. Initial problems with protein stability and lack of useful reference compounds motivated optimization of experimental procedures and conditions. The improved methods enabled the production of pure, folded and dimeric protein, and identified procedures for storage and handling. A new coupled enzymatic assay, using luciferase for detection of pyrophosphate, was developed and used to confirm that the purified enzyme was active after purification and storage. It also confirmed that sensor surfaces prepared with structurally intact protein was active. An SPR‐biosensor assay for fragment library screening and hit confirmation was developed. A thermal shift assay was used in parallel. A library of 90 fragments was efficiently screened by both assays at a single concentration in the presence and absence of the catalytic cofactor Mg2+. Hits were selected on the basis of response levels or ΔTm > 1°C and selectivity for tcFPPS in the presence of Mg2+. Characterization of hits by SPR showed that all had low affinities and the relationships between steady‐state responses and concentrations were not sufficiently hyperbolic for determination of KD‐values. Instead, ranking could be performed from the slope of the linear relationship at low concentrations. This pilot screen confirms that the procedures developed herein enables SPR‐biosensor driven fragment‐based discovery of leads targeting tcFPPS, despite the lack of a reference compound. Significance Statement To enable the discovery of drugs, it is essential to have access to relevant forms of the target protein and valid biochemical methods for studying the protein and effects of compounds that may be evolved into drugs. We have established methods for the discovery of drugs for treatment of American Trypanosomiasis (Chagas disease), using farnesyl pyrophosphate synthase from Trypanosoma cruzi as a target.
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Affiliation(s)
- Giulia Opassi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Helena Nordström
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala, Sweden
| | | | - Valeria Napolitano
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa, Krakow, Poland
| | - Francesca Magari
- Institut für Pharmazeutische Chemie, Phillips-Universität Marburg, Marburg, Germany
| | - Tom Dzus
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Phillips-Universität Marburg, Marburg, Germany
| | - U Helena Danielson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala, Sweden
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