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Salvini CLA, Darlot B, Davison J, Martin MP, Tudhope SJ, Turberville S, Kawamura A, Noble MEM, Wedge SR, Crawford JJ, Waring MJ. Fragment expansion with NUDELs - poised DNA-encoded libraries. Chem Sci 2023; 14:8288-8294. [PMID: 37564419 PMCID: PMC10411621 DOI: 10.1039/d3sc01171b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Optimisation of the affinity of lead compounds is a critical challenge in the identification of drug candidates and chemical probes and is a process that takes many years. Fragment-based drug discovery has become established as one of the methods of choice for drug discovery starting with small, low affinity compounds. Due to their low affinity, the evolution of fragments to desirable levels of affinity is often a key challenge. The accepted best method for increasing the potency of fragments is by iterative fragment growing, which can be very time consuming and complex. Here, we introduce a paradigm for fragment hit optimisation using poised DNA-encoded chemical libraries (DELs). The synthesis of a poised DEL, a partially constructed library that retains a reactive handle, allows the coupling of any active fragment for a specific target protein, allowing rapid discovery of potent ligands. This is illustrated for bromodomain-containing protein 4 (BRD4), in which a weakly binding fragment was coupled to a 42-member poised DEL via Suzuki-Miyaura cross coupling resulting in the identification of an inhibitor with 51 nM affinity in a single step, representing an increase in potency of several orders of magnitude from an original fragment. The potency of the compound was shown to arise from the synergistic combination of substructures, which would have been very difficult to discover by any other method and was rationalised by X-ray crystallography. The compound showed attractive lead-like properties suitable for further optimisation and demonstrated BRD4-dependent cellular pharmacology. This work demonstrates the power of poised DELs to rapidly optimise fragments, representing an attractive generic approach to drug discovery.
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Affiliation(s)
- Catherine L A Salvini
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Benoit Darlot
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Jack Davison
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Susan J Tudhope
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Shannon Turberville
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Akane Kawamura
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Stephen R Wedge
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - James J Crawford
- Genentech Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Michael J Waring
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
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Davison G, Martin MP, Turberville S, Dormen S, Heath R, Heptinstall AB, Lawson M, Miller DC, Ng YM, Sanderson JN, Hope I, Wood DJ, Cano C, Endicott JA, Hardcastle IR, Noble MEM, Waring MJ. Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions. J Med Chem 2022; 65:15416-15432. [PMID: 36367089 PMCID: PMC9706561 DOI: 10.1021/acs.jmedchem.2c01357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Indexed: 11/13/2022]
Abstract
The development of ligands for biological targets is critically dependent on the identification of sites on proteins that bind molecules with high affinity. A set of compounds, called FragLites, can identify such sites, along with the interactions required to gain affinity, by X-ray crystallography. We demonstrate the utility of FragLites in mapping the binding sites of bromodomain proteins BRD4 and ATAD2 and demonstrate that FragLite mapping is comparable to a full fragment screen in identifying ligand binding sites and key interactions. We extend the FragLite set with analogous compounds derived from amino acids (termed PepLites) that mimic the interactions of peptides. The output of the FragLite maps is shown to enable the development of ligands with leadlike potency. This work establishes the use of FragLite and PepLite screening at an early stage in ligand discovery allowing the rapid assessment of tractability of protein targets and informing downstream hit-finding.
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Affiliation(s)
- Gemma Davison
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Mathew P. Martin
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Shannon Turberville
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Selma Dormen
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Richard Heath
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Amy B. Heptinstall
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Marie Lawson
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Duncan C. Miller
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Yi Min Ng
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - James N. Sanderson
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Ian Hope
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Daniel J. Wood
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Céline Cano
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Jane A. Endicott
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Ian R. Hardcastle
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Martin E. M. Noble
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Michael J. Waring
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
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Uguen M, Davison G, Sprenger LJ, Hunter JH, Martin MP, Turberville S, Watt JE, Golding BT, Noble MEM, Stewart HL, Waring MJ. Build-Couple-Transform: A Paradigm for Lead-like Library Synthesis with Scaffold Diversity. J Med Chem 2022; 65:11322-11339. [PMID: 35943172 PMCID: PMC9421646 DOI: 10.1021/acs.jmedchem.2c00897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-throughput screening provides one of the most common ways of finding hit compounds. Lead-like libraries, in particular, provide hits with compatible functional groups and vectors for structural elaboration and physical properties suitable for optimization. Library synthesis approaches can lead to a lack of chemical diversity because they employ parallel derivatization of common building blocks using single reaction types. We address this problem through a "build-couple-transform" paradigm for the generation of lead-like libraries with scaffold diversity. Nineteen transformations of a 4-oxo-2-butenamide scaffold template were optimized, including 1,4-cyclizations, 3,4-cyclizations, reductions, and 1,4-additions. A pool-transformation approach efficiently explored the scope of these transformations for nine different building blocks and synthesized a >170-member library with enhanced chemical space coverage and favorable drug-like properties. Screening revealed hits against CDK2. This work establishes the build-couple-transform concept for the synthesis of lead-like libraries and provides a differentiated approach to libraries with significantly enhanced scaffold diversity.
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Affiliation(s)
- Mélanie Uguen
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Gemma Davison
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Lukas J Sprenger
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - James H Hunter
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Mathew P Martin
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Shannon Turberville
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Jessica E Watt
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Bernard T Golding
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Martin E M Noble
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne NE2 4HH, U.K
| | - Hannah L Stewart
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
| | - Michael J Waring
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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Tripathy D, Vignoli B, Ramesh N, Polanco MJ, Coutelier M, Stephen CD, Canossa M, Monin ML, Aeschlimann P, Turberville S, Aeschlimann D, Schmahmann JD, Hadjivassiliou M, Durr A, Pandey UB, Pennuto M, Basso M. Mutations in TGM6 induce the unfolded protein response in SCA35. Hum Mol Genet 2018; 26:3749-3762. [PMID: 28934387 DOI: 10.1093/hmg/ddx259] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 12/23/2022] Open
Abstract
Spinocerebellar ataxia type 35 (SCA35) is a rare autosomal-dominant neurodegenerative disease caused by mutations in the TGM6 gene, which codes for transglutaminase 6 (TG6). Mutations in TG6 induce cerebellar degeneration by an unknown mechanism. We identified seven patients bearing new mutations in TGM6. To gain insights into the molecular basis of mutant TG6-induced neurotoxicity, we analyzed all the seven new TG6 mutants and the five TG6 mutants previously linked to SCA35. We found that the wild-type (TG6-WT) protein mainly localized to the nucleus and perinuclear area, whereas five TG6 mutations showed nuclear depletion, increased accumulation in the perinuclear area, insolubility and loss of enzymatic function. Aberrant accumulation of these TG6 mutants in the perinuclear area led to activation of the unfolded protein response (UPR), suggesting that specific TG6 mutants elicit an endoplasmic reticulum stress response. Mutations associated with activation of the UPR caused death of primary neurons and reduced the survival of novel Drosophila melanogaster models of SCA35. These results indicate that mutations differently impacting on TG6 function cause neuronal dysfunction and death through diverse mechanisms and highlight the UPR as a potential therapeutic target for patient treatment.
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Affiliation(s)
- Debasmita Tripathy
- Laboratory of Transcriptional Neurobiology, Centre for Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Beatrice Vignoli
- Laboratory of Neural Stem Cells and Neurogenesis, Centre for Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Nandini Ramesh
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria Jose Polanco
- Dulbecco Telethon Institute Lab of Neurodegenerative Diseases, Centre for Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Marie Coutelier
- INSERM U 1127, Centre National de la Recherche Scientifique UMR 7225, UMRS 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France
| | - Christopher D Stephen
- Ataxia Unit, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marco Canossa
- Laboratory of Neural Stem Cells and Neurogenesis, Centre for Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Marie-Lorraine Monin
- INSERM U 1127, Centre National de la Recherche Scientifique UMR 7225, UMRS 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France
| | - Pascale Aeschlimann
- Matrix Biology & Tissue Repair Research Unit, College of Biomedical and Life Sciences, School of Dentistry, Cardiff University, Cardiff, UK
| | - Shannon Turberville
- Matrix Biology & Tissue Repair Research Unit, College of Biomedical and Life Sciences, School of Dentistry, Cardiff University, Cardiff, UK
| | - Daniel Aeschlimann
- Matrix Biology & Tissue Repair Research Unit, College of Biomedical and Life Sciences, School of Dentistry, Cardiff University, Cardiff, UK
| | - Jeremy D Schmahmann
- Ataxia Unit, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marios Hadjivassiliou
- Academic Department of Neurosciences, Royal Hallamshire Hospital, University of Sheffield, Sheffield, UK
| | - Alexandra Durr
- INSERM U 1127, Centre National de la Recherche Scientifique UMR 7225, UMRS 1127, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités, Institut du Cerveau et de la Moelle Epinière, 75013 Paris, France
| | - Udai B Pandey
- Division of Child Neurology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Maria Pennuto
- Dulbecco Telethon Institute Lab of Neurodegenerative Diseases, Centre for Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
| | - Manuela Basso
- Laboratory of Transcriptional Neurobiology, Centre for Integrative Biology (CIBIO), University of Trento, Trento (TN), Italy
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