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Mahía A, Kiib AE, Nisavic M, Svenningsen EB, Palmfeldt J, Poulsen TB. α-Lactam Electrophiles for Covalent Chemical Biology. Angew Chem Int Ed Engl 2023; 62:e202304142. [PMID: 37114559 DOI: 10.1002/anie.202304142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 04/29/2023]
Abstract
Electrophilic groups are one of the key pillars of contemporary chemical biology and medicinal chemistry. For instance, 3-membered N-heterocyclic compounds-such as aziridines, azirines, and oxaziridines-possess unique electronic and structural properties which underlie their potential and applicability as covalent tools. The α-lactams are also members of this group of compounds, however, their utility within the field remains unexplored. Here, we demonstrate an α-lactam reagent (AM2) that is tolerant to aqueous buffers while being reactive towards biologically relevant nucleophiles. Interestingly, carboxylesterases 1 and 2 (CES1/2), both serine hydrolases with key roles in endo- and xenobiotic metabolism, were found as primary covalent targets for AM2 in HepG2 liver cancer cells. All in all, this study constitutes the starting point for the further development and exploration of α-lactam-based electrophilic probes in covalent chemical biology.
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Affiliation(s)
- Alejandro Mahía
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Anders E Kiib
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Marija Nisavic
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Department of Clinical Medicine-Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Esben B Svenningsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine-Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
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McAulay K, Bilsland A, Bon M. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery. Pharmaceuticals (Basel) 2022; 15:1366. [PMID: 36355538 PMCID: PMC9694498 DOI: 10.3390/ph15111366] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 09/27/2023] Open
Abstract
Fragment based drug discovery has long been used for the identification of new ligands and interest in targeted covalent inhibitors has continued to grow in recent years, with high profile drugs such as osimertinib and sotorasib gaining FDA approval. It is therefore unsurprising that covalent fragment-based approaches have become popular and have recently led to the identification of novel targets and binding sites, as well as ligands for targets previously thought to be 'undruggable'. Understanding the properties of such covalent fragments is important, and characterizing and/or predicting reactivity can be highly useful. This review aims to discuss the requirements for an electrophilic fragment library and the importance of differing warhead reactivity. Successful case studies from the world of drug discovery are then be examined.
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Affiliation(s)
- Kirsten McAulay
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Centre for Targeted Protein Degradation, University of Dundee, Nethergate, Dundee DD1 4HN, UK
| | - Alan Bilsland
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marta Bon
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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Karaj E, Sindi SH, Kuganesan N, Perera L, Taylor W, Viranga Tillekeratne LM. Tunable Cysteine-Targeting Electrophilic Heteroaromatic Warheads Induce Ferroptosis. J Med Chem 2022; 65:11788-11817. [PMID: 35984756 PMCID: PMC10408038 DOI: 10.1021/acs.jmedchem.2c00909] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Once considered potential liabilities, the modern era witnesses a renaissance of interest in covalent inhibitors in drug discovery. The available toolbox of electrophilic warheads is limited by constraints on tuning reactivity and selectivity. Following our work on a class of ferroptotic agents termed CETZOLEs, we discovered new tunable heterocyclic electrophiles which are capable of inducing ferroptosis. The biological evaluation demonstrated that thiazoles with an alkyne electrophile at the 2-position selectively induce ferroptosis with high potency. Density functional theory calculations and NMR kinetic studies demonstrated the ability of our heterocycles to undergo thiol addition, an apparent prerequisite for cytotoxicity. Chemoproteomic analysis indicated several potential targets, the most prominent among them being GPX4 protein. These results were further validated by western blot analysis and the cellular thermal shift assay. Incorporation of these heterocycles into appropriate pharmacophores generated highly cytotoxic agents such as the analogue BCP-T.A, with low nM IC50 values in ferroptosis-sensitive cell lines.
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Affiliation(s)
- Endri Karaj
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606
| | - Shaimaa H. Sindi
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606
| | - Nishanth Kuganesan
- Department of Biological Sciences, College of Natural Sciences and Mathematics, University of Toledo, Toledo, OH 43606
| | - Lalith Perera
- Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - William Taylor
- Department of Biological Sciences, College of Natural Sciences and Mathematics, University of Toledo, Toledo, OH 43606
| | - L. M. Viranga Tillekeratne
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH 43606
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Svenningsen EB, Ottosen RN, Jørgensen KH, Nisavic M, Larsen CK, Hansen BK, Wang Y, Lindorff-Larsen K, Tørring T, Hacker SM, Palmfeldt J, Poulsen TB. The covalent reactivity of functionalized 5-hydroxy-butyrolactams is the basis for targeting of fatty acid binding protein 5 (FABP5) by the neurotrophic agent MT-21. RSC Chem Biol 2022; 3:1216-1229. [PMID: 36320884 PMCID: PMC9533406 DOI: 10.1039/d2cb00161f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Covalently acting compounds experience a strong interest within chemical biology both as molecular probes in studies of fundamental biological mechanisms and/or as novel drug candidates. In this context, the identification of new classes of reactive groups is particularly important as these can expose novel reactivity modes and, consequently, expand the ligandable proteome. Here, we investigated the electrophilic reactivity of the 3-acyl-5-hydroxy-1,5-dihydro-2H-pyrrole-2-one (AHPO) scaffold, a heterocyclic motif that is e.g. present in various bioactive natural products. Our investigations were focused on the compound MT-21 – a simplified structural analogue of the natural product epolactaene – which is known to have both neurotrophic activity and ability to trigger apoptotic cell death. We found that the central N-acyl hemiaminal group of MT-21 can function as an electrophilic centre enabling divergent reactivity with both amine- and thiol-based nucleophiles, which furthermore translated to reactivity with proteins in both cell lysates and live cells. We found that in live cells MT-21 strongly engaged the lipid transport protein fatty acid-binding protein 5 (FABP5) by direct binding to a cysteine residue in the bottom of the ligand binding pocket. Through preparation of a series of MT-21 derivatives, we probed the specificity of this interaction which was found to be strongly dependent on subtle structural changes. Our study suggests that MT-21 may be employed as a tool compound in future studies of the biology of FABP5, which remains incompletely understood. Furthermore, our study has also made clear that other natural products containing the AHPO-motif may likewise possess covalent reactivity and that this property may underlie their biological activity. In this work, it is shown that an N-acyl hemiaminal motif present in many natural products can function as an electrophilic centre, mediating covalent reactivity in biological systems, reacting with both thiols and amines.![]()
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Affiliation(s)
| | - Rasmus N. Ottosen
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
| | | | - Marija Nisavic
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
- Department of Clinical Medicine – Research Unit for Molecular Medicine, Aarhus University Hospital, DK-8200 Aarhus N, Denmark
| | - Camilla K. Larsen
- Department of Engineering – Microbial Biosynthesis, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Bente K. Hansen
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark
| | - Yong Wang
- Copenhagen Biocenter, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Thomas Tørring
- Department of Engineering – Microbial Biosynthesis, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Stephan M. Hacker
- Leiden Institute of Chemistry, Leiden University, NL-2333 CC Leiden, The Netherlands
| | - Johan Palmfeldt
- Department of Clinical Medicine – Research Unit for Molecular Medicine, Aarhus University Hospital, DK-8200 Aarhus N, Denmark
| | - Thomas B. Poulsen
- Department of Chemistry, Aarhus University, DK-8000, Aarhus C, Denmark
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