1
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Liu Y, Yu Z, Li P, Yang T, Ding K, Zhang ZM, Tan Y, Li Z. Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles. J Am Chem Soc 2024. [PMID: 39018468 DOI: 10.1021/jacs.4c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhongtang Yu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Peishan Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tao Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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2
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Walther R, Park M, Ashman N, Welch M, Carroll JS, Spring DR. Tuneable thiol exchange linkers for traceless drug release applications in prodrugs and ADCs. Chem Commun (Camb) 2024; 60:7025-7028. [PMID: 38888299 PMCID: PMC11223184 DOI: 10.1039/d4cc01558d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
We describe a versatile and tuneable thiol responsive linker system using thiovinylketones, which relies on the conjugate addition-elimination mechanism of Michael acceptors for the traceless release of therapeutics. In a proof-of-principle study, we translate our findings to exhibit potent thiol-cleavable antibiotic prodrugs and antibody-drug conjugates.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Mahri Park
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Nicola Ashman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, CB2 1QW Cambridge, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, Robinson Way, CB2 0RE Cambridge, UK
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
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3
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [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: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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4
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Tu HF, Jeandin A, Bon C, Brocklehurst C, Lima F, Suero MG. Late-Stage Aryl C-H Bond Cyclopropenylation with Cyclopropenium Cations. Angew Chem Int Ed Engl 2023; 62:e202308379. [PMID: 37459194 DOI: 10.1002/anie.202308379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Herein, we disclose the first regio-, site- and chemoselective late-stage (hetero)aryl C-H bond cyclopropenylation with cyclopropenium cations (CPCs). The process is fast, operationally simple and shows an excellent functional group tolerance in densely-functionalized drug molecules, natural products, agrochemicals and fluorescent dyes. Moreover, we discovered that the installation of the cyclopropene ring in drug molecules could not only be used to shield against metabolic instability but also as a synthetic tool to reach medicinally-relevant sp3 -rich scaffolds exploiting the highly-strained nature of the cyclopropene ring with known transformations.
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Affiliation(s)
- Hang-Fei Tu
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
| | - Aliénor Jeandin
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
- Departament de Química Analítica i Química Orgánica, Universitat Rovira i Virgili, Calle Marcel.lí Domingo, 1, 43007, Tarragona, Spain
| | - Corentin Bon
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Cara Brocklehurst
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Fabio Lima
- Global Discovery Chemistry, Novartis Institutes of BioMedical Research, 4056, Basel, Switzerland
| | - Marcos G Suero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology, Av. Països Catalans, 16, 43007, Tarragona, Spain
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5
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Oppong D, Schiff W, Shivamadhu MC, Ahn YH. Chemistry and biology of enzymes in protein glutathionylation. Curr Opin Chem Biol 2023; 75:102326. [PMID: 37245422 PMCID: PMC10524987 DOI: 10.1016/j.cbpa.2023.102326] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/30/2023]
Abstract
Protein S-glutathionylation is emerging as a central oxidation that regulates redox signaling and biological processes linked to diseases. In recent years, the field of protein S-glutathionylation has expanded by developing biochemical tools for the identification and functional analyses of S-glutathionylation, investigating knockout mouse models, and developing and evaluating chemical inhibitors for enzymes involved in glutathionylation. This review will highlight recent studies of two enzymes, glutathione transferase omega 1 (GSTO1) and glutaredoxin 1 (Grx1), especially introducing their glutathionylation substrates associated with inflammation, cancer, and neurodegeneration and showcasing the advancement of their chemical inhibitors. Lastly, we will feature protein substrates and chemical inducers of LanC-like protein (LanCL), the first enzyme in protein C-glutathionylation.
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Affiliation(s)
- Daniel Oppong
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA
| | - William Schiff
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA
| | | | - Young-Hoon Ahn
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
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6
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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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7
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Koyama T, Takahashi I, Asami T. Cycloprop-2-ene-1-carboxylates: Potential chemical biology tools in the early growth stage of Arabidopsis thaliana. JOURNAL OF PESTICIDE SCIENCE 2023; 48:61-64. [PMID: 37361485 PMCID: PMC10288001 DOI: 10.1584/jpestics.d22-034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/19/2023] [Indexed: 06/28/2023]
Abstract
Cyclopropene derivatives have been used as extremely reactive units in organic chemistry owing to their high ring-strain energy. They have become popular reagents both for bioorthogonal chemistry and for chemical biology because of their small size and ability to be genetically encoded. In this context, we conducted an exploratory study to identify the biologically active cyclopropenes that affect normal plant growth. We synthesized several cycloprop-2-ene-1-carboxylic acid derivatives and evaluated their effects on the early growth stage of Arabidopsis thaliana. Eventually, we identified the chemicals that affect apical hook development in Arabidopsis thaliana. Their mode of action is different from those of ethylene receptor inhibition and gibberellin biosynthesis inhibition. We expect that some of the chemicals reported here can be new tools in chemical biology to determine useful molecular targets for herbicides or plant growth regulators.
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Affiliation(s)
- Tomoyuki Koyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Ikuo Takahashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Tadao Asami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo
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8
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Li S, Zhang P, Xu F, Hu S, Liu J, Tan Y, Tu Z, Sun H, Zhang ZM, He QY, Sun P, Ding K, Li Z. Ynamide Electrophile for the Profiling of Ligandable Carboxyl Residues in Live Cells and the Development of New Covalent Inhibitors. J Med Chem 2022; 65:10408-10418. [PMID: 35880853 DOI: 10.1021/acs.jmedchem.2c00272] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covalent inhibitors with an electrophilic warhead have received considerable attention due to their remarkable pharmacological properties. However, the electrophilic warhead in covalent drugs is often an α, β-unsaturated amide, and the targets are mainly cysteine or lysine residues. Thus, the development of novel electrophiles that can target other amino acids is highly desirable. Ynamide, a useful and versatile building block, is commonly employed in the construction of various compounds in organic synthesis. The performance of this functional group in a proteome-wide environment has been studied here for the first time, and it has been shown that it can efficiently modify carboxyl residues in situ and in vitro. Upon incorporation of this ynamide warhead into the pharmacophores of kinase inhibitors, the resulting compound showed moderate inhibition against the EGFR L858R mutant but not against EGFR WT. This novel electrophilic group can be used in the development of new types of covalent inhibitors.
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Affiliation(s)
- Shengrong Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Pengwei Zhang
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, Guangdong, China
| | - Fang Xu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Shengcao Hu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Jiacong Liu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Yi Tan
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengchao Tu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Qing-Yu He
- Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, Guangdong, China.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
| | - Pinghua Sun
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, China 510632.,MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou 510120, China
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9
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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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10
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Fan Y, Si H, Zhang Z, Zhong L, Sun H, Zhu C, Yin Z, Li H, Tang G, Yao SQ, Sun P, Zhang ZM, Ding K, Li Z. Novel Electrophilic Warhead Targeting a Triple-Negative Breast Cancer Driver in Live Cells Revealed by "Inverse Drug Discovery". J Med Chem 2021; 64:15582-15592. [PMID: 34623802 DOI: 10.1021/acs.jmedchem.0c02024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The "inverse drug discovery" strategy is a potent means of exploring the cellular targets of latent electrophiles not typically used in medicinal chemistry. Cyclopropenone, a powerful electrophile, is generally used in bio-orthogonal reactions mediated by triarylphosphine or in photo-triggered cycloaddition reactions. Here, we have studied, for the first time, the proteome reactivity of cyclopropenones in live cells and discovered that the cyclopropenone warhead can specifically and efficiently modify a triple-negative breast cancer driver, glutathione S-transferase pi-1 (GSTP1), by covalently binding at the catalytic active site. Further structure optimization and signaling pathway validation have led to the discovery of potent inhibitors of GSTP1.
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Affiliation(s)
- Youlong Fan
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Hongfei Si
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhang Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Liang Zhong
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhibin Yin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Pinghua Sun
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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11
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Liu H, Ottosen RN, Jennet KM, Svenningsen EB, Kristensen TF, Biltoft M, Jakobsen MR, Poulsen TB. Macrodiolide Diversification Reveals Broad Immunosuppressive Activity That Impairs the cGAS‐STING Pathway. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Han Liu
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
- Current address: Department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Rasmus N. Ottosen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Kira M. Jennet
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Esben B. Svenningsen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Tobias F. Kristensen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
| | - Mette Biltoft
- STipe Therapeutics ApS, c/o The Kitchen Peter Sabroes Gade 7 8000 Aarhus C Denmark
| | - Martin R. Jakobsen
- STipe Therapeutics ApS, c/o The Kitchen Peter Sabroes Gade 7 8000 Aarhus C Denmark
- Department of Biomedicine Aarhus University Høegh-Guldbergs Gade 10 8000 Aarhus C Denmark
| | - Thomas B. Poulsen
- Department of Chemistry Aarhus University Langelandsgade 140 8000 Aarhus C Denmark
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12
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Liu H, Ottosen RN, Jennet KM, Svenningsen EB, Kristensen TF, Biltoft M, Jakobsen MR, Poulsen TB. Macrodiolide Diversification Reveals Broad Immunosuppressive Activity That Impairs the cGAS-STING Pathway. Angew Chem Int Ed Engl 2021; 60:18734-18741. [PMID: 34124819 DOI: 10.1002/anie.202105793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Indexed: 02/02/2023]
Abstract
The development of new immunomodulatory agents can impact various areas of medicine. In particular, compounds with the ability to modulate innate immunological pathways hold significant unexplored potential. Herein, we report a modular synthetic approach to the macrodiolide natural product (-)-vermiculine, an agent previously shown to possess diverse biological effects, including cytotoxic and immunosuppressive activity. The synthesis allows for a high degree of flexibility in modifying the macrocyclic framework, including the formation of all possible stereoisomers. In total, 18 analogues were prepared. Two analogues with minor structural modifications showed clearly enhanced cancer cell line selectivity and reduced toxicity. Moreover, these compounds possessed broad inhibitory activity against innate immunological pathways in human PBMCs, including the DNA-sensing cGAS-STING pathway. Initial mechanistic characterization suggests a surprising impairment of the STING-TBK1 interaction.
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Affiliation(s)
- Han Liu
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.,Current address: Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, P. R. China
| | - Rasmus N Ottosen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Kira M Jennet
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Esben B Svenningsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Tobias F Kristensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Mette Biltoft
- STipe Therapeutics ApS, c/o The Kitchen, Peter Sabroes Gade 7, 8000, Aarhus C, Denmark
| | - Martin R Jakobsen
- STipe Therapeutics ApS, c/o The Kitchen, Peter Sabroes Gade 7, 8000, Aarhus C, Denmark.,Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
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13
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Cordon MB, Jacobsen KM, Nielsen CS, Hjerrild P, Poulsen TB. Forward Chemical Genetic Screen for Oxygen-Dependent Cytotoxins Uncovers New Covalent Fragments that Target GPX4. Chembiochem 2021; 23:e202100253. [PMID: 34252249 DOI: 10.1002/cbic.202100253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Indexed: 11/09/2022]
Abstract
The identification of growth inhibitory compounds with the ability to selectively target the cellular oxygenation state may be of therapeutic interest. Here, a phenotypic screen of a covalent fragment library revealed diverse compounds containing propiolamide warheads with selective toxicity for liver cancer cells in normoxic conditions. Target identification and validation through CETSA and direct pulldown experiments demonstrated that several compounds target glutathione peroxidase 4 (GPX4) and induce ferroptotic cell death. Although being an oxidative cell death mechanism, ferroptosis can be induced also under hypoxic conditions. Prompted by the selective toxicity discovered in the screen, we mapped the oxygen-dependence of several ferroptosis-inducing compounds across three different cell lines. These studies revealed combinations with notable reductions in sensitivity under hypoxic conditions. These observations are mechanistically interesting and may be relevant for the use of ferroptosis-inducers as anti-cancer agents.
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Affiliation(s)
- Marie B Cordon
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Kristian M Jacobsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Cecilie S Nielsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Per Hjerrild
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
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14
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Poulsen TB. Total Synthesis of Natural Products Containing Enamine or Enol Ether Derivatives. Acc Chem Res 2021; 54:1830-1842. [PMID: 33660974 DOI: 10.1021/acs.accounts.0c00851] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Enamine and enol ethers are nucleophilic functional groups that are well known to most chemists. When enamine or enol ethers are present in natural products, they are nearly exclusively found as derivatives having a direct connection to electron-withdrawing groups for stabilization, and the resulting larger entities, such as enamides or enol acylates, can be further extended or modified in the framework of natural products. The restricted conformational space that is associated with even simple enamine and enol ether derivatives can be a strong determinant of the overall molecular structure, and the more polarized derivatives can endow some natural products with electrophilic properties and thus facilitate covalent interactions with biological targets.In this Account, I describe our efforts (published since 2016) to prepare natural products from several different classes that all feature enamine or enol ether derivatives as key functionalities. Our choice of targets has been guided by a desire to illuminate unknown biological mechanisms associated with the compounds or, alternatively, to improve upon known biological activities that appear to be promising from a biomedical perspective. In the present text, however, the exclusive focus will be on the syntheses.First, I will discuss the basic properties of the functional groups and briefly present a small collection of illustrative and inspirational examples from the literature for their construction in different complex settings. Next, I will provide an overview of our work on the macrocyclic APD-CLD natural products, rakicidin A and BE-43547A1, involving the development of an efficient macrocyclization strategy and the development of methods to construct the hallmark APD group: a modified enamide. The synthesis of the meroterpenoid strongylophorine-26 is discussed next, where we developed an oxidative quinone methoxylation to build a vinylogous ester group in the final step of the synthesis and employed FeCl3-mediated cascade reactions for the rapid assembly of the overall scaffold to enable a short semisynthesis from isocupressic acid. An efficient core scaffold assembly was also in focus in our synthesis of the alkaloid streptazone A with the signature enaminone system being assembled through a rhodium-catalyzed Pauson-Khand reaction. Sequential, site-selective redox manipulations were developed to arrive at strepatzone A and additional members of the natural product family. Finally, I discuss our work to prepare analogs of complex polyether ionophores featuring functionalized tetronic acids as cation-binding groups. A method for the construction of a suitably protected chloromethylidene-modified tetronate is presented which enabled its installation in the full structure through a C-acylation reaction. This work exemplifies how components of abundant polyether ionophores can be recycled and used to access new structures which may possess enhanced biological activities.
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Affiliation(s)
- Thomas B. Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
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15
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Escorihuela J, Looijen WJE, Wang X, Aquino AJA, Lischka H, Zuilhof H. Cycloaddition of Strained Cyclic Alkenes and Ortho-Quinones: A Distortion/Interaction Analysis. J Org Chem 2020; 85:13557-13566. [PMID: 33105075 PMCID: PMC7656516 DOI: 10.1021/acs.joc.0c01674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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The
chemistry of strained unsaturated cyclic compounds has experienced
remarkable growth in recent years via the development of metal–free
click reactions. Among these reactions, the cycloaddition of cyclopropenes
and their analogues to ortho-quinones has been established
as a highly promising click reaction. The present work investigates
the mechanism involved in the cycloaddition of strained dienes to ortho-quinones and structural factors that would influence
this reaction. For this purpose, we use B97D density functional theory
calculations throughout, and for relevant cases, we use spin component–scaled
MP2 calculations and single–point domain-based local pair natural
orbital coupled cluster (DLPNO-CCSD(T)) calculations. The outcomes
are analyzed in detail using the distortion/interaction model, and
suggestions for future experimental work are made.
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Affiliation(s)
- Jorge Escorihuela
- Departament de Quı́mica Orgànica, Universitat de València, Av. Vicent Andrés Estellés s/n, 46100 Burjassot, Valencia, Spain
| | - Wilhelmus J E Looijen
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Xiao Wang
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China
| | - Adelia J A Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Institute for Soil Research, University of Natural Resources and Life Sciences, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria.,Department of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria.,Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
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16
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Prasad Raiguru B, Nayak S, Ranjan Mishra D, Das T, Mohapatra S, Priyadarsini Mishra N. Synthetic Applications of Cyclopropene and Cyclopropenone: Recent Progress and Developments. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000193] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Sabita Nayak
- Department of ChemistryRavenshaw University Cuttack Odisha India
| | | | - Tapaswini Das
- Department of ChemistryRavenshaw University Cuttack Odisha India
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17
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Vicente R. C–C Bond Cleavages of Cyclopropenes: Operating for Selective Ring-Opening Reactions. Chem Rev 2020; 121:162-226. [DOI: 10.1021/acs.chemrev.0c00151] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Rubén Vicente
- Facultad de Quı́mica, Departamento de Quı́mica Orgánica e Inorgánica, Instituto de Quı́mica Organometálica Enrique Moles, Universidad de Oviedo, 33006 Oviedo, Spain
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