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Bailly C. Covalent binding of withanolides to cysteines of protein targets. Biochem Pharmacol 2024; 226:116405. [PMID: 38969301 DOI: 10.1016/j.bcp.2024.116405] [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] [Received: 03/29/2024] [Revised: 05/26/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
Withanolides represent an important category of natural products with a steroidal lactone core. Many of them contain an α,β-unsaturated carbonyl moiety with a high reactivity toward sulfhydryl groups, including protein cysteine thiols. Different withanolides endowed with marked antitumor and anti-inflammatory have been shown to form stable covalent complexes with exposed cysteines present in the active site of oncogenic kinases (BTK, IKKβ, Zap70), metabolism enzymes (Prdx-1/6, Pin1, PHGDH), transcription factors (Nrf2, NFκB, C/EBPβ) and other structural and signaling molecules (GFAP, β-tubulin, p97, Hsp90, vimentin, Mpro, IPO5, NEMO, …). The present review analyzed the covalent complexes formed through Michael addition alkylation reactions between six major withanolides (withaferin A, physalin A, withangulatin A, 4β-hydroxywithanolide E, withanone and tubocapsanolide A) and key cysteine residues of about 20 proteins and the resulting biological effects. The covalent conjugation of the α,β-unsaturated carbonyl system of withanolides with reactive protein thiols can occur with a large set of soluble and membrane proteins. It points to a general mechanism, well described with the leading natural product withaferin A, but likely valid for most withanolides harboring a reactive (electrophilic) enone moiety susceptible to react covalently with cysteinyl residues of proteins. The multiplicity of reactive proteins should be taken into account when studying the mechanism of action of new withanolides. Proteomic and network analyses shall be implemented to capture and compare the cysteine covalent-binding map for the major withanolides, so as to identify the protein targets at the origin of their activity and/or unwanted effects. Screening of the cysteinome will help understanding the mechanism of action and designing cysteine-reactive electrophilic drug candidates.
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Affiliation(s)
- Christian Bailly
- CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, OncoLille Institute, University of Lille, F-59000 Lille, France; Institute of Pharmaceutical Chemistry Albert Lespagnol (ICPAL), Faculty of Pharmacy, University of Lille, F-59006 Lille, France; OncoWitan, Scientific Consulting Office, F-59290 Lille, France.
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2
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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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Liang W, Krabill AD, Gallagher KS, Muli C, Qu Z, Trader D, Zhang ZY, Dai M. Natural Product-Inspired Molecules for Covalent Inhibition of SHP2 Tyrosine Phosphatase. Tetrahedron 2024; 156:133918. [PMID: 38618612 PMCID: PMC11008911 DOI: 10.1016/j.tet.2024.133918] [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] [Indexed: 04/16/2024]
Abstract
Natural products have been playing indispensable roles in the development of lifesaving drug molecules. They are also valuable sources for covalent protein modifiers. However, they often are scarce in nature and have complex chemical structures, which are limiting their further biomedical development. Thus, natural product-inspired small molecules which still contain the essence of the parent natural products but are readily available and amenable for structural modification, are important and desirable in searching for lead compounds for various disease treatment. Inspired by the complex and diverse ent-kaurene diterpenoids with significant biological activities, we have created a synthetically accessible and focused covalent library by incorporating the bicyclo[3.2.1]octane α-methylene ketone, which is considered as the pharmacophore of ent-kaurene diterpenoids, as half of the structure, and replacing the other half with much less complex but more druglike scaffolds. From this library, we have identified and characterized selective covalent inhibitors of protein tyrosine phosphatase SHP2, an important anti-cancer therapeutic target. The success of this study demonstrated the importance of creating and evaluating natural product-inspired library as well as their application in targeting challenging disease targets.
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Affiliation(s)
- Weida Liang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Katelyn S Gallagher
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Christine Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Zihan Qu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Darci Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
| | - Mingji Dai
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA 30322, United States
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MacLean MR, Walker OL, Arun RP, Fernando W, Marcato P. Informed by Cancer Stem Cells of Solid Tumors: Advances in Treatments Targeting Tumor-Promoting Factors and Pathways. Int J Mol Sci 2024; 25:4102. [PMID: 38612911 PMCID: PMC11012648 DOI: 10.3390/ijms25074102] [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] [Received: 02/28/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer stem cells (CSCs) represent a subpopulation within tumors that promote cancer progression, metastasis, and recurrence due to their self-renewal capacity and resistance to conventional therapies. CSC-specific markers and signaling pathways highly active in CSCs have emerged as a promising strategy for improving patient outcomes. This review provides a comprehensive overview of the therapeutic targets associated with CSCs of solid tumors across various cancer types, including key molecular markers aldehyde dehydrogenases, CD44, epithelial cellular adhesion molecule, and CD133 and signaling pathways such as Wnt/β-catenin, Notch, and Sonic Hedgehog. We discuss a wide array of therapeutic modalities ranging from targeted antibodies, small molecule inhibitors, and near-infrared photoimmunotherapy to advanced genetic approaches like RNA interference, CRISPR/Cas9 technology, aptamers, antisense oligonucleotides, chimeric antigen receptor (CAR) T cells, CAR natural killer cells, bispecific T cell engagers, immunotoxins, drug-antibody conjugates, therapeutic peptides, and dendritic cell vaccines. This review spans developments from preclinical investigations to ongoing clinical trials, highlighting the innovative targeting strategies that have been informed by CSC-associated pathways and molecules to overcome therapeutic resistance. We aim to provide insights into the potential of these therapies to revolutionize cancer treatment, underscoring the critical need for a multi-faceted approach in the battle against cancer. This comprehensive analysis demonstrates how advances made in the CSC field have informed significant developments in novel targeted therapeutic approaches, with the ultimate goal of achieving more effective and durable responses in cancer patients.
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Affiliation(s)
- Maya R. MacLean
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.M.); (O.L.W.); (R.P.A.); (W.F.)
| | - Olivia L. Walker
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.M.); (O.L.W.); (R.P.A.); (W.F.)
| | - Raj Pranap Arun
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.M.); (O.L.W.); (R.P.A.); (W.F.)
| | - Wasundara Fernando
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.M.); (O.L.W.); (R.P.A.); (W.F.)
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
| | - Paola Marcato
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; (M.R.M.); (O.L.W.); (R.P.A.); (W.F.)
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Nova Scotia Health Authority, Halifax, NS B3H 4R2, Canada
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Luo S, Long H, Lou F, Liu Y, Wang H, Pu J, Ji P, Jin X. Chronic restraint stress promotes oral squamous cell carcinoma development by inhibiting ALDH3A1 via stress response hormone. BMC Oral Health 2024; 24:43. [PMID: 38191346 PMCID: PMC10773021 DOI: 10.1186/s12903-023-03787-1] [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: 03/07/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Chronic restraint stress (CRS) has iteratively been reported to be possibly implicated in the development of numerous cancer types. However, its role in oral squamous cell carcinoma (OSCC) has not been well elucidated. Here we intended to evaluate the role and mechanism. METHODS The effects of CRS were investigated in xenograft models of OSCC by using transcriptome sequencing, LC-MS, ELISA and RT-PCR. Moreover, the role of CRS and ALDH3A1 on OSCC cells was researched by using Trans-well, flow cytometry, western blotting, immunofluorescence, ATP activity and OCR assay. Furthermore, immunohistochemical staining was employed to observe the cell proliferation and invasion of OSCC in xenotransplantation models. RESULTS CRS promoted the progression of OSCC in xenograft models, stimulated the secretion of norepinephrine and the expression of ADRB2, but decreased the expression of ALDH3A1. Moreover, CRS changed energy metabolism and increased mitochondrial metabolism markers. However, ALDH3A1 overexpression suppressed proliferation, EMT and mitochondrial metabolism of OSCC cells. CONCLUSION Inhibition of ALDH3A1 expression plays a pivotal role in CRS promoting tumorigenic potential of OSCC cells, and the regulatory of ALDH3A1 on mitochondrial metabolism may be involved in this process.
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Affiliation(s)
- Shihong Luo
- College of Stomatology, Chongqing Medical University, Chongqing, 401147, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, 401147, China
| | - Huiqing Long
- College of Stomatology, Chongqing Medical University, Chongqing, 401147, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, 401147, China
| | - Fangzhi Lou
- College of Stomatology, Chongqing Medical University, Chongqing, 401147, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, 401147, China
| | - Yiyun Liu
- NHC Key Laboratory of Diagnosis and Treatment On Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Haiyang Wang
- NHC Key Laboratory of Diagnosis and Treatment On Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Juncai Pu
- NHC Key Laboratory of Diagnosis and Treatment On Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400042, China
| | - Ping Ji
- College of Stomatology, Chongqing Medical University, Chongqing, 401147, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, 401147, China
| | - Xin Jin
- College of Stomatology, Chongqing Medical University, Chongqing, 401147, China.
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, 401147, China.
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Shao Q, Duong TN, Park I, Nomura DK. Covalent 14-3-3 Molecular Glues and Heterobifunctional Molecules Against Nuclear Transcription Factors and Regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.06.565850. [PMID: 37986959 PMCID: PMC10659333 DOI: 10.1101/2023.11.06.565850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
14-3-3 proteins have the unique ability to bind and sequester a multitude of diverse phosphorylated signaling proteins and transcription factors. Many previous studies have shown that 14-3-3 interactions with specific phosphorylated substrate proteins can be enhanced through small-molecule natural product or fully synthetic molecular glue interactions. However, enhancing 14-3-3 interactions with both therapeutically intractable transcription factor substrates as well as potential neo-substrates to sequester and inhibit their function has remained elusive. One of the 14-3-3 proteins, 14-3-3σ or SFN, has a cysteine C38 at the substrate binding interface near sites where previous 14-3-3 molecular glues have been found to bind. In this study, we screened a fully synthetic cysteine-reactive covalent ligand library to identify molecular glues that enhance interaction of 14-3-3σ with not only druggable transcription factors such as estrogen receptor (ERα), but also challenging oncogenic transcription factors such as YAP and TAZ that are part of the Hippo transducer pathway. We identified a hit EN171 that covalently targets 14-3-3 to enhance 14-3-3 interactions with ERα, YAP, and TAZ leading to impaired estrogen receptor and Hippo pathway transcriptional activity. We further demonstrate that EN171 could not only be used as a molecular glue to enhance native protein interactions, but also could be used as a covalent 14-3-3 recruiter in heterobifunctional molecules to sequester nuclear neo-substrates such as BRD4 into the cytosol. Overall, our study reveals a covalent ligand that acts as a novel 14-3-3 molecular glue for challenging transcription factors such as YAP and TAZ and also demonstrates that these glues can be potentially utilized in heterobifunctional molecules to sequester nuclear neo-substrates out of the nucleus and into the cytosol to enable targeted protein localization.
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Affiliation(s)
- Qian Shao
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Tuong Nghi Duong
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Inji Park
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Daniel K Nomura
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
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Chen Y, Yan H, Yan L, Wang X, Che X, Hou K, Yang Y, Li X, Li Y, Zhang Y, Hu X. Hypoxia-induced ALDH3A1 promotes the proliferation of non-small-cell lung cancer by regulating energy metabolism reprogramming. Cell Death Dis 2023; 14:617. [PMID: 37730658 PMCID: PMC10511739 DOI: 10.1038/s41419-023-06142-y] [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: 02/05/2023] [Revised: 08/24/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
Aldehyde dehydrogenase 3A1 (ALDH3A1) is an NAD+-dependent enzyme that is closely related to tumor development. However, its role in non-small-cell lung cancer (NSCLC) has not been elucidated. This study aimed to clarify the mechanism of ALDH3A1 and identify potential therapeutic targets for NSCLC. Here, for the first time, we found that ALDH3A1 expression could be induced by a hypoxic environment in NSCLC. ALDH3A1 was highly expressed in NSCLC tissue, especially in some late-stage patients, and was associated with a poor prognosis. In mechanistic terms, ALDH3A1 enhances glycolysis and suppresses oxidative phosphorylation (OXPHOS) to promote cell proliferation by activating the HIF-1α/LDHA pathway in NSCLC. In addition, the results showed that ALDH3A1 was a target of β-elemene. ALDH3A1 can be downregulated by β-elemene to inhibit glycolysis and enhance OXPHOS, thus suppressing NSCLC proliferation in vitro and in vivo. In conclusion, hypoxia-induced ALDH3A1 is related to the energy metabolic status of tumors and the efficacy of β-elemene, providing a new theoretical basis for better clinical applications in NSCLC.
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Affiliation(s)
- Yang Chen
- Department of Respiratory and Infectious Disease of Geriatrics, The First Hospital of China Medical University, 110001, Shenyang, China
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Hongfei Yan
- Department of Medical Oncology, The First Hospital of China Medical University, 110001, Shenyang, China
- Key laboratory of anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, 110001, Shenyang, China
| | - Lirong Yan
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, NO.155, North Nanjing Street, Heping District, 110001, Shenyang, China
| | - Ximing Wang
- Department of Respiratory and Infectious Disease of Geriatrics, The First Hospital of China Medical University, 110001, Shenyang, China
| | - Xiaofang Che
- Department of Medical Oncology, The First Hospital of China Medical University, 110001, Shenyang, China
- Key laboratory of anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, 110001, Shenyang, China
- Liaoning Province Clinical Research Center for Cancer, 110001, Shenyang, China
| | - Kezuo Hou
- Department of Medical Oncology, The First Hospital of China Medical University, 110001, Shenyang, China
- Key laboratory of anticancer Drugs and Biotherapy of Liaoning Province, The First Hospital of China Medical University, 110001, Shenyang, China
- Liaoning Province Clinical Research Center for Cancer, 110001, Shenyang, China
| | - Yi Yang
- Laboratory Animal Center, China Medical University, 110001, Shenyang, China
| | - Xuena Li
- Department of Nuclear Medicine, The First Hospital of China Medical University, 110001, Shenyang, China
| | - Yaming Li
- Department of Nuclear Medicine, The First Hospital of China Medical University, 110001, Shenyang, China
| | - Ye Zhang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, NO.155, North Nanjing Street, Heping District, 110001, Shenyang, China.
| | - Xuejun Hu
- Department of Respiratory and Infectious Disease of Geriatrics, The First Hospital of China Medical University, 110001, Shenyang, China.
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Yamane D, Tetsukawa R, Zenmyo N, Tabata K, Yoshida Y, Matsunaga N, Shindo N, Ojida A. Expanding the Chemistry of Dihaloacetamides as Tunable Electrophiles for Reversible Covalent Targeting of Cysteines. J Med Chem 2023. [PMID: 37393576 DOI: 10.1021/acs.jmedchem.3c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The choice of an appropriate electrophile is crucial in the design of targeted covalent inhibitors (TCIs). In this report, we systematically investigated the glutathione (GSH) reactivity of various haloacetamides and the aqueous stability of their thiol adducts. Our findings revealed that dihaloacetamides cover a broad range of GSH reactivity depending on the combination of the halogen atoms and the structure of the amine scaffold. Among the dihaloacetamides, dichloroacetamide (DCA) exhibited slightly lower GSH reactivity than chlorofluoroacetamide (CFA). The DCA-thiol adduct is readily hydrolyzed under aqueous conditions, but it can stably exist in the solvent-sequestered binding pocket of the protein. These reactivity profiles of DCA were successfully exploited in the design of TCIs targeting noncatalytic cysteines of KRASG12C and EGFRL858R/T790M. These inhibitors exhibited strong antiproliferative activities against cancer cells. Our findings provide valuable insights for designing dihaloacetamide-based reversible covalent inhibitors.
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Affiliation(s)
- Daiki Yamane
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ryo Tetsukawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoki Zenmyo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kaori Tabata
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuya Yoshida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Belcher BP, Ward CC, Nomura DK. Ligandability of E3 Ligases for Targeted Protein Degradation Applications. Biochemistry 2023; 62:588-600. [PMID: 34473924 PMCID: PMC8928483 DOI: 10.1021/acs.biochem.1c00464] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Targeted protein degradation (TPD) using proteolysis targeting chimeras (PROTACs) and molecular glue degraders has arisen as a powerful therapeutic modality for eliminating disease-causing proteins from cells. PROTACs and molecular glue degraders employ heterobifunctional or monovalent small molecules, respectively, to chemically induce the proximity of target proteins with E3 ubiquitin ligases to ubiquitinate and degrade specific proteins via the proteasome. Whereas TPD is an attractive therapeutic strategy for expanding the druggable proteome, only a relatively small number of E3 ligases out of the >600 E3 ligases encoded by the human genome have been exploited by small molecules for TPD applications. Here we review the existing E3 ligases that have thus far been successfully exploited for TPD and discuss chemoproteomics-enabled covalent screening strategies for discovering new E3 ligase recruiters. We also provide a chemoproteomic map of reactive cysteines within hundreds of E3 ligases that may represent potential ligandable sites that can be pharmacologically interrogated to uncover additional E3 ligase recruiters.
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Affiliation(s)
- Bridget P. Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Carl C. Ward
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA,correspondence to
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10
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Gilbert K, Vuorinen A, Aatkar A, Pogány P, Pettinger J, Grant EK, Kirkpatrick JM, Rittinger K, House D, Burley GA, Bush JT. Profiling Sulfur(VI) Fluorides as Reactive Functionalities for Chemical Biology Tools and Expansion of the Ligandable Proteome. ACS Chem Biol 2023; 18:285-295. [PMID: 36649130 PMCID: PMC9942091 DOI: 10.1021/acschembio.2c00633] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Here, we report a comprehensive profiling of sulfur(VI) fluorides (SVI-Fs) as reactive groups for chemical biology applications. SVI-Fs are reactive functionalities that modify lysine, tyrosine, histidine, and serine sidechains. A panel of SVI-Fs were studied with respect to hydrolytic stability and reactivity with nucleophilic amino acid sidechains. The use of SVI-Fs to covalently modify carbonic anhydrase II (CAII) and a range of kinases was then investigated. Finally, the SVI-F panel was used in live cell chemoproteomic workflows, identifying novel protein targets based on the type of SVI-F used. This work highlights how SVI-F reactivity can be used as a tool to expand the liganded proteome.
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Affiliation(s)
- Katharine
E. Gilbert
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom,University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Aini Vuorinen
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Arron Aatkar
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom,University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom
| | - Peter Pogány
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | - Jonathan Pettinger
- Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Emma K. Grant
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom
| | | | - Katrin Rittinger
- The
Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, United Kingdom
| | - David House
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom,Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom
| | - Glenn A. Burley
- University
of Strathclyde, 295 Cathedral Street, GlasgowG11XL, United Kingdom,
| | - Jacob T. Bush
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, HertfordshireSG1 2NY, United Kingdom,Crick-GSK
Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, StevenageSG1 2NY, United Kingdom,
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11
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Henning NJ, Boike L, Spradlin JN, Ward CC, Liu G, Zhang E, Belcher BP, Brittain SM, Hesse MJ, Dovala D, McGregor LM, Valdez Misiolek R, Plasschaert LW, Rowlands DJ, Wang F, Frank AO, Fuller D, Estes AR, Randal KL, Panidapu A, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Deubiquitinase-targeting chimeras for targeted protein stabilization. Nat Chem Biol 2022; 18:412-421. [PMID: 35210618 PMCID: PMC10125259 DOI: 10.1038/s41589-022-00971-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/09/2022] [Indexed: 12/12/2022]
Abstract
Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS.
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Affiliation(s)
- Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Bridget P Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthew J Hesse
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dustin Dovala
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Lynn M McGregor
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Feng Wang
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Andreas O Frank
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Daniel Fuller
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Abigail R Estes
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Katelyn L Randal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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12
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Knight S, Gianni D, Hendricks A. Fragment-based screening: A new paradigm for ligand and target discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:3-7. [PMID: 35058174 DOI: 10.1016/j.slasd.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Significant advances in fragment-based screening, including the emergence of Fully Functionalised Fragments (FFFs) and innovations in Covalent Fragment screening are providing a new paradigm for ligand and target discovery. FFFs offer some key distinct advantages over other screening modalities such as small molecules and genetic screens, including 1) An ability to access diverse chemical space employing a relatively small compound set 2) Ease of screen optimisation given there is no requirement for genetic manipulation and 3) Built-in proteomics tools to facilitate rapid target deconvolution directly in cells. Covalent fragments enable exploration of novel druggable nodes through irreversible fragment-cysteine interactions, complementing their fully functionalized counterparts. Both FFFs and Covalent fragments present the phenotypic screening community with an additional and complementary approach for disease centric target identification.
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Affiliation(s)
- Sinéad Knight
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK; Bioscience, Sygnature Discovery Ltd, Alderley Park, Cheshire, UK.
| | - Davide Gianni
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Adam Hendricks
- Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, Boston, USA; Civetta Therapeutics, 10 Wilson Road, Cambridge, MA 02140
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13
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Shindo N, Ojida A. Recent progress in covalent warheads for in vivo targeting of endogenous proteins. Bioorg Med Chem 2021; 47:116386. [PMID: 34509863 DOI: 10.1016/j.bmc.2021.116386] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/21/2023]
Abstract
Covalent drugs exert potent and durable activity by chemical modification of the endogenous target protein in vivo. To maximize the pharmacological efficacy while alleviating the risk of toxicity due to nonspecific off-target reactions, current covalent drug discovery focuses on the development of targeted covalent inhibitors (TCIs), wherein a reactive group (warhead) is strategically incorporated onto a reversible ligand of the target protein to facilitate specific covalent engagement. Various aspects of warheads, such as intrinsic reactivity, chemoselectivity, mode of reaction, and reversibility of the covalent engagement, would affect the target selectivity of TCIs. Although TCIs clinically approved to date largely rely on Michael acceptor-type electrophiles for cysteine targeting, a wide array of novel warheads have been devised and tested in TCI development in recent years. In this short review, we provide an overview of recent progress in chemistry for selective covalent targeting of proteins and their applications in TCI designs.
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Affiliation(s)
- Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan.
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14
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Fan F, Yin R, Wang L, Zhao S, Lv D, Yang K, Geng S, Yang N, Zhang X, Wang H. ALDH3A1 driving tumor metastasis is mediated by p53/BAG1 in lung adenocarcinoma. J Cancer 2021; 12:4780-4790. [PMID: 34234849 PMCID: PMC8247369 DOI: 10.7150/jca.58250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/22/2021] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a lethal malignancy with metastasis, a major tumor feature that predominantly correlated with progression, but the molecules that mediated tumor metastasis remain elusive. To declare the critical regulatory genes, RNA sequencing data in LUAD patients was acquired from The Cancer Genome Atlas (TCGA) and found that ALDH3A1 was distinctly highly expressed in LUAD patients with metastasis (M1) compared with those without metastasis (M0), linked to the property of cancer stem cell and epithelial-mesenchymal transition (EMT). Besides, high ALDH3A1 expression predicted a poor prognosis. Knockdown of ALDH3A1 showed decreased proliferation, migration, and invasion in A549 cell line. Furthermore, BAG1 was regulated by ALDH3A1 through p53, enhanced cell proliferation, and predicted clinical prognosis. Our findings collectively uncovered a novel mechanism that orchestrates tumor cells' metastasis, and decreasing ALDH3A1 represented a potential therapeutic target for reprogramming metastasis.
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Affiliation(s)
- Feifei Fan
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ruxue Yin
- Department of rheumatism and immunology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Liuya Wang
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shunxin Zhao
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Dan Lv
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Kangli Yang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Shen Geng
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Ningning Yang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xiaohong Zhang
- Department of Respiratory Medicine, Zhengzhou Central Hospital, Zhengzhou 450052, China
| | - Hongmin Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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15
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Conway LP, Li W, Parker CG. Chemoproteomic-enabled phenotypic screening. Cell Chem Biol 2021; 28:371-393. [PMID: 33577749 DOI: 10.1016/j.chembiol.2021.01.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/26/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022]
Abstract
The ID of disease-modifying, chemically accessible targets remains a central priority of modern therapeutic discovery. The phenotypic screening of small-molecule libraries not only represents an attractive approach to identify compounds that may serve as drug leads but also serves as an opportunity to uncover compounds with novel mechanisms of action (MoAs). However, a major bottleneck of phenotypic screens continues to be the ID of pharmacologically relevant target(s) for compounds of interest. The field of chemoproteomics aims to map proteome-wide small-molecule interactions in complex, native systems, and has proved a key technology to unravel the protein targets of pharmacological modulators. In this review, we discuss the application of modern chemoproteomic methods to identify protein targets of phenotypic screening hits and investigate MoAs, with a specific focus on the development of chemoproteomic-enabled compound libraries to streamline target discovery.
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Affiliation(s)
- Louis P Conway
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
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16
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Abstract
In the first decade of targeted covalent inhibition, scientists have successfully reversed the previous trend that had impeded the use of covalent inhibition in drug development. Successes in the clinic, mainly in the field of kinase inhibitors, are existing proof that safe covalent inhibitors can be designed and employed to develop effective treatments. The case of KRASG12C covalent inhibitors entering clinical trials in 2019 has been among the hottest topics discussed in drug discovery, raising expectations for the future of the field. In this perspective, an overview of the milestones hit with targeted covalent inhibitors, as well as the promise and the needs of current research, are presented. While recent results have confirmed the potential that was foreseen, many questions remain unexplored in this branch of precision medicine.
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17
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Tokunaga K, Sato M, Kuwata K, Miura C, Fuchida H, Matsunaga N, Koyanagi S, Ohdo S, Shindo N, Ojida A. Bicyclobutane Carboxylic Amide as a Cysteine-Directed Strained Electrophile for Selective Targeting of Proteins. J Am Chem Soc 2020; 142:18522-18531. [PMID: 33047956 DOI: 10.1021/jacs.0c07490] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Expanding the repertoire of electrophiles with unique reactivity features would facilitate the development of covalent inhibitors with desirable reactivity profiles. We herein introduce bicyclo[1.1.0]butane (BCB) carboxylic amide as a new class of thiol-reactive electrophiles for selective and irreversible inhibition of targeted proteins. We first streamlined the synthetic routes to generate a variety of BCB amides. The strain-driven nucleophilic addition to BCB amides proceeded chemoselectively with cysteine thiols under neutral aqueous conditions, the rate of which was significantly slower than that of acrylamide. This reactivity profile of BCB amide was successfully exploited to develop covalent ligands targeting Bruton's tyrosine kinase (BTK). By tuning BCB amide reactivity and optimizing its disposition on the ligand, we obtained a selective covalent inhibitor of BTK. The in-gel activity-based protein profiling and mass spectrometry-based chemical proteomics revealed that the selected BCB amide had a higher target selectivity for BTK in human cells than did a Michael acceptor probe. Further chemical proteomic study revealed that BTK probes bearing different classes of electrophiles exhibited distinct off-target profiles. This result suggests that incorporation of BCB amide as a cysteine-directed electrophile could expand the capability to develop covalent inhibitors with the desired proteome reactivity profile.
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Affiliation(s)
- Keisuke Tokunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mami Sato
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furocho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Chizuru Miura
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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18
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Design and Applications of Bifunctional Small Molecules in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140534. [PMID: 32871274 DOI: 10.1016/j.bbapap.2020.140534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/17/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
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19
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Perez M, Bak DW, Bergholtz SE, Crooks DR, Arimilli BS, Yang Y, Weerapana E, Linehan WM, Meier JL. Heterogeneous adaptation of cysteine reactivity to a covalent oncometabolite. J Biol Chem 2020; 295:13410-13418. [PMID: 32820045 DOI: 10.1074/jbc.ac120.014993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
An important context in which metabolism influences tumorigenesis is the genetic cancer syndrome hereditary leiomyomatosis and renal cell carcinoma (HLRCC), a disease in which mutation of the tricarboxylic acid cycle enzyme fumarate hydratase (FH) causes hyperaccumulation of fumarate. This electrophilic oncometabolite can alter gene activity at the level of transcription, via reversible inhibition of epigenetic dioxygenases, as well as posttranslationally, via covalent modification of cysteine residues. To better understand the potential for metabolites to influence posttranslational modifications important to tumorigenesis and cancer cell growth, here we report a chemoproteomic analysis of a kidney-derived HLRCC cell line. Using a general reactivity probe, we generated a data set of proteomic cysteine residues sensitive to the reduction in fumarate levels caused by genetic reintroduction of active FH into HLRCC cell lines. This revealed a broad up-regulation of cysteine reactivity upon FH rescue, which evidence suggests is caused by an approximately equal proportion of transcriptional and posttranslational modification-mediated regulation. Gene ontology analysis highlighted several new targets and pathways potentially modulated by FH mutation. Comparison of the new data set with prior studies highlights considerable heterogeneity in the adaptive response of cysteine-containing proteins in different models of HLRCC. This is consistent with emerging studies indicating the existence of cell- and tissue-specific cysteine-omes, further emphasizing the need for characterization of diverse models. Our analysis provides a resource for understanding the proteomic adaptation to fumarate accumulation and a foundation for future efforts to exploit this knowledge for cancer therapy.
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Affiliation(s)
- Minervo Perez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | - Sarah E Bergholtz
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Bhargav Srinivas Arimilli
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Youfeng Yang
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.
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20
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Craven GB, Affron DP, Kösel T, Wong TLM, Jukes ZH, Liu CT, Morgan RML, Armstrong A, Mann DJ. Multiparameter Kinetic Analysis for Covalent Fragment Optimization by Using Quantitative Irreversible Tethering (qIT). Chembiochem 2020; 21:3417-3422. [PMID: 32659037 PMCID: PMC7754465 DOI: 10.1002/cbic.202000457] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 12/23/2022]
Abstract
Chemical probes that covalently modify cysteine residues in a protein‐specific manner are valuable tools for biological investigations. Covalent fragments are increasingly implemented as probe starting points, but the complex relationship between fragment structure and binding kinetics makes covalent fragment optimization uniquely challenging. We describe a new technique in covalent probe discovery that enables data‐driven optimization of covalent fragment potency and selectivity. This platform extends beyond the existing repertoire of methods for identifying covalent fragment hits by facilitating rapid multiparameter kinetic analysis of covalent structure–activity relationships through the simultaneous determination of Ki, kinact and intrinsic reactivity. By applying this approach to develop novel probes against electrophile‐sensitive kinases, we showcase the utility of the platform in hit identification and highlight how multiparameter kinetic analysis enabled a successful fragment‐merging strategy.
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Affiliation(s)
- Gregory B Craven
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.,Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Dominic P Affron
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Teresa Kösel
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Tsz Lam M Wong
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Zoë H Jukes
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Chun-Ting Liu
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Rhodri M L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - David J Mann
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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21
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Ding M, Tegel H, Sivertsson Å, Hober S, Snijder A, Ormö M, Strömstedt PE, Davies R, Holmberg Schiavone L. Secretome-Based Screening in Target Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:535-551. [PMID: 32425085 PMCID: PMC7309359 DOI: 10.1177/2472555220917113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022]
Abstract
Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.
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Affiliation(s)
- Mei Ding
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Hanna Tegel
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Sivertsson
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH, Royal Institute of Technology, Stockholm, Sweden
| | - Arjan Snijder
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Mats Ormö
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Per-Erik Strömstedt
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Rick Davies
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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22
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Qu Y, He Y, Yang Y, Li S, An W, Li Z, Wang X, Han Z, Qin L. ALDH3A1 acts as a prognostic biomarker and inhibits the epithelial mesenchymal transition of oral squamous cell carcinoma through IL-6/STAT3 signaling pathway. J Cancer 2020; 11:2621-2631. [PMID: 32201532 PMCID: PMC7066020 DOI: 10.7150/jca.40171] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/20/2020] [Indexed: 12/21/2022] Open
Abstract
Objectives: Aldehyde dehydrogenase 3A1 (ALDH3A1) is a member of the ALDH superfamily and its relationship with oral squamous cell carcinoma (OSCC) still unknown. In our subject, we aimed to reveal the expression pattern and clinical value of ALDH3A1 in OSCC and its biological function in OSCC cell lines. Materials and methods: The expression level of ALDH3A1 in paired OSCC tissues and adjacent noncancerous tissues were detected by quantitative real-time PCR, Western blot and immunohistochemistry. The relationship between ALDH3A1 expression and clinical characteristics was analyzed. Besides, cell-counting kit 8, colony formation, wound healing, transwell invasion, apoptosis and cell cycle assays were employed to assess the role of ALDH3A1 in OSCC cells. To explore the influence of ALDH3A1 on OSCC epithelial-to-mesenchymal transition (EMT), the expression of EMT markers (E-cadherin, vimentin, snail, MMP3) on OSCC cells were detected, and possible mechanisms were analyzed. Results: In OSCC tissues, ALDH3A1 was significantly decreased compared to the adjacent normal tissues. Lower ALDH3A1 expression in OSCC tissues was associated with a higher incidence of lymph node metastasis (LNM). Moreover, the overall survival of OSCC with low ALDH3A1 expression was significantly worse compared to that of OSCC with high ALDH3A1 expression. Restored expression of ALDH3A1 suppressed cell proliferation, migration and invasion in OSCC cells. Further experiments showed that ALDH3A1 might inhibit EMT in OSCC via a regulation of the IL-6/STAT3 signal pathway. Conclusion: These data indicate that ALDH3A1 may serve as a biomarker and may be developed into a novel treatment for OSCC.
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Affiliation(s)
- Yi Qu
- Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Ying He
- Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Yang Yang
- Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Shaoqing Li
- Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Wei An
- Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Zhilin Li
- Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Xue Wang
- Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Zhengxue Han
- Professor and Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
| | - Lizheng Qin
- Professor and Medical Doctor, Department of Oral and Maxillofacial & Head and Neck Oncology, Beijing Stomatological Hospital, Capital Medical University, Beijing, China, 100050
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23
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Xu J, Li X, Ding K, Li Z. Applications of Activity-Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery. Chem Asian J 2019; 15:34-41. [PMID: 31762171 DOI: 10.1002/asia.201901500] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Indexed: 01/12/2023]
Abstract
Activity-based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high-throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity-based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.
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Affiliation(s)
- Jiaqian Xu
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China.,Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong SAR, 999077, China
| | - Xiaoqian Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Ke Ding
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou City Key Laboratory of Precision Chemical Drug Development, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China
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24
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Ward CC, Kleinman JI, Brittain SM, Lee PS, Chung CYS, Kim K, Petri Y, Thomas JR, Tallarico JA, McKenna JM, Schirle M, Nomura DK. Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications. ACS Chem Biol 2019; 14:2430-2440. [PMID: 31059647 DOI: 10.1021/acschembio.8b01083] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Targeted protein degradation has arisen as a powerful strategy for drug discovery allowing the targeting of undruggable proteins for proteasomal degradation. This approach most often employs heterobifunctional degraders consisting of a protein-targeting ligand linked to an E3 ligase recruiter to ubiquitinate and mark proteins of interest for proteasomal degradation. One challenge with this approach, however, is that only a few E3 ligase recruiters currently exist for targeted protein degradation applications, despite the hundreds of known E3 ligases in the human genome. Here, we utilized activity-based protein profiling (ABPP)-based covalent ligand screening approaches to identify cysteine-reactive small-molecules that react with the E3 ubiquitin ligase RNF4 and provide chemical starting points for the design of RNF4-based degraders. The hit covalent ligand from this screen reacted with either of two zinc-coordinating cysteines in the RING domain, C132 and C135, with no effect on RNF4 activity. We further optimized the potency of this hit and incorporated this potential RNF4 recruiter into a bifunctional degrader linked to JQ1, an inhibitor of the BET family of bromodomain proteins. We demonstrate that the resulting compound CCW 28-3 is capable of degrading BRD4 in a proteasome- and RNF4-dependent manner. In this study, we have shown the feasibility of using chemoproteomics-enabled covalent ligand screening platforms to expand the scope of E3 ligase recruiters that can be exploited for targeted protein degradation applications.
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Affiliation(s)
- Carl C. Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jordan I. Kleinman
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Scott M. Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Lee
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Clive Yik Sham Chung
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Kenneth Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Yana Petri
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jason R. Thomas
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M. McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K. Nomura
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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25
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Chung CYS, Shin HR, Berdan CA, Ford B, Ward CC, Olzmann JA, Zoncu R, Nomura DK. Covalent targeting of the vacuolar H +-ATPase activates autophagy via mTORC1 inhibition. Nat Chem Biol 2019; 15:776-785. [PMID: 31285595 PMCID: PMC6641988 DOI: 10.1038/s41589-019-0308-4] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis. A major route for activating autophagy involves inhibition of the mTORC1 kinase, but current mTORC1-targeting compounds do not allow complete and selective mTORC1 blockade. Here, we have coupled screening of a covalent ligand library with activity-based protein profiling to discover EN6, a small-molecule in vivo activator of autophagy that covalently targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which activates mTORC1 via the Rag guanosine triphosphatases. EN6-mediated ATP6V1A modification decouples the v-ATPase from the Rags, leading to inhibition of mTORC1 signaling, increased lysosomal acidification and activation of autophagy. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in a lysosome-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling.
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Affiliation(s)
- Clive Yik-Sham Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Hijai R Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Charles A Berdan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Breanna Ford
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA.
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26
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Haymond A, Davis JB, Espina V. Proteomics for cancer drug design. Expert Rev Proteomics 2019; 16:647-664. [PMID: 31353977 PMCID: PMC6736641 DOI: 10.1080/14789450.2019.1650025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/26/2019] [Indexed: 12/29/2022]
Abstract
Introduction: Signal transduction cascades drive cellular proliferation, apoptosis, immune, and survival pathways. Proteins have emerged as actionable drug targets because they are often dysregulated in cancer, due to underlying genetic mutations, or dysregulated signaling pathways. Cancer drug development relies on proteomic technologies to identify potential biomarkers, mechanisms-of-action, and to identify protein binding hot spots. Areas covered: Brief summaries of proteomic technologies for drug discovery include mass spectrometry, reverse phase protein arrays, chemoproteomics, and fragment based screening. Protein-protein interface mapping is presented as a promising method for peptide therapeutic development. The topic of biosimilar therapeutics is presented as an opportunity to apply proteomic technologies to this new class of cancer drug. Expert opinion: Proteomic technologies are indispensable for drug discovery. A suite of technologies including mass spectrometry, reverse phase protein arrays, and protein-protein interaction mapping provide complimentary information for drug development. These assays have matured into well controlled, robust technologies. Recent regulatory approval of biosimilar therapeutics provides another opportunity to decipher the molecular nuances of their unique mechanisms of action. The ability to identify previously hidden protein hot spots is expanding the gamut of potential drug targets. Proteomic profiling permits lead compound evaluation beyond the one drug, one target paradigm.
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Affiliation(s)
- Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Justin B Davis
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
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27
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S-glycosylation-based cysteine profiling reveals regulation of glycolysis by itaconate. Nat Chem Biol 2019; 15:983-991. [DOI: 10.1038/s41589-019-0323-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/12/2019] [Indexed: 01/19/2023]
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28
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Spradlin JN, Hu X, Ward CC, Brittain SM, Jones MD, Ou L, To M, Proudfoot A, Ornelas E, Woldegiorgis M, Olzmann JA, Bussiere DE, Thomas JR, Tallarico JA, McKenna JM, Schirle M, Maimone TJ, Nomura DK. Harnessing the anti-cancer natural product nimbolide for targeted protein degradation. Nat Chem Biol 2019; 15:747-755. [PMID: 31209351 PMCID: PMC6592714 DOI: 10.1038/s41589-019-0304-8] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 05/08/2019] [Indexed: 12/22/2022]
Abstract
Nimbolide, a terpenoid natural product derived from the Neem tree, impairs cancer pathogenicity; however, the direct targets and mechanisms by which nimbolide exerts its effects are poorly understood. Here, we used activity-based protein profiling (ABPP) chemoproteomic platforms to discover that nimbolide reacts with a novel functional cysteine crucial for substrate recognition in the E3 ubiquitin ligase RNF114. Nimbolide impairs breast cancer cell proliferation in-part by disrupting RNF114 substrate recognition, leading to inhibition of ubiquitination and degradation of the tumor-suppressors such as p21, resulting in their rapid stabilization. We further demonstrate that nimbolide can be harnessed to recruit RNF114 as an E3 ligase in targeted protein degradation applications and show that synthetically simpler scaffolds are also capable of accessing this unique reactive site. Our study highlights the utility of ABPP platforms in uncovering unique druggable modalities accessed by natural products for cancer therapy and targeted protein degradation applications.
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Affiliation(s)
- Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Xirui Hu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Michael D Jones
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lisha Ou
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Milton To
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew Proudfoot
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | | | | | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Dirksen E Bussiere
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Jason R Thomas
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA.,Vertex Pharmaceuticals, Boston, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.,Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA. .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. .,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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29
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Ye Z, Wang F, Yan F, Wang L, Li B, Liu T, Hu F, Jiang M, Li W, Fu Z. Bioinformatic identification of candidate biomarkers and related transcription factors in nasopharyngeal carcinoma. World J Surg Oncol 2019; 17:60. [PMID: 30935420 PMCID: PMC6444505 DOI: 10.1186/s12957-019-1605-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/20/2019] [Indexed: 12/24/2022] Open
Abstract
Background The incidence of nasopharyngeal carcinoma (NPC) is rare, but a certain amount of mortality remains in NPC patients. Our study aimed to identify candidate genes as biomarkers for NPC screening, diagnosis, and therapy. Methods We investigated two microarray profile datasets GSE64634 and GSE12452 to screen the potential differentially expressed genes (DEGs) in NPC. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs were also performed. A protein-protein interaction (PPI) network of DEGs was constructed by STRING and visualized by Cytoscape software. The associated transcriptional factor regulatory network of the DEGs was also constructed. Results A total of 152 DEGs were identified from the GSE64634 and GSE12452 datasets, including 10 upregulated and 142 downregulated genes. Gene functional enrichment analysis indicated that these DEGs were enriched in the cilium movement, antimicrobial humoral response, O-glycan processing, mucosal immune response, carbohydrate transmembrane transporter activity, hormone biosynthetic process, neurotransmitter biosynthetic process, and drug metabolism-cytochrome P450 pathway. Five hub genes (DNALI1, RSPH4A, RSPH9, DNAI2, and ALDH3A1) and one significant module (score = 5.6) were obtained from the PPI network. Key transcriptional factors, such as SPI1, SIN3B, and GATA2, were identified with close interactions with these five hub DEGs from the gene-transcriptional factor network. Conclusions With the integrated bioinformatic analysis, numerous DEGs related to NPC were screened, and the hub DEGs we identified may be potential biomarkers for NPC.
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Affiliation(s)
- Zhimin Ye
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Fangzheng Wang
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Fengqin Yan
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Lei Wang
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Bin Li
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Tongxin Liu
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Fujun Hu
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Mingxiang Jiang
- Department of Radiology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Weiyang Li
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhenfu Fu
- Department of Radiation Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China. .,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, Zhejiang, China.
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30
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Liu W, Zhang Z, Zhang ZM, Hao P, Ding K, Li Z. Integrated phenotypic screening and activity-based protein profiling to reveal potential therapy targets of pancreatic cancer. Chem Commun (Camb) 2019; 55:1596-1599. [PMID: 30656306 DOI: 10.1039/c8cc08753a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pancreatic cancer has been defined as one of the most complex and challenging cancers to treat, but very few valid therapeutic targets have been identified to date. To address this issue, a 61-compound library was readily created by Ugi reaction followed by phenotypic screening, leading to the discovery of two most potent inhibitors, P21 and P26, which significantly impair BxPC-3 pancreatic cancer cell survival. A series of interacting protein hits, such as GSTO1, FAM213A, RAB6A/6B/39A and USMG5, were subsequently identified by quantitative chemoproteomics studies. The main cellular target, GSTO1, was further validated as a novel pancreatic cancer therapeutic target.
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Affiliation(s)
- Wenyan Liu
- School of Pharmacy, Jinan University; Guangzhou City Key Laboratory of Precision Chemical Drug Development; International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of People's Republic of China, 601 Huangpu Avenue West, Guangzhou, 510632, China.
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31
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Huang Z, Ogasawara D, Seneviratne UI, Cognetta AB, am Ende CW, Nason DM, Lapham K, Litchfield J, Johnson DS, Cravatt BF. Global Portrait of Protein Targets of Metabolites of the Neurotoxic Compound BIA 10-2474. ACS Chem Biol 2019; 14:192-197. [PMID: 30702848 DOI: 10.1021/acschembio.8b01097] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Clinical investigation of the fatty acid amide hydrolase (FAAH) inhibitor BIA 10-2474 resulted in serious adverse neurological events. Structurally unrelated FAAH inhibitors tested in humans have not presented safety concerns, suggesting that BIA 10-2474 has off-target activities. A recent activity-based protein profiling (ABPP) study revealed that BIA 10-2474 and one of its major metabolites inhibit multiple members of the serine hydrolase class to which FAAH belongs. Here, we extend these studies by performing a proteome-wide analysis of covalent targets of BIA 10-2474 metabolites. Using alkynylated probes for click chemistry-ABPP in human cells, we show that des-methylated metabolites of BIA 10-2474 covalently modify the conserved catalytic cysteine in aldehyde dehydrogenases, including ALDH2, which has been implicated in protecting the brain from oxidative stress-related damage. These findings indicate that BIA 10-2474 and its metabolites have the potential to inhibit multiple mechanistically distinct enzyme classes involved in nervous system function.
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Affiliation(s)
- Zhen Huang
- Medicine Design, Chemical Biology, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Daisuke Ogasawara
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Uthpala I. Seneviratne
- Medicine Design, Chemical Biology, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Armand B. Cognetta
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Christopher W. am Ende
- Medicine Design, Medicinal Chemistry, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Deane M. Nason
- Medicine Design, Medicinal Chemistry, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kimberly Lapham
- Medicine Design, Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - John Litchfield
- Medicine Design, Pharmacokinetics, Dynamics and Metabolism, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Douglas S. Johnson
- Medicine Design, Chemical Biology, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Benjamin F. Cravatt
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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32
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Craven GB, Affron DP, Raymond PN, Mann DJ, Armstrong A. Vinyl sulfonamide synthesis for irreversible tethering via a novel α-selenoether protection strategy. MEDCHEMCOMM 2019; 10:158-163. [PMID: 30774862 DOI: 10.1039/c8md00566d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/11/2018] [Indexed: 12/22/2022]
Abstract
Vinyl sulfonamides are valuable electrophiles for targeted protein modification and inhibition. We describe a novel approach to the synthesis of terminal vinyl sulfonamides which uses mild oxidative conditions to induce elimination of an α-selenoether masking group. The method complements traditional synthetic approaches and typically yields vinyl sulfonamides in high purity after aqueous work-up without requiring column chromatography of the final electrophilic product. The methodology is applied to the synthesis of covalent fragments for use in irreversible protein tethering and crucially enables the attachment of diverse fragments to the vinyl sulfonamide warhead via a chemical linker. Using thymidylate synthase as a model system, ethylene glycol is identified as an effective linker for irreversible protein tethering.
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Affiliation(s)
- Gregory B Craven
- Department of Chemistry , Imperial College London , Molecular Sciences Research Hub , White City Campus, Wood Lane , London W12 0BZ , UK .
| | - Dominic P Affron
- Department of Chemistry , Imperial College London , Molecular Sciences Research Hub , White City Campus, Wood Lane , London W12 0BZ , UK .
| | - Philip N Raymond
- Department of Chemistry , Imperial College London , Molecular Sciences Research Hub , White City Campus, Wood Lane , London W12 0BZ , UK .
| | - David J Mann
- Department of Life Sciences , Imperial College London , South Kensington Campus , London SW7 2AZ , UK
| | - Alan Armstrong
- Department of Chemistry , Imperial College London , Molecular Sciences Research Hub , White City Campus, Wood Lane , London W12 0BZ , UK .
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