1
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Chauhan P, V R, Kumar M, Molla R, Mishra SD, Basa S, Rai V. Chemical technology principles for selective bioconjugation of proteins and antibodies. Chem Soc Rev 2024; 53:380-449. [PMID: 38095227 DOI: 10.1039/d3cs00715d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.
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Affiliation(s)
- Preeti Chauhan
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Ragendu V
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Mohan Kumar
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Rajib Molla
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Surya Dev Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Sneha Basa
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
| | - Vishal Rai
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, 462 066, India.
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2
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Homer JA, Xu L, Kayambu N, Zheng Q, Choi EJ, Kim BM, Sharpless KB, Zuilhof H, Dong J, Moses JE. Sulfur fluoride exchange. NATURE REVIEWS. METHODS PRIMERS 2023; 3:58. [PMID: 38873592 PMCID: PMC11171465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Sulfur Fluoride Exchange (SuFEx) is a click reaction par excellence that has revolutionized multiple research fields. In this Primer, we delve into the essential elements of SuFEx operation, catalysis, and SuFExable connective hubs. We also explore the cutting-edge applications of SuFEx in drug development, polymer science, and biochemistry. Additionally, we examine the potential limitations and promising prospects for this versatile click reaction.
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Affiliation(s)
- Joshua A. Homer
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
| | - Long Xu
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Namitharan Kayambu
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Qinheng Zheng
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
- Current affiliation: Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Eun Joung Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Byeong Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- School of Pharmaceutical Science & Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jiajia Dong
- Institute of Translational Medicine, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - John E. Moses
- Cancer Center, Cold Spring Harbor Laboratory, 1 Bungtown Road, NY 11724, USA
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3
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Chatterjee S, Shioi R, Kool ET. Sulfonylation of RNA 2'-OH groups. ACS CENTRAL SCIENCE 2023; 9:531-539. [PMID: 36968531 PMCID: PMC10037496 DOI: 10.1021/acscentsci.2c01237] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 06/18/2023]
Abstract
The nucleophilic reactivity of RNA 2'-OH groups in water has proven broadly useful in probing, labeling, and conjugating RNA. To date, reactions selective to ribose 2'-OH have been limited to bond formation with short-lived carbonyl electrophiles. Here we report that many activated small-molecule sulfonyl species can exhibit extended lifetimes in water and retain 2'-OH reactivity. The data establish favorable aqueous solubility for selected reagents and successful RNA-selective reactions at stoichiometric and superstoichiometric yields, particularly for aryl sulfonyltriazole species. We report that the latter are considerably more stable than most prior carbon electrophiles in aqueous environments and tolerate silica chromatography. Furthermore, an azide-substituted sulfonyltriazole reagent is developed to introduce labels into RNA via click chemistry. In addition to high-yield reactions, we find that RNA sulfonylation can also be performed under conditions that give trace yields necessary for structure mapping. Like acylation, the reaction occurs with selectivity for unpaired nucleotides over those in the duplex structure, and a sulfonate adduct causes reverse transcriptase stops, suggesting potential use in RNA structure analysis. Probing of rRNA is demonstrated in human cells, indicating possible cell permeability. The sulfonyl reagent class enables a new level of control, selectivity, versatility, and ease of preparation for RNA applications.
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Affiliation(s)
- Sayantan Chatterjee
- Department of Chemistry, Stanford
University, Stanford, California 94305, United States
| | - Ryuta Shioi
- Department of Chemistry, Stanford
University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford
University, Stanford, California 94305, United States
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4
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Carneiro SN, Khasnavis SR, Lee J, Butler TW, Majmudar JD, Am Ende CW, Ball ND. Sulfur(VI) fluorides as tools in biomolecular and medicinal chemistry. Org Biomol Chem 2023; 21:1356-1372. [PMID: 36662157 PMCID: PMC9929716 DOI: 10.1039/d2ob01891h] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023]
Abstract
Recent advances in the synthesis of sulfur(VI)-fluorides has enabled incredible growth in their application in biomolecular chemistry. This review aims to serve as a primer highlighting synthetic strategies toward a diversity of S(VI) fluorides and their application in chemical biology, bioconjugation, and medicinal chemistry.
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Affiliation(s)
- Sabrina N Carneiro
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
| | - Samuel R Khasnavis
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
| | - Jisun Lee
- Pfizer Worldwide Research, Development, Groton, Connecticut 06340, USA.
| | - Todd W Butler
- Pfizer Worldwide Research, Development, Groton, Connecticut 06340, USA.
| | - Jaimeen D Majmudar
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, USA
| | | | - Nicholas D Ball
- Department of Chemistry, Pomona College, Claremont, California 91711, USA.
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5
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Chemical and biology of Sulfur (VI) Fluoride Exchange (SuFEx) Click Chemistry for Drug Discovery. Bioorg Chem 2022; 130:106227. [DOI: 10.1016/j.bioorg.2022.106227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/05/2022] [Accepted: 10/22/2022] [Indexed: 11/19/2022]
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6
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Yang T, Cuesta A, Wan X, Craven GB, Hirakawa B, Khamphavong P, May JR, Kath JC, Lapek JD, Niessen S, Burlingame AL, Carelli JD, Taunton J. Reversible lysine-targeted probes reveal residence time-based kinase selectivity. Nat Chem Biol 2022; 18:934-941. [PMID: 35590003 PMCID: PMC9970282 DOI: 10.1038/s41589-022-01019-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 03/23/2022] [Indexed: 12/21/2022]
Abstract
The expansion of the target landscape of covalent inhibitors requires the engagement of nucleophiles beyond cysteine. Although the conserved catalytic lysine in protein kinases is an attractive candidate for a covalent approach, selectivity remains an obvious challenge. Moreover, few covalent inhibitors have been shown to engage the kinase catalytic lysine in animals. We hypothesized that reversible, lysine-targeted inhibitors could provide sustained kinase engagement in vivo, with selectivity driven in part by differences in residence time. By strategically linking benzaldehydes to a promiscuous kinase binding scaffold, we developed chemoproteomic probes that reversibly and covalently engage >200 protein kinases in cells and mice. Probe-kinase residence time was dramatically enhanced by a hydroxyl group ortho to the aldehyde. Remarkably, only a few kinases, including Aurora A, showed sustained, quasi-irreversible occupancy in vivo, the structural basis for which was revealed by X-ray crystallography. We anticipate broad application of salicylaldehyde-based probes to proteins that lack a druggable cysteine.
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Affiliation(s)
- Tangpo Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Xiaobo Wan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States,Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Gregory B. Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158 United States
| | - Brad Hirakawa
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Penney Khamphavong
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Jeffrey R. May
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - John C. Kath
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - John D. Lapek
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Sherry Niessen
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jordan D. Carelli
- Pfizer Global Research and Development La Jolla, San Diego, California 92121, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
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7
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Mingione VR, Foda Z, Paung Y, Philipose H, Rangwala AM, Shan Y, Seeliger MA. Validation of an allosteric binding site of Src kinase identified by unbiased ligand binding simulations. J Mol Biol 2022; 434:167628. [PMID: 35595169 DOI: 10.1016/j.jmb.2022.167628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
Abstract
Allostery plays a primary role in regulating protein activity, making it an important mechanism in human disease and drug discovery. Identifying allosteric regulatory sites to explore their biological significance and therapeutic potential is invaluable to drug discovery; however, identification remains a challenge. Allosteric sites are often "cryptic" without clear geometric or chemical features. Since allosteric regulatory sites are often less conserved in protein kinases than the orthosteric ATP binding site, allosteric ligands are commonly more specific than ATP competitive inhibitors. We present a generalizable computational protocol to predict allosteric ligand binding sites based on unbiased ligand binding simulation trajectories. We demonstrate the feasibility of this protocol by revisiting our previously published ligand binding simulations using the first identified viral proto-oncogene, Src kinase, as a model system. The binding paths for kinase inhibitor PP1 uncovered three metastable intermediate states before binding the high-affinity ATP-binding pocket, revealing two previously known allosteric sites and one novel site. Herein, we validate the novel site using a combination of virtual screening and experimental assays to identify a v-type allosteric small-molecule inhibitor that targets this novel site with specificity for Src over closely related kinases. This study provides a proof-of-concept for employing unbiased ligand binding simulations to identify cryptic allosteric binding sites and is widely applicable to other protein-ligand systems.
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Affiliation(s)
- Victoria R Mingione
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Zachariah Foda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - YiTing Paung
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hannah Philipose
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Aziz M Rangwala
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yibing Shan
- Antidote Health Foundation for Cure of Cancer, Cambridge, MA 02139, USA.
| | - Markus A Seeliger
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA.
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8
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Yamanushkin P, Kaya K, Feliciano MAM, Gold B. SuFExable NH-Pyrazoles via 1,3-Dipolar Cycloadditions of Diazo Compounds with Bromoethenylsulfonyl Fluoride. J Org Chem 2022; 87:3868-3873. [PMID: 35143195 DOI: 10.1021/acs.joc.1c03105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
"Click" reactions have transformed the molecular sciences. Augmenting cycloaddition reactions, sulfur(VI) fluoride exchange (SuFEx) chemistry has diversified the landscape of molecular assembly. Herein, we report a facile strategy to access SuFExable NH-pyrazoles via strain and catalyst-free 1,3-dipolar cycloadditions of stabilized diazo compounds under mild conditions. Subsequent SuFEx proceeds efficiently with various N- and O-nucleophiles. Access to SuFExable NH-pyrazoles─a class of compounds containing two common pharmacophores─enables future opportunities within drug discovery, chemical biology, materials chemistry, and related fields.
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Affiliation(s)
- Pavel Yamanushkin
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Kemal Kaya
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States.,Department of Biochemistry, Kütahya Dumlupınar University, 43100 Kütahya, Turkey
| | - Mark Aldren M Feliciano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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9
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Ma Z, Shan L, Ma X, Hu X, Guo Y, Chen QY, Liu C. Arenesulfonyl fluoride synthesis via one-pot copper-free Sandmeyer-type three-component reaction of aryl amine, K2S2O5, and NFSI. J Fluor Chem 2022. [DOI: 10.1016/j.jfluchem.2022.109948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Structural insights into the potency and selectivity of covalent pan-FGFR inhibitors. Commun Chem 2022; 5:5. [PMID: 36697561 PMCID: PMC9814232 DOI: 10.1038/s42004-021-00623-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 12/22/2021] [Indexed: 01/28/2023] Open
Abstract
FIIN-2, TAS-120 (Futibatinib) and PRN1371 are highly potent pan-FGFR covalent inhibitors targeting the p-loop cysteine of FGFR proteins, of which TAS-120 and PRN1371 are currently in clinical trials. It is critical to analyze their target selectivity and their abilities to overcome gatekeeper mutations. In this study, we demonstrate that FIIN-2 and TAS-120 form covalent adducts with SRC, while PRN1371 does not. FIIN-2 and TAS-120 inhibit SRC and YES activities, while PRN1371 does not. Moreover, FIIN-2, TAS-120 and PRN1371 exhibit different potencies against different FGFR gatekeeper mutants. In addition, the co-crystal structures of SRC/FIIN-2, SRC/TAS-120 and FGFR4/PRN1371 complexes reveal structural basis for kinase targeting and gatekeeper mutations. Taken together, our study not only provides insight into the potency and selectivity of covalent pan-FGFR inhibitors, but also sheds light on the development of next-generation FGFR covalent inhibitors with high potency, high selectivity, and stronger ability to overcome gatekeeper mutations.
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11
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Chen X, Huang Y, Xu W, Cai Y, Yang Y. 4-Aminopyrazolopyrimidine scaffold and its deformation in the design of tyrosine and serine/threonine kinase inhibitors in medicinal chemistry. RSC Med Chem 2022; 13:1008-1028. [DOI: 10.1039/d2md00139j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/08/2022] [Indexed: 11/21/2022] Open
Abstract
Deformation of the 4-aminopyrazolopyrimidine scaffold in designing small-molecule inhibitors.
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Affiliation(s)
- Xiaolu Chen
- Department of Pharmacy, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Yajiao Huang
- Department of Pharmacy, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
| | - Wanghan Xu
- Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou 311202, Zhejiang, P. R. China
| | - Yuepiao Cai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yuanrong Yang
- Department of Pharmacy, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, Hubei 434020, China
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12
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Ferlenghi F, Scalvini L, Vacondio F, Castelli R, Bozza N, Marseglia G, Rivara S, Lodola A, La Monica S, Minari R, Petronini PG, Alfieri R, Tiseo M, Mor M. A sulfonyl fluoride derivative inhibits EGFR L858R/T790M/C797S by covalent modification of the catalytic lysine. Eur J Med Chem 2021; 225:113786. [PMID: 34464874 DOI: 10.1016/j.ejmech.2021.113786] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
The emergence of the C797S mutation in EGFR is a frequent mechanism of resistance to osimertinib in the treatment of non-small cell lung cancer (NSCLC). In the present work, we report the design, synthesis and biochemical characterization of UPR1444 (compound 11), a new sulfonyl fluoride derivative which potently and irreversibly inhibits EGFRL858R/T790M/C797S through the formation of a sulfonamide bond with the catalytic residue Lys745. Enzymatic assays show that compound 11 displayed an inhibitory activity on EGFRWT comparable to that of osimertinib, and it resulted more selective than the sulfonyl fluoride probe XO44, recently reported to inhibit a significant part of the kinome. Neither compound 11 nor XO44 inhibited EGFRdel19/T790M/C797S triple mutant. When tested in Ba/F3 cells expressing EGFRL858R/T790M/C797S, compound 11 resulted significantly more potent than osimertinib at inhibiting both EGFR autophosphorylation and proliferation, even if the inhibition of EGFR autophosphorylation by compound 11 in Ba/F3 cells was not long lasting.
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Affiliation(s)
| | - Laura Scalvini
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Nicole Bozza
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | - Silvia Rivara
- Department of Food and Drug, University of Parma, Parma, Italy
| | - Alessio Lodola
- Department of Food and Drug, University of Parma, Parma, Italy.
| | - Silvia La Monica
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Roberta Minari
- Medical Oncology, University Hospital of Parma, Parma, Italy
| | | | - Roberta Alfieri
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Marcello Tiseo
- Department of Medicine and Surgery, University of Parma, Parma, Italy; Medical Oncology, University Hospital of Parma, Parma, Italy
| | - Marco Mor
- Department of Food and Drug, University of Parma, Parma, Italy
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13
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Cu-catalyzed endo-selective asymmetric 1,3-dipolar cycloaddition of azomethine ylides with ethenesulfonyl fluorides: Efficient access to chiral pyrrolidine-3-sulfonyl fluorides. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.05.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Dong X, Jiang W, Hua D, Wang X, Xu L, Wu X. Radical-mediated vicinal addition of alkoxysulfonyl/fluorosulfonyl and trifluoromethyl groups to aryl alkyl alkynes. Chem Sci 2021; 12:11762-11768. [PMID: 34659713 PMCID: PMC8442677 DOI: 10.1039/d1sc03315h] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/02/2021] [Indexed: 12/18/2022] Open
Abstract
The addition of sulfonyl radicals to alkenes and alkynes is a valuable method for constructing useful highly functionalized sulfonyl compounds. The underexplored alkoxy- and fluorosulfonyl radicals are easily accessed by CF3 radical addition to readily available allylsulfonic acid derivatives and then β-fragmentation. These substituted sulfonyl radicals add to aryl alkyl alkynes to give vinyl radicals that are trapped by trifluoromethyl transfer to provide tetra-substituted alkenes bearing the privileged alkoxy- or fluorosulfonyl group on one carbon and a trifluoromethyl group on the other. This process exhibits broad functional group compatibility and allows for the late-stage functionalization of drug molecules, demonstrating its potential in drug discovery and chemical biology. An unprecedented method for vicinal addition of alkoxysulfonyl/fluorosulfonyl and trifluoromethyl groups to aryl alkyl alkynes has been developed to afford useful alkenylsulfonate esters and alkenylsulfonyl fluorides.![]()
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Affiliation(s)
- Xinrui Dong
- State Key Laboratory of Natural Medicines, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University Nanjing 211198 China
| | - Wenhua Jiang
- State Key Laboratory of Natural Medicines, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University Nanjing 211198 China
| | - Dexiang Hua
- State Key Laboratory of Natural Medicines, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University Nanjing 211198 China
| | - Xiaohui Wang
- State Key Laboratory of Natural Medicines, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University Nanjing 211198 China
| | - Liang Xu
- School of Chemistry and Chemical Engineering, Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University Shihezi 832003 China
| | - Xiaoxing Wu
- State Key Laboratory of Natural Medicines, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University Nanjing 211198 China
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15
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Concomitant use of a dual Src/ABL kinase inhibitor eliminates the in vitro efficacy of blinatumomab against Ph+ ALL. Blood 2021; 137:939-944. [PMID: 32898857 DOI: 10.1182/blood.2020005655] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
Blinatumomab is currently approved for use as a single agent in relapsed and refractory acute lymphoblastic leukemia (ALL). Cytotoxicity is mediated via signaling through the T-cell receptor (TCR). There is now much interest in combining blinatumomab with targeted therapies, particularly in Philadelphia chromosome-positive ALL (Ph+ ALL). However, some second- and third-generation ABL inhibitors also potently inhibit Src family kinases that are important in TCR signaling. We combined ABL inhibitors and dual Src/ABL inhibitors with blinatumomab in vitro from both healthy donor samples and primary samples from patients with Ph+ ALL. Blinatumomab alone led to both T-cell proliferation and elimination of target CD19+ cells and enhanced production of interferon-γ (IFN-γ). The addition of the ABL inhibitors imatinib or nilotinib to blinatumomab did not inhibit T-cell proliferation or IFN-γ production. However, the addition of dasatinib or ponatinib inhibited T-cell proliferation and IFN-γ production. Importantly, there was no loss of CD19+ cells treated with blinatumomab plus dasatinib or ponatinib in healthy samples or samples with a resistant ABL T315I mutation by dasatinib in combination with blinatumomab. These in vitro findings bring pause to the excitement of combination therapies, highlighting the importance of maintaining T-cell function with targeted therapies.
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16
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Liu Y, Lv S, Peng L, Xie C, Gao L, Sun H, Lin L, Ding K, Li Z. Development and application of novel electrophilic warheads in target identification and drug discovery. Biochem Pharmacol 2021; 190:114636. [PMID: 34062128 DOI: 10.1016/j.bcp.2021.114636] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
Nucleophilic amino acids play important roles in maintenance of protein structure and function, covalent modification of such amino acid residues by therapeutic agents is an efficient way to treat human diseases. Most of current clinical drugs are structurally limited to α,β-unsaturated amide as an electrophilic warhead. To alleviate this issue, many novel electrophiles have been developed in recent years that can covalently bind to different amino acid residues and provides a unique way to interrogate proteins, including "undruggable" targets. With an activity-based protein profiling (ABPP) approach, the activity and functionality of a protein and its binding sites can be assessed. This facilitates an understanding of protein function, and contributes to the discovery of new druggable targets and lead compounds. Meanwhile, many novel inhibitors bearing new reactive warhead were developed and displayed remarkable pharmaceutical properties. In this perspective, we have reviewed the recent remarkable progress of novel electrophiles and their applications in target identification and drug discovery.
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Affiliation(s)
- Yue Liu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shumin Lv
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Lijie Peng
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Chengliang Xie
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou 510000, China
| | - Liqian Gao
- School of Pharmaceutical Science (Shenzhen), Sun Yat-sen University, Guangzhou 510000, China
| | - Hongyan Sun
- Department of Chemistry, City University of Hong Kong, Hong Kong 999077, China
| | - Ligen Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China.
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China; MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China.
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17
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Structural insights into redox-active cysteine residues of the Src family kinases. Redox Biol 2021; 41:101934. [PMID: 33765616 PMCID: PMC8022254 DOI: 10.1016/j.redox.2021.101934] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/18/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022] Open
Abstract
The Src Family Kinases (SFKs) are pivotal regulators of cellular signal transduction and highly sought-after targets in drug discovery. Their actions within cells are controlled by alterations in protein phosphorylation that switch the SFKs from autoinhibited to active states. The SFKs are also well recognized to contain redox-active cysteine residues where oxidation of certain residues directly contribute to kinase function. To more completely understand the factors that influence cysteine oxidation within the SFKs, a review is presented of the local structural environments surrounding SFK cysteine residues compared to their quantified oxidation in vivo from the Oximouse database. Generally, cysteine local structure and degree of redox sensitivity vary with respect to sequence conservation. Cysteine residues found in conserved positions are more mildly redox-active as they are found in hydrophobic environments and not fully exposed to solvent. Non-conserved redox-active cysteines are generally the most reactive with direct solvent access and/or in hydrophilic environments. Results from this analysis motivate future efforts to conduct comprehensive proteome-wide analysis of redox-sensitivity, conservation, and local structural environments of proteins containing reactive cysteine residues.
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18
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Watanabe T, Abe H, Shibasaki M. Catalytic Asymmetric Total Synthesis of Leucinostatin A. CHEM REC 2020; 21:175-187. [PMID: 33107684 DOI: 10.1002/tcr.202000108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/05/2020] [Indexed: 12/30/2022]
Abstract
This review describes our efforts toward achieving catalytic asymmetric total synthesis of leucinostatin A, a compound that interferes with the tumor-stroma interaction. The synthesis utilizes four catalytic asymmetric reactions, including direct-type reactions exemplified by high atom-economy, and three C-C bond forming reactions. Thorough analysis of the NMR data, HPLC profiles, and biologic activity led us to unambiguously revise the absolute configuration regarding the 6-position of the AHMOD residue side chain from S (reported) to R. Other examples of previously reported important studies on the stereoselective synthesis of HyLeu and AHMOD are also described.
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Affiliation(s)
- Takumi Watanabe
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Hikaru Abe
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
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19
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Alvarez Dorta D, Deniaud D, Mével M, Gouin SG. Tyrosine Conjugation Methods for Protein Labelling. Chemistry 2020; 26:14257-14269. [DOI: 10.1002/chem.202001992] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/09/2020] [Indexed: 12/23/2022]
Affiliation(s)
| | - David Deniaud
- CNRS, CEISAM UMR, 6230 Université de Nantes 44000 Nantes France
| | - Mathieu Mével
- CHU de Nantes, INSERM UMR 1089 Université de Nantes 44200 Nantes France
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20
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Zhong T, Pang MK, Chen ZD, Zhang B, Weng J, Lu G. Copper-free Sandmeyer-type Reaction for the Synthesis of Sulfonyl Fluorides. Org Lett 2020; 22:3072-3078. [DOI: 10.1021/acs.orglett.0c00823] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tao Zhong
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Meng-Ke Pang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Zhi-Da Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Bin Zhang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Jiang Weng
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Gui Lu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
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21
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Parker CG, Pratt MR. Click Chemistry in Proteomic Investigations. Cell 2020; 180:605-632. [PMID: 32059777 PMCID: PMC7087397 DOI: 10.1016/j.cell.2020.01.025] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/09/2020] [Accepted: 01/16/2020] [Indexed: 01/20/2023]
Abstract
Despite advances in genetic and proteomic techniques, a complete portrait of the proteome and its complement of dynamic interactions and modifications remains a lofty, and as of yet, unrealized, objective. Specifically, traditional biological and analytical approaches have not been able to address key questions relating to the interactions of proteins with small molecules, including drugs, drug candidates, metabolites, or protein post-translational modifications (PTMs). Fortunately, chemists have bridged this experimental gap through the creation of bioorthogonal reactions. These reactions allow for the incorporation of chemical groups with highly selective reactivity into small molecules or protein modifications without perturbing their biological function, enabling the selective installation of an analysis tag for downstream investigations. The introduction of chemical strategies to parse and enrich subsets of the "functional" proteome has empowered mass spectrometry (MS)-based methods to delve more deeply and precisely into the biochemical state of cells and its perturbations by small molecules. In this Primer, we discuss how one of the most versatile bioorthogonal reactions, "click chemistry", has been exploited to overcome limitations of biological approaches to enable the selective marking and functional investigation of critical protein-small-molecule interactions and PTMs in native biological environments.
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Affiliation(s)
- Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Matthew R Pratt
- Departments of Chemistry and Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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22
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Dalton SE, Campos S. Covalent Small Molecules as Enabling Platforms for Drug Discovery. Chembiochem 2020; 21:1080-1100. [DOI: 10.1002/cbic.201900674] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel E. Dalton
- Astex Pharmaceuticals 436 Cambridge Science Park Milton Road Cambridge CB4 0QA UK
| | - Sebastien Campos
- PharmaronDrug Discovery Services Europe Hertford Road Hoddesdon Hertfordshire EN11 9BU UK
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23
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Cuesta A, Wan X, Burlingame AL, Taunton J. Ligand Conformational Bias Drives Enantioselective Modification of a Surface-Exposed Lysine on Hsp90. J Am Chem Soc 2020; 142:3392-3400. [DOI: 10.1021/jacs.9b09684] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Xiaobo Wan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
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24
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Tsukidate T, Li Q, Hang HC. Targeted and proteome-wide analysis of metabolite-protein interactions. Curr Opin Chem Biol 2020; 54:19-27. [PMID: 31790852 PMCID: PMC7131882 DOI: 10.1016/j.cbpa.2019.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 12/31/2022]
Abstract
Understanding the molecular mechanisms of endogenous and environmental metabolites is crucial for basic biology and drug discovery. With the genome, proteome, and metabolome of many organisms being readily available, researchers now have the opportunity to dissect how key metabolites regulate complex cellular pathways in vivo. Nonetheless, characterizing the specific and functional protein targets of key metabolites associated with specific cellular phenotypes remains a major challenge. Innovations in chemical biology are now poised to address this fundamental limitation in physiology and disease. In this review, we highlight recent advances in chemoproteomics for targeted and proteome-wide analysis of metabolite-protein interactions that have enabled the discovery of unpredicted metabolite-protein interactions and facilitated the development of new small molecule therapeutics.
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Affiliation(s)
- Taku Tsukidate
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, United States
| | - Qiang Li
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, United States
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY, 10065, United States.
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25
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Chen J, Huang BQ, Wang ZQ, Zhang XJ, Yan M. Asymmetric Conjugate Addition of Ethylene Sulfonyl Fluorides to 3-Amido-2-oxindoles: Synthesis of Chiral Spirocyclic Oxindole Sultams. Org Lett 2019; 21:9742-9746. [DOI: 10.1021/acs.orglett.9b03911] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Jie Chen
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Bao-qin Huang
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zeng-qing Wang
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xue-jing Zhang
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ming Yan
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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26
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Leng J, Alharbi NS, Qin HL. Construction of α-(Hetero)aryl Ethenesulfonyl Fluorides for SuFEx Click Chemistry. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jing Leng
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Njud S. Alharbi
- Biotechnology Research group; Deportment of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Hua-Li Qin
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
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27
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Charoenpattarapreeda J, Tan YS, Iegre J, Walsh SJ, Fowler E, Eapen RS, Wu Y, Sore HF, Verma CS, Itzhaki L, Spring DR. Targeted covalent inhibitors of MDM2 using electrophile-bearing stapled peptides. Chem Commun (Camb) 2019; 55:7914-7917. [PMID: 31225847 DOI: 10.1039/c9cc04022f] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, we describe the development of a novel staple with an electrophilic warhead to enable the generation of stapled peptide covalent inhibitors of the p53-MDM2 protein-protein interaction (PPI). The peptide developed showed complete and selective covalent binding resulting in potent inhibition of p53-MDM2 PPI.
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Affiliation(s)
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Jessica Iegre
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Stephen J Walsh
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Elaine Fowler
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Rohan S Eapen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Yuteng Wu
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Hannah F Sore
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore and Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore and School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 673551, Singapore
| | - Laura Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
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28
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Huang YM, Wang SM, Leng J, Moku B, Zhao C, Alharbi NS, Qin HL. Converting (E)-(Hetero)arylethanesulfonyl Fluorides to (Z)-(Hetero)arylethanesulfonyl Fluorides Under Light Irradiation. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900799] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yu-Mei Huang
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Shi-Meng Wang
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Jing Leng
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Balakrishna Moku
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Chuang Zhao
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Njud S. Alharbi
- Biotechnology Research group; Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Hua-Li Qin
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
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29
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David AHG, García-Cerezo P, Campaña AG, Santoyo-González F, Blanco V. [2]Rotaxane End-Capping Synthesis by Click Michael-Type Addition to the Vinyl Sulfonyl Group. Chemistry 2019; 25:6170-6179. [PMID: 30762912 DOI: 10.1002/chem.201900156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Indexed: 01/23/2023]
Abstract
We report the application of the click Michael-type addition reaction to vinyl sulfone or vinyl sulfonate groups in the synthesis of rotaxanes through the threading-and-capping method. This methodology has proven to be efficient and versatile as it allowed the preparation of rotaxanes using template approaches based on different noncovalent interactions (i.e., donor-acceptor π-π interactions or hydrogen bonding) in yields of generally 60-80 % and up to 91 % aided by the mild conditions required (room temperature or 0 °C and a mild base such as Et3 N or 4-(N,N-dimethylamino)pyridine (DMAP)). Furthermore, the use of vinyl sulfonate moieties, which are suitable motifs for coupling-and-decoupling (CAD) chemistry, implies another advantage because it allows the controlled chemical disassembly of the rotaxanes into their components through nucleophilic substitution of the sulfonates resulting from the capping step with a thiol under mild conditions (Cs2 CO3 and room temperature).
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Affiliation(s)
- Arthur H G David
- Departamento de Química Orgánica, Universidad de Granada, Facultad de Ciencias, Avda. Fuente Nueva, S/N, 18071, Granada, Spain
| | - Pablo García-Cerezo
- Departamento de Química Orgánica, Universidad de Granada, Facultad de Ciencias, Avda. Fuente Nueva, S/N, 18071, Granada, Spain
| | - Araceli G Campaña
- Departamento de Química Orgánica, Universidad de Granada, Facultad de Ciencias, Avda. Fuente Nueva, S/N, 18071, Granada, Spain
| | - Francisco Santoyo-González
- Departamento de Química Orgánica, Universidad de Granada, Facultad de Ciencias, Avda. Fuente Nueva, S/N, 18071, Granada, Spain
| | - Victor Blanco
- Departamento de Química Orgánica, Universidad de Granada, Facultad de Ciencias, Avda. Fuente Nueva, S/N, 18071, Granada, Spain
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30
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Abstract
Covalent inhibitors are widely used in drug discovery and chemical biology. Although covalent inhibitors are frequently designed to react with noncatalytic cysteines, many ligand binding sites lack an accessible cysteine. Here, we review recent advances in the chemical biology of lysine-targeted covalent inhibitors and chemoproteomic probes. By analyzing crystal structures of proteins bound to common metabolites and enzyme cofactors, we identify a large set of mostly unexplored lysines that are potentially targetable with covalent inhibitors. In addition, we describe mass spectrometry-based approaches for determining proteome-wide lysine ligandability and lysine-reactive chemoproteomic probes for assessing drug-target engagement. Finally, we discuss the design of amine-reactive inhibitors that form reversible covalent bonds with their protein targets.
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Affiliation(s)
- Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA; ,
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA; ,
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31
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Barrow AS, Smedley CJ, Zheng Q, Li S, Dong J, Moses JE. The growing applications of SuFEx click chemistry. Chem Soc Rev 2019; 48:4731-4758. [DOI: 10.1039/c8cs00960k] [Citation(s) in RCA: 181] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
SuFEx (Sulfur Fluoride Exchange) is a modular, next generation family of click reactions, geared towards the rapid and reliable assembly of functional molecules.
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Affiliation(s)
- A. S. Barrow
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - C. J. Smedley
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
| | - Q. Zheng
- Department of Chemistry
- The Scripps Research Institute
- La Jolla
- USA
| | - S. Li
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou 510275
- P. R. China
| | - J. Dong
- Key Laboratory of Organofluorine Chemistry
- Center for Excellence in Molecular Synthesis
- Shanghai Institute of Organic Chemistry
- University of Chinese Academy of Sciences
- Chinese Academy of Sciences
| | - J. E. Moses
- La Trobe Institute for Molecular Science
- La Trobe University
- Melbourne
- Australia
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32
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Heppner DE, Dustin CM, Liao C, Hristova M, Veith C, Little AC, Ahlers BA, White SL, Deng B, Lam YW, Li J, van der Vliet A. Direct cysteine sulfenylation drives activation of the Src kinase. Nat Commun 2018; 9:4522. [PMID: 30375386 PMCID: PMC6207713 DOI: 10.1038/s41467-018-06790-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/19/2018] [Indexed: 01/17/2023] Open
Abstract
The Src kinase controls aspects of cell biology and its activity is regulated by intramolecular structural changes induced by protein interactions and tyrosine phosphorylation. Recent studies indicate that Src is additionally regulated by redox-dependent mechanisms, involving oxidative modification(s) of cysteines within the Src protein, although the nature and molecular-level impact of Src cysteine oxidation are unknown. Using a combination of biochemical and cell-based studies, we establish the critical importance of two Src cysteine residues, Cys-185 and Cys-277, as targets for H2O2-mediated sulfenylation (Cys-SOH) in redox-dependent kinase activation in response to NADPH oxidase-dependent signaling. Molecular dynamics and metadynamics simulations reveal the structural impact of sulfenylation of these cysteines, indicating that Cys-277-SOH enables solvent exposure of Tyr-416 to promote its (auto)phosphorylation, and that Cys-185-SOH destabilizes pTyr-527 binding to the SH2 domain. These redox-dependent Src activation mechanisms offer opportunities for development of Src-selective inhibitors in treatment of diseases where Src is aberrantly activated.
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Affiliation(s)
- David E Heppner
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA.
| | - Christopher M Dustin
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Chenyi Liao
- Department of Chemistry, College of Arts and Sciences, University of Vermont, 82 University Place, Burlington, VT, 05405, USA
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Carmen Veith
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Andrew C Little
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Bethany A Ahlers
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Sheryl L White
- Department of Neurological Sciences, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA
| | - Bin Deng
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Ying-Wai Lam
- Department of Biology, College of Arts and Sciences, University of Vermont, 109 Carrigan Drive, Burlington, VT, 05405, USA
| | - Jianing Li
- Department of Chemistry, College of Arts and Sciences, University of Vermont, 82 University Place, Burlington, VT, 05405, USA.
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine University of Vermont, 149 Beaumont Avenue, Burlington, VT, 05405, USA.
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33
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Martín‐Gago P, Olsen CA. Arylfluorosulfate-Based Electrophiles for Covalent Protein Labeling: A New Addition to the Arsenal. Angew Chem Int Ed Engl 2018; 58:957-966. [PMID: 30024079 PMCID: PMC6518939 DOI: 10.1002/anie.201806037] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/18/2018] [Indexed: 01/15/2023]
Abstract
Selective covalent modification of a targeted protein is a powerful tool in chemical biology and drug discovery, with applications ranging from identification and characterization of proteins and their functions to the development of targeted covalent inhibitors. Most covalent ligands contain an affinity motif and an electrophilic warhead that reacts with a nucleophilic residue of the targeted protein. Because the electrophilic warhead is prone to react and modify off‐target nucleophiles, its reactivity should be balanced carefully to maximize target selectivity. Arylfluorosulfates have recently emerged as latent electrophiles for selective labeling of context‐specific tyrosine and lysine residues in protein pockets. Here, we review the recent but intense introduction of arylfluorosulfates into the arsenal of available warheads for selective covalent modification of proteins. We highlight the untapped potential of this functional group for use in chemical biology and drug discovery.
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Affiliation(s)
- Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversity of CopenhagenUniversitetsparken 22100CopenhagenDenmark
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34
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Martín‐Gago P, Olsen CA. Arylfluorsulfat‐basierte Elektrophile für die kovalente Proteinmarkierung. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806037] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pablo Martín‐Gago
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversität Kopenhagen Universitetsparken 2 2100 Kopenhagen Dänemark
| | - Christian A. Olsen
- Center for Biopharmaceuticals &, Department of Drug Design and PharmacologyUniversität Kopenhagen Universitetsparken 2 2100 Kopenhagen Dänemark
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35
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Ocasio CA, Warkentin AA, McIntyre PJ, Barkovich KJ, Vesely C, Spencer J, Shokat KM, Bayliss R. Type II Kinase Inhibitors Targeting Cys-Gatekeeper Kinases Display Orthogonality with Wild Type and Ala/Gly-Gatekeeper Kinases. ACS Chem Biol 2018; 13:2956-2965. [PMID: 30239186 DOI: 10.1021/acschembio.8b00592] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Analogue-sensitive (AS) kinases contain large to small mutations in the gatekeeper position rendering them susceptible to inhibition with bulky analogues of pyrazolopyrimidine-based Src kinase inhibitors (e.g., PP1). This "bump-hole" method has been utilized for at least 85 of ∼520 kinases, but many kinases are intolerant to this approach. To expand the scope of AS kinase technology, we designed type II kinase inhibitors, ASDO2/6 (analogue-sensitive "DFG-out" kinase inhibitors 2 and 6), that target the "DFG-out" conformation of Cys-gatekeeper kinases with submicromolar potency. We validated this system in vitro against Greatwall kinase (GWL), Aurora-A kinase, and cyclin-dependent kinase-1 and in cells using M110C-GWL-expressing mouse embryonic fibroblasts. These Cys-gatekeeper kinases were sensitive to ASDO2/6 inhibition but not AS kinase inhibitor 3MB-PP1 and vice versa. These compounds, with AS kinase inhibitors, have the potential to inhibit multiple AS kinases independently with applications in systems level and translational kinase research as well as the rational design of type II kinase inhibitors targeting endogenous kinases.
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Affiliation(s)
- Cory A Ocasio
- Genome Damage and Stability Centre, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9RQ , U.K
| | - Alexander A Warkentin
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Patrick J McIntyre
- Department of Molecular and Cell Biology , University of Leicester , Henry Wellcome Building , Leicester LE1 9HN , U.K
| | - Krister J Barkovich
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Clare Vesely
- Genome Damage and Stability Centre, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9RQ , U.K
| | - John Spencer
- Department of Chemistry, School of Life Sciences , University of Sussex , Falmer, Brighton BN1 9QJ , U.K
| | - Kevan M Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology , University of California, San Francisco , 600 16th Street , San Francisco , California 94158-2280 , United States
| | - Richard Bayliss
- School of Molecular and Cellular Biology, Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , U.K
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36
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Thomas J, Fokin VV. Regioselective Synthesis of Fluorosulfonyl 1,2,3-Triazoles from Bromovinylsulfonyl Fluoride. Org Lett 2018; 20:3749-3752. [DOI: 10.1021/acs.orglett.8b01309] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joice Thomas
- The Bridge@USC and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Valery V. Fokin
- The Bridge@USC and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
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37
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Site-selective covalent reactions on proteinogenic amino acids. Curr Opin Biotechnol 2017; 48:220-227. [DOI: 10.1016/j.copbio.2017.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/05/2017] [Indexed: 11/20/2022]
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38
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Pettinger J, Jones K, Cheeseman MD. Lysine-Targeting Covalent Inhibitors. Angew Chem Int Ed Engl 2017; 56:15200-15209. [PMID: 28853194 DOI: 10.1002/anie.201707630] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/23/2017] [Indexed: 12/11/2022]
Abstract
Targeted covalent inhibitors have gained widespread attention in drug discovery as a validated method to circumvent acquired resistance in oncology. This strategy exploits small-molecule/protein crystal structures to design tightly binding ligands with appropriately positioned electrophilic warheads. Whilst most focus has been on targeting binding-site cysteine residues, targeting nucleophilic lysine residues can also represent a viable approach to irreversible inhibition. However, owing to the basicity of the ϵ-amino group in lysine, this strategy generates a number of specific challenges. Herein, we review the key principles for inhibitor design, give historical examples, and present recent developments that demonstrate the potential of lysine targeting for future drug discovery.
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Matthew D Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit, The Institute of Cancer Research, London, SW7 3RP, UK
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39
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Affiliation(s)
- Jonathan Pettinger
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Keith Jones
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
| | - Matthew D. Cheeseman
- Cancer Research, UK, Cancer Therapeutics Unit; The Institute of Cancer Research; London SW7 3RP Großbritannien
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40
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Maity S, Sadlowski CM, George Lin JM, Chen CH, Peng LH, Lee ES, Vegesna GK, Lee C, Kim SH, Mochly-Rosen D, Kumar S, Murthy N. Thiophene bridged aldehydes (TBAs) image ALDH activity in cells via modulation of intramolecular charge transfer. Chem Sci 2017; 8:7143-7151. [PMID: 29081945 PMCID: PMC5635522 DOI: 10.1039/c7sc03017g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/01/2017] [Indexed: 12/15/2022] Open
Abstract
Aldehyde dehydrogenases (ALDHs) catalyze the oxidation of an aldehyde to a carboxylic acid and are implicated in the etiology of numerous diseases. However, despite their importance, imaging ALDH activity in cells is challenging due to a lack of fluorescent imaging probes. In this report, we present a new family of fluorescent probes composed of an oligothiophene flanked by an aldehyde and an electron donor, termed thiophene-bridged aldehydes (TBAs), which can image ALDH activity in cells. The TBAs image ALDH activity via a fluorescence sensing mechanism based on the modulation of intramolecular charge transfer (ICT) and this enables the TBAs and their ALDH-mediated oxidized products, thiophene-bridged carboxylates (TBCs), to have distinguishable fluorescence spectra. Herein, we show that the TBAs can image ALDH activity in cells via fluorescence microscopy, flow cytometry, and in a plate reader. Using TBA we were able to develop a cell-based high throughput assay for ALDH inhibitors, for the first time, and screened a large, 1460-entry electrophile library against A549 cells. We identified α,β-substituted acrylamides as potent electrophile fragments that can inhibit ALDH activity in cells. These inhibitors sensitized drug-resistant glioblastoma cells to the FDA approved anti-cancer drug, temozolomide. The TBAs have the potential to make the analysis of ALDH activity in cells routinely possible given their ability to spectrally distinguish between an aldehyde and a carboxylic acid.
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Affiliation(s)
- Santanu Maity
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Corinne M Sadlowski
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Jung-Ming George Lin
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
- The UC Berkeley-UCSF Graduate Program in Bioengineering , UC Berkeley , Berkeley , California , USA
| | - Che-Hong Chen
- Department of Chemical and Systems Biology , Stanford University , School of Medicine , Stanford , CA 94305-5174 , USA
| | - Li-Hua Peng
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Eun-Soo Lee
- Korea Research Institute of Standards and Science , 267 Gajeong-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Giri K Vegesna
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Charles Lee
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
| | - Se-Hwa Kim
- Korea Research Institute of Standards and Science , 267 Gajeong-ro, Yuseong-gu , Daejeon , Republic of Korea
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology , Stanford University , School of Medicine , Stanford , CA 94305-5174 , USA
| | - Sanjay Kumar
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
- The UC Berkeley-UCSF Graduate Program in Bioengineering , UC Berkeley , Berkeley , California , USA
| | - Niren Murthy
- Department of Bioengineering , University of California , 140 Hearst Memorial Mining Building , Berkeley , CA 94720 , USA .
- The UC Berkeley-UCSF Graduate Program in Bioengineering , UC Berkeley , Berkeley , California , USA
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41
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Dasari R, La Clair JJ, Kornienko A. Irreversible Protein Labeling by Paal-Knorr Conjugation. Chembiochem 2017; 18:1792-1796. [PMID: 28715110 PMCID: PMC5766258 DOI: 10.1002/cbic.201700210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 01/07/2023]
Abstract
The application of new chemical reactions in a biological context has advanced bioconjugation methods for both fundamental research and commercial arenas. Recent adaptations of reactions such as Huisgen 1,3-dipolar or Diels-Alder cycloadditions have enabled the labeling of specific residues in biomolecules by the attachment of molecules carrying azides, alkynes, or strained alkenes. Although these are fundamental tools, there is a need for the discovery of reactions that can label native proteins. We report herein the adaptation of the Paal-Knorr reaction to label lysine residues in proteins via pyrrole linkages.
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Affiliation(s)
- Ramesh Dasari
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163, USA
| | - Alexander Kornienko
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
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42
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Fadeyi OO, Hoth LR, Choi C, Feng X, Gopalsamy A, Hett EC, Kyne RE, Robinson RP, Jones LH. Covalent Enzyme Inhibition through Fluorosulfate Modification of a Noncatalytic Serine Residue. ACS Chem Biol 2017; 12:2015-2020. [PMID: 28718624 DOI: 10.1021/acschembio.7b00403] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Irreversible enzyme inhibitors and covalent chemical biology probes often utilize the reaction of a protein cysteine residue with an appropriately positioned electrophile (e.g., acrylamide) on the ligand template. However, cysteine residues are not always available for site-specific protein labeling, and therefore new approaches are needed to expand the toolkit of appropriate electrophiles ("warheads") that target alternative amino acids. We previously described the rational targeting of tyrosine residues in the active site of a protein (the mRNA decapping scavenger enzyme, DcpS) using inhibitors armed with a sulfonyl fluoride electrophile. These inhibitors subsequently enabled the development of clickable probe technology to measure drug-target occupancy in live cells. Here we describe a fluorosulfate-containing inhibitor (aryl fluorosulfate probe (FS-p1)) with excellent chemical and metabolic stability that reacts selectively with a noncatalytic serine residue in the same active site of DcpS as confirmed by peptide mapping experiments. Our results suggest that noncatalytic serine targeting using fluorosulfate electrophilic warheads could be a suitable strategy for the development of covalent inhibitor drugs and chemical probes.
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Affiliation(s)
- Olugbeminiyi O. Fadeyi
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lise R. Hoth
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Chulho Choi
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Xidong Feng
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ariamala Gopalsamy
- Medicine
Design, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Erik C. Hett
- Medicine
Design, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Robert E. Kyne
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ralph P. Robinson
- Medicine
Design, Pfizer Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Lyn H. Jones
- Medicine
Design, Pfizer Inc., 610 Main Street, Cambridge, Massachusetts 02139, United States
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43
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Liu M, Ji Z, Zhang M, Xia J. Versatile Site-Selective Protein Reaction Guided by WW Domain–Peptide Motif Interaction. Bioconjug Chem 2017; 28:2199-2205. [DOI: 10.1021/acs.bioconjchem.7b00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miao Liu
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Zeyang Ji
- Division
of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Mingjie Zhang
- Division
of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiang Xia
- Department
of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
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44
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Zhao Z, Xie L, Bourne PE. Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome. PLoS One 2017; 12:e0179936. [PMID: 28628649 PMCID: PMC5476283 DOI: 10.1371/journal.pone.0179936] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/06/2017] [Indexed: 11/18/2022] Open
Abstract
Protein kinases are critical drug targets for treating a large variety of human diseases. Type-III kinase inhibitors have attracted increasing attention as highly selective therapeutics. Thus, understanding the binding mechanism of existing type-III kinase inhibitors provides useful insights into designing new type-III kinase inhibitors. In this work, we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-site information on the binding characteristics of MEK type-III kinase inhibitors. We hypothesize that the helix-folding activation loop is a hallmark allosteric binding site for type-III inhibitors. Subsequently, we screened and predicted allosteric binding sites across the human kinome, suggesting other kinases as potential targets suitable for type-III inhibitors.
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Affiliation(s)
- Zheng Zhao
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland, United States of America
| | - Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, United States of America
- The Graduate Center, The City University of New York, New York, United States of America
| | - Philip E. Bourne
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland, United States of America
- Office of the Director, National Institutes of Health, Bethesda, Maryland, United States of America
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45
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Zha GF, Zheng Q, Leng J, Wu P, Qin HL, Sharpless KB. Palladium-Catalyzed Fluorosulfonylvinylation of Organic Iodides. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701162] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gao-Feng Zha
- State Key Laboratory of Silicate Materials for Architectures, and School of Chemistry; Chemical Engineering and Life Science; Wuhan University of Technology; Wuhan 430070 China
| | - Qinheng Zheng
- Department of Chemistry; The Scripps Research Institute; La Jolla CA 92037 USA
| | - Jing Leng
- State Key Laboratory of Silicate Materials for Architectures, and School of Chemistry; Chemical Engineering and Life Science; Wuhan University of Technology; Wuhan 430070 China
| | - Peng Wu
- Department of Chemical Physiology; The Scripps Research Institute; La Jolla CA 92037 USA
| | - Hua-Li Qin
- State Key Laboratory of Silicate Materials for Architectures, and School of Chemistry; Chemical Engineering and Life Science; Wuhan University of Technology; Wuhan 430070 China
| | - K. Barry Sharpless
- Department of Chemistry; The Scripps Research Institute; La Jolla CA 92037 USA
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46
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Zha GF, Zheng Q, Leng J, Wu P, Qin HL, Sharpless KB. Palladium-Catalyzed Fluorosulfonylvinylation of Organic Iodides. Angew Chem Int Ed Engl 2017; 56:4849-4852. [PMID: 28370917 DOI: 10.1002/anie.201701162] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/07/2017] [Indexed: 11/06/2022]
Abstract
A palladium-catalyzed fluorosulfonylvinylation reaction of organic iodides is described. Catalytic Pd(OAc)2 with a stoichiometric amount of silver(I) trifluoroacetate enables the coupling process between either an (hetero)aryl or alkenyl iodide with ethenesulfonyl fluoride (ESF). The method is demonstrated in the successful syntheses of eighty-eight otherwise difficult to access compounds, in up to 99 % yields, including the unprecedented 2-heteroarylethenesulfonyl fluorides and 1,3-dienylsulfonyl fluorides.
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Affiliation(s)
- Gao-Feng Zha
- State Key Laboratory of Silicate Materials for Architectures, and School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, China
| | - Qinheng Zheng
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jing Leng
- State Key Laboratory of Silicate Materials for Architectures, and School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, China
| | - Peng Wu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hua-Li Qin
- State Key Laboratory of Silicate Materials for Architectures, and School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan, 430070, China
| | - K Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
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47
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Jackson PA, Widen JC, Harki DA, Brummond KM. Covalent Modifiers: A Chemical Perspective on the Reactivity of α,β-Unsaturated Carbonyls with Thiols via Hetero-Michael Addition Reactions. J Med Chem 2017; 60:839-885. [PMID: 27996267 PMCID: PMC5308545 DOI: 10.1021/acs.jmedchem.6b00788] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although Michael acceptors display a potent and broad spectrum of bioactivity, they have largely been ignored in drug discovery because of their presumed indiscriminate reactivity. As such, a dearth of information exists relevant to the thiol reactivity of natural products and their analogues possessing this moiety. In the midst of recently approved acrylamide-containing drugs, it is clear that a good understanding of the hetero-Michael addition reaction and the relative reactivities of biological thiols with Michael acceptors under physiological conditions is needed for the design and use of these compounds as biological tools and potential therapeutics. This Perspective provides information that will contribute to this understanding, such as kinetics of thiol addition reactions, bioactivities, as well as steric and electronic factors that influence the electrophilicity and reversibility of Michael acceptors. This Perspective is focused on α,β-unsaturated carbonyls given their preponderance in bioactive natural products.
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Affiliation(s)
- Paul A. Jackson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - John C. Widen
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kay M. Brummond
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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48
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Zhao Q, Ouyang X, Wan X, Gajiwala KS, Kath JC, Jones LH, Burlingame AL, Taunton J. Broad-Spectrum Kinase Profiling in Live Cells with Lysine-Targeted Sulfonyl Fluoride Probes. J Am Chem Soc 2017; 139:680-685. [PMID: 28051857 PMCID: PMC5858558 DOI: 10.1021/jacs.6b08536] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein kinases comprise a large family of structurally related enzymes. A major goal in kinase-inhibitor development is to selectively engage the desired kinase while avoiding myriad off-target kinases. However, quantifying inhibitor interactions with multiple endogenous kinases in live cells remains an unmet challenge. Here, we report the design of sulfonyl fluoride probes that covalently label a broad swath of the intracellular kinome with high efficiency. Protein crystallography and mass spectrometry confirmed a chemoselective reaction between the sulfonyl fluoride and a conserved lysine in the ATP binding site. Optimized probe 2 (XO44) covalently modified up to 133 endogenous kinases, efficiently competing with high intracellular concentrations of ATP. We employed probe 2 and label-free mass spectrometry to quantify intracellular kinase engagement by the approved drug, dasatinib. The data revealed saturable dasatinib binding to a small subset of kinase targets at clinically relevant concentrations, highlighting the utility of lysine-targeted sulfonyl fluoride probes in demanding chemoproteomic applications.
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Affiliation(s)
- Qian Zhao
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
- Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Xiaohu Ouyang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Xiaobo Wan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
| | - Ketan S. Gajiwala
- Worldwide Research and Development, Pfizer, San Diego, California 92121, United States
| | - John C. Kath
- Worldwide Research and Development, Pfizer, San Diego, California 92121, United States
| | - Lyn H. Jones
- Medicine Design, Pfizer, Cambridge, Massachusetts 02139, United States
| | - Alma L. Burlingame
- Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
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49
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Cruz CM, Ortega-Muñoz M, López-Jaramillo FJ, Hernández-Mateo F, Blanco V, Santoyo-González F. Vinyl Sulfonates: A Click Function for Coupling-and-Decoupling Chemistry and their Applications. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600628] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carlos M. Cruz
- Departamento de Química Orgánica; Facultad de Ciencias; Universidad de Granada; 18071 Granada Spain
| | - Mariano Ortega-Muñoz
- Departamento de Química Orgánica; Facultad de Ciencias; Universidad de Granada; 18071 Granada Spain
| | | | - Fernando Hernández-Mateo
- Departamento de Química Orgánica; Facultad de Ciencias; Universidad de Granada; 18071 Granada Spain
| | - Victor Blanco
- Departamento de Química Orgánica; Facultad de Ciencias; Universidad de Granada; 18071 Granada Spain
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50
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Heppner DE, Hristova M, Dustin CM, Danyal K, Habibovic A, van der Vliet A. The NADPH Oxidases DUOX1 and NOX2 Play Distinct Roles in Redox Regulation of Epidermal Growth Factor Receptor Signaling. J Biol Chem 2016; 291:23282-23293. [PMID: 27650496 DOI: 10.1074/jbc.m116.749028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Indexed: 12/31/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) plays a critical role in regulating airway epithelial homeostasis and responses to injury. Activation of EGFR is regulated by redox-dependent processes involving reversible cysteine oxidation by reactive oxygen species (ROS) and involves both ligand-dependent and -independent mechanisms, but the precise source(s) of ROS and the molecular mechanisms that control tyrosine kinase activity are incompletely understood. Here, we demonstrate that stimulation of EGFR activation by ATP in airway epithelial cells is closely associated with dynamic reversible oxidation of cysteine residues via sequential sulfenylation and S-glutathionylation within EGFR and the non-receptor-tyrosine kinase Src. Moreover, the intrinsic kinase activity of recombinant Src or EGFR was in both cases enhanced by H2O2 but not by GSSG, indicating that the intermediate sulfenylation is the activating modification. H2O2-induced increase in EGFR tyrosine kinase activity was not observed with the C797S variant, confirming Cys-797 as the redox-sensitive cysteine residue that regulates kinase activity. Redox-dependent regulation of EGFR activation in airway epithelial cells was found to strongly depend on activation of either the NADPH oxidase DUOX1 or the homolog NOX2, depending on the activation mechanism. Whereas DUOX1 and Src play a primary role in EGFR transactivation by wound-derived signals such as ATP, direct ligand-dependent EGFR activation primarily involves NOX2 with a secondary role for DUOX1 and Src. Collectively, our findings establish that redox-dependent EGFR kinase activation involves a dynamic and reversible cysteine oxidation mechanism and that this activation mechanism variably involves DUOX1 and NOX2.
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Affiliation(s)
- David E Heppner
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Milena Hristova
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Christopher M Dustin
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Karamatullah Danyal
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Aida Habibovic
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
| | - Albert van der Vliet
- From the Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont 05405
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