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Liu Y, Yu Z, Li P, Yang T, Ding K, Zhang ZM, Tan Y, Li Z. Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles. J Am Chem Soc 2024. [PMID: 39018468 DOI: 10.1021/jacs.4c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhongtang Yu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Peishan Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tao Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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Nambu H, Onuki Y, Aso K, Kanamori M, Tomohara K, Tsuge K, Yakura T. Ring expansion of spirocyclopropanes with stabilized sulfonium ylides: highly diastereoselective synthesis of cyclobutanes. Chem Commun (Camb) 2024; 60:4537-4540. [PMID: 38507284 DOI: 10.1039/d3cc06033k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
A novel method was devised for regioselective ring expansion of Meldrum's acid-derived spirocyclopropanes to spirocyclobutanes with stabilized sulfonium ylides, affording 1,2-trans-disubstituted 6,8-dioxaspiro[3.5]nonane-5,9-diones in up to 87% yields without the formation of any isomers. The aforementioned reaction was also applied to the barbituric acid-derived spirocyclopropane, resulting in the formation of the corresponding cyclobutanes.
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Affiliation(s)
- Hisanori Nambu
- Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan.
- Laboratory of Pharmaceutical Manufacturing Chemistry, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan.
| | - Yuta Onuki
- Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan.
| | - Kana Aso
- Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan.
| | - Momoka Kanamori
- Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan.
| | - Keisuke Tomohara
- Laboratory of Pharmaceutical Manufacturing Chemistry, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan.
| | - Kiyoshi Tsuge
- Graduate School of Science and Engineering, University of Toyama, Gofuku, Toyama 930-8555, Japan
| | - Takayuki Yakura
- Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan.
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Abstract
Cyclopropanes that carry an electron-accepting group react as electrophiles in polar, ring-opening reactions. Analogous reactions at cyclopropanes with additional C2 substituents allow one to access difunctionalized products. Consequently, functionalized cyclopropanes are frequently used building blocks in organic synthesis. The polarization of the C1-C2 bond in 1-acceptor-2-donor-substituted cyclopropanes not only favorably enhances reactivity toward nucleophiles but also directs the nucleophilic attack toward the already substituted C2 position. Monitoring the kinetics of non-catalytic ring-opening reactions with a series of thiophenolates and other strong nucleophiles, such as azide ions, in DMSO provided the inherent SN2 reactivity of electrophilic cyclopropanes. The experimentally determined second-order rate constants k 2 for cyclopropane ring-opening reactions were then compared to those of related Michael additions. Interestingly, cyclopropanes with aryl substituents at the C2 position reacted faster than their unsubstituted analogues. Variation of the electronic properties of the aryl groups at C2 gave rise to parabolic Hammett relationships.
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Affiliation(s)
- Andreas Eitzinger
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5–13, 81377München, Germany
| | - Armin R. Ofial
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr. 5–13, 81377München, Germany
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4
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Vartanova AE, Levina II, Ratmanova NK, Andreev IA, Ivanova OA, Trushkov IV. Ambident reactivity of 5-aminopyrazoles towards donor-acceptor cyclopropanes. Org Biomol Chem 2022; 20:7795-7802. [PMID: 36148530 DOI: 10.1039/d2ob01490d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lewis acid-catalysed reactions of donor-acceptor cyclopropanes with 1,3-disubstituted 5-aminopyrazoles were investigated. Under catalysis with gallium(III) chloride, products of the three-membered ring opening via a nucleophilic attack of the exocyclic amino group were obtained in a chemoselective manner. Oppositely, in the presence of scandium(III) triflate, products of either N-alkylation or C(4)-alkylation, or a mixture of both were formed. The products of the C(4) alkylation were transformed in one step into tetrahydropyrazolo[3,4-b]azepines that are attractive for medicinal chemistry and pharmacology.
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Affiliation(s)
- Anna E Vartanova
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky pr. 47, Moscow 119334, Russian Federation.
| | - Irina I Levina
- N. M. Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina 4, Moscow 119334, Russian Federation
| | - Nina K Ratmanova
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky pr. 47, Moscow 119334, Russian Federation. .,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela 1, Moscow 117997, Russian Federation
| | - Ivan A Andreev
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky pr. 47, Moscow 119334, Russian Federation. .,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela 1, Moscow 117997, Russian Federation
| | - Olga A Ivanova
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky pr. 47, Moscow 119334, Russian Federation. .,Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow, 119991, Russian Federation
| | - Igor V Trushkov
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky pr. 47, Moscow 119334, Russian Federation.
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Andreev I, Boichenko M, Ratmanova N, Ivanova O, Levina I, Khrustalev V, Sedov I, Trushkov I. 4‐(Dimethylamino)pyridinium Azide in Protic Ionic Liquid Media as a Stable Equivalent of Hydrazoic Acid. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ivan Andreev
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology RUSSIAN FEDERATION
| | - Maksim Boichenko
- Lomonosov Moscow State University Department of Chemistry RUSSIAN FEDERATION
| | - Nina Ratmanova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology RUSSIAN FEDERATION
| | | | - Irina Levina
- FSBSI Institute of Biochemical Physics named after N M Emanuel of the Russian Academy of Sciences RUSSIAN FEDERATION
| | | | - Igor Sedov
- Kazan Federal University RUSSIAN FEDERATION
| | - Igor Trushkov
- N.D. Zelinsky Institute of Organic Chemistry RUSSIAN FEDERATION
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An F, Jangra H, Wei Y, Shi M, Zipse H, Ofial AR. Reactivities of allenic and olefinic Michael acceptors towards phosphines. Chem Commun (Camb) 2022; 58:3358-3361. [PMID: 35188503 DOI: 10.1039/d1cc06786a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The kinetics of the reactions of tributylphosphine with allenic and olefinic Michael acceptors in dichloromethane at 20 °C was followed by photometric and NMR spectroscopic methods. Combination with DFT-calculated methyl anion affinities revealed the relevance of retroaddition barriers in phosphine-catalysed reactions when mixtures of allenic and olefinic substrates are used.
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Affiliation(s)
- Feng An
- Department Chemie, Ludwig-Maximilians-Universtität München, Butenandtstr. 5-13, München 81377, Germany.
| | - Harish Jangra
- Department Chemie, Ludwig-Maximilians-Universtität München, Butenandtstr. 5-13, München 81377, Germany.
| | - Yin Wei
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, P. R. China.
| | - Min Shi
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Road, Shanghai 200032, P. R. China. .,Key Laboratory for Advanced Materials and Institute of Fine Chemicals, East China University of Science and Technology, 130 MeiLong Road, Shanghai 200237, P. R. China
| | - Hendrik Zipse
- Department Chemie, Ludwig-Maximilians-Universtität München, Butenandtstr. 5-13, München 81377, Germany.
| | - Armin R Ofial
- Department Chemie, Ludwig-Maximilians-Universtität München, Butenandtstr. 5-13, München 81377, Germany.
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