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Islamov II, Dzhemileva LU, Gaisin IV, Dzhemilev UM, D′yakonov VA. New Polyether Macrocycles as Promising Antitumor Agents-Targeted Synthesis and Induction of Mitochondrial Apoptosis. ACS OMEGA 2024; 9:19923-19931. [PMID: 38737069 PMCID: PMC11079895 DOI: 10.1021/acsomega.3c09566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024]
Abstract
A series of previously unknown aromatic polyether macrodiolides containing a cis,cis-1,5-diene moiety in the molecule were synthesized in 47-74% yields. Macrocycle compounds were first obtained by intermolecular esterification of aromatic polyether diols with α,ω-alka-nZ,(n+4)Z-dienedioic acids mediated by N-(3-(dimethylamino)propyl)-N'-ethylcarbodiimide hydrochloride (EDC·HCl) and 4-(dimethylamino)pyridine (DMAP). For the synthesized compounds, studies of cytotoxicity on tumor (Jurkat, K562, U937), conditionally normal (HEK293) cell lines, and normal fibroblasts were carried out. CC50 was determined, and the therapeutic selectivity index of cytotoxic action (SI) in comparison with normal fibroblasts was evaluated. With the involvement of modern methods of flow cytometry for the most promising macrocycles, their effect on mitochondria and the cell cycle was investigated. It was found that a new macrocycle exhibits pronounced apoptosis-inducing activity toward Jurkat cells and can retard cell division by blocking at the G1/S checkpoint. Also, it was shown that the synthesized macrodiolides influence mitochondria due to their high ability to penetrate the mitochondrial membrane.
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Affiliation(s)
- Ilgiz I. Islamov
- Institute
of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
| | - Lilya U. Dzhemileva
- N.
D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, Moscow 119991, Russian Federation
- State
Scientific Center of the Russian Federation Federal State Budgetary
Institution, “National Medical Research
Center of Endocrinology” of the Ministry of Health
of the Russian Federation, st. Dmitry Ulyanov, 11, Moscow 117292, Russian Federation
| | - Ilgam V. Gaisin
- Institute
of Petrochemistry and Catalysis, Russian Academy of Sciences, 141 Prospekt Oktyabrya, Ufa 450075, Russian Federation
| | - Usein M. Dzhemilev
- N.
D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, Moscow 119991, Russian Federation
| | - Vladimir A. D′yakonov
- N.
D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, Moscow 119991, Russian Federation
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2
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Suarez AFL, Nguyen TQN, Chang L, Tooh YW, Yong RHS, Leow LC, Koh IYF, Chen H, Koh JWH, Selvanayagam A, Lim V, Tan YE, Agatha I, Winnerdy FR, Morinaka BI. Functional and Promiscuity Studies of Three-Residue Cyclophane Forming Enzymes Show Nonnative C-C Cross-Linked Products and Leader-Dependent Cyclization. ACS Chem Biol 2024; 19:774-783. [PMID: 38417140 DOI: 10.1021/acschembio.3c00795] [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: 03/01/2024]
Abstract
Enzymes catalyzing peptide macrocyclization are important biochemical tools in drug discovery. The three-residue cyclophane-forming enzymes (3-CyFEs) are an emerging family of post-translational modifying enzymes that catalyze the formation of three-residue peptide cyclophanes. In this report, we introduce three additional 3-CyFEs, including ChlB, WnsB, and FnnB, that catalyze cyclophane formation on Tyr, Trp, and Phe, respectively. To understand the promiscuity of these enzymes and those previously reported (MscB, HaaB, and YxdB), we tested single amino acid substitutions at the three-residue motif of modification (Ω1X2X3, Ω1 = aromatic). Collectively, we observe that substrate promiscuity is observed at the Ω1 and X2 positions, but a greater specificity is observed for the X3 residue. Two nonnative cyclophane products were characterized showing a Phe-C3 to Arg-Cβ and His-C2 to Pro-Cβ cross-links, respectively. We also tested the leader dependence of selected 3-CyFEs and show that a predicted helix region is important for cyclophane formation. These results demonstrate the biocatalytic potential of these maturases and allow rational design of substrates to obtain a diverse array of genetically encoded 3-residue cyclophanes.
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Affiliation(s)
| | - Thi Quynh Ngoc Nguyen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Litao Chang
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi Wei Tooh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Rubin How Sheng Yong
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Li Chuan Leow
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Ivan Yu Fan Koh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Huiyi Chen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Jeffery Wei Heng Koh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Vernon Lim
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi En Tan
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Irene Agatha
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Fernaldo R Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
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3
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Zhu D, Mu T, Li ZL, Luo HY, Cao RF, Xue XS, Chen ZM. Enantioselective Synthesis of Planar-Chiral Sulfur-Containing Cyclophanes by Chiral Sulfide Catalyzed Electrophilic Sulfenylation of Arenes. Angew Chem Int Ed Engl 2024; 63:e202318625. [PMID: 38231132 DOI: 10.1002/anie.202318625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/05/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
An efficient catalytic asymmetric electrophilic sulfenylation reaction for the synthesis of planar-chiral sulfur-containing cyclophanes has been developed for the first time. This was achieved by using a new Lewis base catalyst and a new ortho-trifluoromethyl-substituted sulfenylating reagent. Using the substrates with low rotational energy barrier, the transformation proceeded through a dynamic kinetic resolution, and the high rotational energy barrier of the substrates allowed the reaction to undergo a kinetic resolution process. Meanwhile, this transformation was compatible with a desymmetrization process when the symmetric substrates were used. Various planar-chiral sulfur-containing cyclophanes were readily obtained in moderate to excellent yields with moderate to excellent enantioselectivities (up to 97 % yield and 95 % ee). This approach was used to synthesize pharmaceutically relevant planar-chiral sulfur-containing molecules. Density functional theory calculations showed that π-π interactions between the sulfenyl group and the aromatic ring in the substrate play a crucial role in enantioinduction in this sulfenylation reaction.
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Affiliation(s)
- Deng Zhu
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Tong Mu
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200232, P. R. China
| | - Ze-Long Li
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Hui-Yun Luo
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Ren-Fei Cao
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xiao-Song Xue
- Key Laboratory of Fluorine and Nitrogen Chemistry and Advanced Materials, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200232, P. R. China
- School of Chemistry and Material Sciences, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, P. R. China
| | - Zhi-Min Chen
- School of Chemistry and Chemical Engineering, Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin, 300071, P. R. China
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4
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Wang J, Wang M, Wen Y, Teng P, Li C, Zhao C. N-Heterocyclic Carbene-Catalyzed Highly Enantioselective Macrolactonization to Access Planar-Chiral Macrocycles. Org Lett 2024; 26:1040-1045. [PMID: 38295348 DOI: 10.1021/acs.orglett.3c04200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
An N-heterocyclic carbene (NHC)-catalyzed atroposelective macrolactonization has been disclosed. This approach affords planar-chiral macrocycles in high yields with excellent enantioselectivities over a broad substrate scope. Controlled experiments suggest that the enantioselectivity might arise from the cation-n interaction between the acyl azolium and the electron-rich moiety in the substrate. This mechanism is supported by density functional theory calculations, which also suggest an important π-π interaction in stabilizing the transition state.
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Affiliation(s)
- Jiaming Wang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Meng Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yilu Wen
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Peng Teng
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Zhejiang 310058, China
| | - Chenyang Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Changgui Zhao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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5
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Dong Z, Li J, Yao T, Zhao C. Palladium-Catalyzed Enantioselective C-H Olefination to Access Planar-Chiral Cyclophanes by Dynamic Kinetic Resolution. Angew Chem Int Ed Engl 2023:e202315603. [PMID: 37919238 DOI: 10.1002/anie.202315603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
Planar-chiral cyclophanes have received increasing attention for drug discovery and catalyst design. However, the catalytically asymmetric synthesis of planar-chiral cyclophanes has been a longstanding challenge. We describe the first Pd(II)-catalyzed enantioselective C-H olefination of prochiral cyclophanes. The low rotational barrier of less hindered benzene ring in the substrates allows the reaction to proceed through a dynamic kinetic resolution. This approach exhibits broad substrate scope, providing the planar-chiral cyclophanes in high yields (up to 99 %) with excellent enantioselectivities (up to >99 % ee). The ansa chain length scope studies reveal that the chirality of the cyclophanes arises from the bond rotation constraint of the benzene ring around the macrocycle plane, rather than the C-N axis. The C-H activation approach is also applicable to the late-stage modification of bioactive molecules and pharmaceuticals.
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Affiliation(s)
- Ziyang Dong
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875 (P. R., China
| | - Jia Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875 (P. R., China
| | - Ting Yao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875 (P. R., China
| | - Changgui Zhao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875 (P. R., China
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6
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Wang YJ, Liu CY, Wang YL, Zhang FX, Lu YF, Dai SY, Li C, Sun Y, Pei YH. Cytotoxic Cyclodepsipeptides and Cyclopentane Derivatives from a Plant-Associated Fungus Fusarium sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:2592-2602. [PMID: 36288556 DOI: 10.1021/acs.jnatprod.2c00555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this work, four new cyclodepsipeptides, fusarihexins C-E (1-3) and enniatin Q (4), four new cyclopentane derivatives, fusarilins A-D (5-8), together with eight known compounds (9-16), were isolated from cultures of the endophytic fungus Fusarium sp. The structures of the isolated compounds were elucidated by analysis of HRMS and NMR spectroscopic data. The absolute configurations were determined using Marfey's method, a modified Mosher's method, single-crystal X-ray diffraction analysis, and ECD analysis. The antitumor activities of the isolated compounds in vitro were evaluated. Cyclodepsipeptides displayed cytotoxicities against the Huh-7, MRMT-1, and HepG-2 cell lines. Compounds 4, 9, 10, and 12 with IC50 values of 1.0-9.1 μM exhibited the most potent cytotoxicities against the three cell lines as compared to the positive control-5-fluorouracil. Compounds 1-3 and 11 exhibited moderate cytotoxic activities (IC50 values of 10.7-20.1 μM).
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Affiliation(s)
- Ya-Jing Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Chun-Yue Liu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Yan-Lei Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Feng-Xiang Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, Guilin 541004, People's Republic of China
| | - Yong-Fu Lu
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Si-Yang Dai
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Chang Li
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
| | - Yi Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Yue-Hu Pei
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150081, People's Republic of China
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7
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Sugiyama R, Suarez AFL, Morishita Y, Nguyen TQN, Tooh YW, Roslan MNHB, Lo Choy J, Su Q, Goh WY, Gunawan GA, Wong FT, Morinaka BI. The Biosynthetic Landscape of Triceptides Reveals Radical SAM Enzymes That Catalyze Cyclophane Formation on Tyr- and His-Containing Motifs. J Am Chem Soc 2022; 144:11580-11593. [PMID: 35729768 DOI: 10.1021/jacs.2c00521] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptide-derived cyclophanes inhabit a unique niche in the chemical space of macrocyclic peptides with several examples of pharmaceutical importance. Although both synthetic and biocatalytic methods are available for constructing these macrocycles, versatile (bio)catalysts able to incorporate a variety of amino acids that compose the macrocycle would be useful for the creation of diverse peptide cyclophanes. In this report, we synergized the use of bioinformatic tools to map the biosynthetic landscape of radical SAM enzymes (3-CyFEs) that catalyze three-residue cyclophane formation in the biosynthesis of a new family of RiPP natural products, the triceptides. This analysis revealed 3940 (3113 unique) putative precursor sequences predicted to be modified by 3-CyFEs. Several uncharacterized maturase systems were identified that encode unique precursor types. Functional studies were carried out in vivo in Escherichia coli to identify modified precursors containing His and Tyr residues. NMR analysis of the products revealed that Tyr and His can also be incorporated into cyclophane macrocycles by 3-CyFEs. Collectively, all aromatic amino acids can be incorporated by 3-CyFEs, and the cyclophane formation strictly occurs via a C(sp2)-C(sp3) cross-link between the (hetero)aromatic ring to Cβ. In addition to 3-CyFEs, we functionally validated an Fe(II)/α-ketoglutarate-dependent hydroxylase, resulting in β-hydroxylated residues within the cyclophane rings. This study reveals the potential breadth of triceptide precursors and a systematic approach for studying these enzymes to broaden the diversity of peptide macrocycles.
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Affiliation(s)
- Ryosuke Sugiyama
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Yohei Morishita
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Thi Quynh Ngoc Nguyen
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Yi Wei Tooh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | | | - Justin Lo Choy
- Department of Pharmacology and Toxicology, University of Toronto, Toronto M5S 1A8, Canada
| | - Qi Su
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Wei Yang Goh
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
| | - Gregory Adrian Gunawan
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore.,Molecular Engineering Lab, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Organic & Biomolecular Chemistry, Institute of Sustainability for Chemicals, Energy and Environment, A*STAR, Singapore 138665, Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Singapore Institute of Food and Biotechnology Innovation, A*STAR, Singapore 138673, Singapore
| | - Brandon I Morinaka
- Department of Pharmacy, National University of Singapore, Singapore 117544, Singapore
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