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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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2
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Kulkarni A, Zhou J, Biyani N, Kathad U, Banerjee PP, Srivastava S, Prucsi Z, Solarczyk K, Bhatia K, Ewesuedo RB, Sharma P. LP-184, a Novel Acylfulvene Molecule, Exhibits Anticancer Activity against Diverse Solid Tumors with Homologous Recombination Deficiency. CANCER RESEARCH COMMUNICATIONS 2024; 4:1199-1210. [PMID: 38630886 PMCID: PMC11072798 DOI: 10.1158/2767-9764.crc-23-0554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Homologous recombination (HR)-related gene alterations are present in a significant subset of prostate, breast, ovarian, pancreatic, lung, and colon cancers rendering these tumors as potential responders to specific DNA damaging agents. A small molecule acylfulvene prodrug, LP-184, metabolizes to an active compound by the oxidoreductase activity of enzyme prostaglandin reductase 1 (PTGR1), which is frequently elevated in multiple solid tumor types. Prior work demonstrated that cancer cell lines deficient in a spectrum of DNA damage repair (DDR) pathway genes show increased susceptibility to LP-184. Here, we investigated the potential of LP-184 in targeting multiple tumors with impaired HR function and its mechanism of action as a DNA damaging agent. LP-184 induced elevated DNA double-strand breaks in HR deficient (HRD) cancer cells. Depletion of key HR components BRCA2 or ataxia telangiectasia mutated (ATM) in cancer cells conferred up to 12-fold increased sensitivity to the LP-184. LP-184 showed nanomolar potency in a diverse range of HRD cancer models, including prostate cancer organoids, leiomyosarcoma cell lines, and patient-derived tumor graft models of lung, pancreatic, and prostate cancers. LP-184 demonstrated complete, durable tumor regression in 10 patient-derived xenograft (PDX) models of HRD triple-negative breast cancer (TNBC) including those resistant to PARP inhibitors (PARPi). LP-184 further displayed strong synergy with PARPi in ovarian and prostate cancer cell lines as well as in TNBC PDX models. These preclinical findings illustrate the potential of LP-184 as a pan-HRD cancer therapeutic. Taken together, our results support continued clinical evaluation of LP-184 in a large subset of HRD solid tumors. SIGNIFICANCE New agents with activity against DDR-deficient solid tumors refractory to standard-of-care therapies are needed. We report multiple findings supporting the potential for LP-184, a novel alkylating agent with three FDA orphan drug designations, to fill this void clinically: strong nanomolar potency; sustained, durable regression of solid tumor xenografts; synthetic lethality with HR defects. LP-184 adult phase IA trial to assess safety in advanced solid tumors is ongoing.
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Affiliation(s)
| | | | | | | | - Partha P. Banerjee
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Shiv Srivastava
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
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3
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Han H, Zhang P, Xie Z, Qi J, Wang P, Li C, Xue Z, Wu R, Liu C. Functional Characterization of Sesquiterpene Synthases and P450 Enzymes in Flammulina velutipes for Biosynthesis of Spiro [4.5] Decane Terpene. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38606577 DOI: 10.1021/acs.jafc.4c01636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Flammulina velutipes, a popular edible mushroom, contains sesquiterpenes with potential health benefits. We characterized 12 sesquiterpene synthases and one P450 enzyme in F. velutipes using Aspergillus oryzae as a heterologous expression system, culminating in the biosynthesis of 16 distinct sesquiterpene compounds. An enzyme encoded by the axeB gene responsible for the synthesis of the spiro [4.5] decane compound axenol was discovered, and the mechanism of spirocycle formation was elucidated through quantum mechanical calculations. Furthermore, we delineated the role of a P450 enzyme colocated with AxeB in producing the novel compound 3-oxo-axenol. Our findings highlight the diverse array of sesquiterpene skeletons and functional groups biosynthesized by these enzymes in F. velutipes and underscore the effectiveness of the A. oryzae system as a heterologous host for expressing genes in the Basidiomycota genome. These insights into the biosynthesis of bioactive compounds in F. velutipes have significant implications for functional food and drug development.
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Affiliation(s)
- Haiyan Han
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ping Zhang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Zhekai Xie
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jianzhao Qi
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Pengchao Wang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chang Li
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, HarBin Medical University, Harbin 150081, China
| | - Zheyong Xue
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ruibo Wu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
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Son K, Takhaveev V, Mor V, Yu H, Dillier E, Zilio N, Püllen NJL, Ivanov D, Ulrich HD, Sturla SJ, Schärer OD. Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes. Nat Commun 2024; 15:1388. [PMID: 38360910 PMCID: PMC10869700 DOI: 10.1038/s41467-024-45664-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Most genotoxic anticancer agents fail in tumors with intact DNA repair. Therefore, trabectedin, anagent more toxic to cells with active DNA repair, specifically transcription-coupled nucleotide excision repair (TC-NER), provides therapeutic opportunities. To unlock the potential of trabectedin and inform its application in precision oncology, an understanding of the mechanism of the drug's TC-NER-dependent toxicity is needed. Here, we determine that abortive TC-NER of trabectedin-DNA adducts forms persistent single-strand breaks (SSBs) as the adducts block the second of the two sequential NER incisions. We map the 3'-hydroxyl groups of SSBs originating from the first NER incision at trabectedin lesions, recording TC-NER on a genome-wide scale. Trabectedin-induced SSBs primarily occur in transcribed strands of active genes and peak near transcription start sites. Frequent SSBs are also found outside gene bodies, connecting TC-NER to divergent transcription from promoters. This work advances the use of trabectedin for precision oncology and for studying TC-NER and transcription.
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Affiliation(s)
- Kook Son
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Visesato Mor
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Hobin Yu
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea
| | - Emma Dillier
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Nicola Zilio
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Nikolai J L Püllen
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Dmitri Ivanov
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland.
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea.
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.
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5
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Lal B, Kulkarni A, McDermott J, Rais R, Alt J, Wu Y, Lopez-Bertoni H, Sall S, Kathad U, Zhou J, Slusher BS, Bhatia K, Laterra J. Preclinical Efficacy of LP-184, a Tumor Site Activated Synthetic Lethal Therapeutic, in Glioblastoma. Clin Cancer Res 2023; 29:4209-4218. [PMID: 37494541 DOI: 10.1158/1078-0432.ccr-23-0673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/15/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Glioblastoma (GBM) is the most common brain malignancy with median survival <2 years. Standard-of-care temozolomide has marginal efficacy in approximately 70% of patients due to MGMT expression. LP-184 is an acylfulvene-derived prodrug activated by the oxidoreductase PTGR1 that alkylates at N3-adenine, not reported to be repaired by MGMT. This article examines LP-184 efficacy against preclinical GBM models and identifies molecular predictors of LP-184 efficacy in clinical GBM. EXPERIMENTAL DESIGN LP-184 effects on GBM cell viability and DNA damage were determined using cell lines, primary PDX-derived cells and patient-derived neurospheres. GBM cell sensitivities to LP-184 relative to temozolomide and MGMT expression were examined. Pharmacokinetics and CNS bioavailability were evaluated in mice with GBM xenografts. LP-184 effects on GBM xenograft growth and animal survival were determined. Machine learning, bioinformatic tools, and clinical databases identified molecular predictors of GBM cells and tumors to LP-184 responsiveness. RESULTS LP-184 inhibited viability of multiple GBM cell isolates including temozolomide-resistant and MGMT-expressing cells at IC50 = approximately 22-310 nmol/L. Pharmacokinetics showed favorable AUCbrain/plasma and AUCtumor/plasma ratios of 0.11 (brain Cmax = 839 nmol/L) and 0.2 (tumor Cmax = 2,530 nmol/L), respectively. LP-184 induced regression of GBM xenografts and prolonged survival of mice bearing orthotopic xenografts. Bioinformatic analyses identified PTGR1 elevation in clinical GBM subtypes and associated LP-184 sensitivity with EGFR signaling, low nucleotide excision repair (NER), and low ERCC3 expression. Spironolactone, which induces ERCC3 degradation, decreased LP-184 IC50 3 to 6 fold and enhanced GBM xenograft antitumor responses. CONCLUSIONS These results establish LP-184 as a promising chemotherapeutic for GBM with enhanced efficacy in intrinsic or spironolactone-induced TC-NER-deficient tumors.
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Affiliation(s)
- Bachchu Lal
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
| | | | | | - Rana Rais
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jesse Alt
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ying Wu
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sophie Sall
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
| | | | | | - Barbara S Slusher
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Johns Hopkins Drug Discovery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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6
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Wu J, Yang X, Duan Y, Wang P, Qi J, Gao JM, Liu C. Biosynthesis of Sesquiterpenes in Basidiomycetes: A Review. J Fungi (Basel) 2022; 8:jof8090913. [PMID: 36135638 PMCID: PMC9501842 DOI: 10.3390/jof8090913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/10/2022] [Accepted: 08/26/2022] [Indexed: 11/19/2022] Open
Abstract
Sesquiterpenes are common small-molecule natural products with a wide range of promising applications and are biosynthesized by sesquiterpene synthase (STS). Basidiomycetes are valuable and important biological resources. To date, hundreds of related sesquiterpenoids have been discovered in basidiomycetes, and the biosynthetic pathways of some of these compounds have been elucidated. This review summarizes 122 STSs and 2 fusion enzymes STSs identified from 26 species of basidiomycetes over the past 20 years. The biological functions of enzymes and compound structures are described, and related research is discussed.
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Affiliation(s)
- Jiajun Wu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiaoran Yang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yingce Duan
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Pengchao Wang
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jianzhao Qi
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China
| | - Chengwei Liu
- Key Laboratory for Enzyme and Enzyme-like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence:
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7
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Yamac M, Engür Öztürk S, Cantürk Z, Dikmen M. Comparative Analysis of Antioxidant and Anticancer Activities of Fruiting bodies, Mycelial Biomass and Culture Liquid of Omphalotus olearius OBCC 2503 (Agaricomycetes) from Turkey. Int J Med Mushrooms 2022; 24:61-72. [DOI: 10.1615/intjmedmushrooms.2022045033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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8
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Dai Q, Zhang FL, Feng T. Sesquiterpenoids Specially Produced by Fungi: Structures, Biological Activities, Chemical and Biosynthesis (2015-2020). J Fungi (Basel) 2021; 7:1026. [PMID: 34947008 PMCID: PMC8705726 DOI: 10.3390/jof7121026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 11/28/2021] [Accepted: 11/28/2021] [Indexed: 12/28/2022] Open
Abstract
Fungi are widely distributed in the terrestrial environment, freshwater, and marine habitat. Only approximately 100,000 of these have been classified although there are about 5.1 million characteristic fungi all over the world. These eukaryotic microbes produce specialized metabolites and participate in a variety of ecological functions, such as quorum detection, chemical defense, allelopathy, and maintenance of symbiosis. Fungi therefore remain an important resource for the screening and discovery of biologically active natural products. Sesquiterpenoids are arguably the richest natural products from plants and micro-organisms. The rearrangement of the 15 high-ductility carbons gave rise to a large number of different skeletons. At the same time, abundant structural variations lead to a diversification of biological activity. This review examines the isolation, structural determination, bioactivities, and synthesis of sesquiterpenoids that were specially produced by fungi over the past five years (2015-2020).
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Affiliation(s)
| | | | - Tao Feng
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, China; (Q.D.); (F.-L.Z.)
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9
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Tang JJ, Wang MR, Dong S, Huang LF, He QR, Gao JM. 1,10-Seco-Eudesmane sesquiterpenoids as a new type of anti-neuroinflammatory agents by suppressing TLR4/NF-κB/MAPK pathways. Eur J Med Chem 2021; 224:113713. [PMID: 34315042 DOI: 10.1016/j.ejmech.2021.113713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/14/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022]
Abstract
Dysregulation of neuroinflammation is a key pathological factor in the progressive neuronal damage of neurodegenerative diseases. An in-house natural products library of 1407 compounds were screened against neuroinflammation in lipopolysaccharide (LPS)-activated microglia cells to identify a novel hit 1,6-O,O-diacetylbritannilactone (OABL) with anti-neuroinflammatory activity. Furthermore, a 1,10-seco-eudesmane sesquiterpenoid library containing 33 compounds was constructed by semisynthesis of a major component 1-O-acetylbritannilactone (ABL) from the traditional Chinese medicinal herb Inula Britannica L. Compound 15 was identified as a promising anti-neuroinflammatory agent by nitrite oxide (NO) production screening. 15 could attenuate tumor necrosis factor-α (TNF-α) and prostaglandin E2 (PGE2) productions, and inhibit the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) at a submicromolar level. Mechanistic study revealed that 15 significantly modulated TLR4/NF-kB and p38 MAPK pathways, and upregulated the anti-oxidant response HO-1. Besides, 15 promoted the conversion of the microglia from M1 to M2 phenotype by increasing levels of arginase-1 and IL-10. The structure-activity relationships (SARs) analysis indicated that the α-methylene-γ-lactone motifs, epoxidation of C5=C10 bond and bromination of C14 were important to the activity. Parallel artificial membrane permeation assay (PAMPA) also demonstrated that 15 and OABL can overcome the blood-brain barrier (BBB). In all, compound 15 is a promising anti-neuroinflammatory lead with potent anti-inflammatory effects via the blockage of TLR4/NF-κB/MAPK pathways, favorable BBB penetration property, and low cytotoxicity.
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Affiliation(s)
- Jiang-Jiang Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, PR China.
| | - Min-Ran Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, PR China
| | - Shuai Dong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, PR China
| | - Lan-Fang Huang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, PR China
| | - Qiu-Rui He
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, PR China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, PR China.
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10
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Topka S, Steinsnyder Z, Ravichandran V, Tkachuk K, Kemel Y, Bandlamudi C, Winkel Madsen M, Furberg H, Ouerfelli O, Rudin CM, Iyer G, Lipkin SM, Mukherjee S, Solit DB, Berger MF, Bajorin DF, Rosenberg JE, Taylor BS, de Stanchina E, Vijai J, Offit K. Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer. Clin Cancer Res 2021; 27:1997-2010. [PMID: 33199492 DOI: 10.1158/1078-0432.ccr-20-3322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/19/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Nucleotide excision repair (NER) gene alterations constitute potential cancer therapeutic targets. We explored the prevalence of NER gene alterations across cancers and putative therapeutic strategies targeting these vulnerabilities. EXPERIMENTAL DESIGN We interrogated our institutional dataset with mutational data from more than 40,000 patients with cancer to assess the frequency of putative deleterious alterations in four key NER genes. Gene-edited isogenic pairs of wild-type and mutant ERCC2 or ERCC3 cell lines were created and used to assess response to several candidate drugs. RESULTS We found that putative damaging germline and somatic alterations in NER genes were present with frequencies up to 10% across multiple cancer types. Both in vitro and in vivo studies showed significantly enhanced sensitivity to the sesquiterpene irofulven in cells harboring specific clinically observed heterozygous mutations in ERCC2 or ERCC3. Sensitivity of NER mutants to irofulven was greater than to a current standard-of-care agent, cisplatin. Hypomorphic ERCC2/3-mutant cells had impaired ability to repair irofulven-induced DNA damage. Transcriptomic profiling of tumor tissues suggested codependencies between DNA repair pathways, indicating a potential benefit of combination therapies, which were confirmed by in vitro studies. CONCLUSIONS These findings provide novel insights into a synthetic lethal relationship between clinically observed NER gene deficiencies and sensitivity to irofulven and its potential synergistic combination with other drugs.See related commentary by Jiang and Greenberg, p. 1833.
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Affiliation(s)
- Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vignesh Ravichandran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Helena Furberg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ouathek Ouerfelli
- Chemical Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F Bajorin
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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11
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Kathad U, Kulkarni A, McDermott JR, Wegner J, Carr P, Biyani N, Modali R, Richard JP, Sharma P, Bhatia K. A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications. BMC Bioinformatics 2021; 22:102. [PMID: 33653269 PMCID: PMC7923321 DOI: 10.1186/s12859-021-04040-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Non-targeted cytotoxics with anticancer activity are often developed through preclinical stages using response criteria observed in cell lines and xenografts. A panel of the NCI-60 cell lines is frequently the first line to define tumor types that are optimally responsive. Open data on the gene expression of the NCI-60 cell lines, provides a unique opportunity to add another dimension to the preclinical development of such drugs by interrogating correlations with gene expression patterns. Machine learning can be used to reduce the complexity of whole genome gene expression patterns to derive manageable signatures of response. Application of machine learning in early phases of preclinical development is likely to allow a better positioning and ultimate clinical success of molecules. LP-184 is a highly potent novel alkylating agent where the preclinical development is being guided by a dedicated machine learning-derived response signature. We show the feasibility and the accuracy of such a signature of response by accurately predicting the response to LP-184 validated using wet lab derived IC50s on a panel of cell lines. RESULTS We applied our proprietary RADR® platform to an NCI-60 discovery dataset encompassing LP-184 IC50s and publicly available gene expression data. We used multiple feature selection layers followed by the XGBoost regression model and reduced the complexity of 20,000 gene expression values to generate a 16-gene signature leading to the identification of a set of predictive candidate biomarkers which form an LP-184 response gene signature. We further validated this signature and predicted response to an additional panel of cell lines. Considering fold change differences and correlation between actual and predicted LP-184 IC50 values as validation performance measures, we obtained 86% accuracy at four-fold cut-off, and a strong (r = 0.70) and significant (p value 1.36e-06) correlation between actual and predicted LP-184 sensitivity. In agreement with the perceived mechanism of action of LP-184, PTGR1 emerged as the top weighted gene. CONCLUSION Integration of a machine learning-derived signature of response with in vitro assessment of LP-184 efficacy facilitated the derivation of manageable yet robust biomarkers which can be used to predict drug sensitivity with high accuracy and clinical value.
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Affiliation(s)
- Umesh Kathad
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA.
| | - Aditya Kulkarni
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | | | - Jordan Wegner
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Peter Carr
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Neha Biyani
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Rama Modali
- REPROCELL USA Inc., 9000 Virginia Manor Rd, Ste 207, Beltsville, MD, 20705, USA
| | | | - Panna Sharma
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Kishor Bhatia
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
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12
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Yong JY, Li WR, Wang XJ, Su GZ, Li M, Zhang JP, Jia HL, Li YH, Wang RB, Gan M, Ma SG. Illihenin A: An Antiviral Sesquiterpenoid with a Cage-like Tricyclo[6.2.2.01,5]dodecane Skeleton from Illicium henryi. J Org Chem 2021; 86:2017-2022. [DOI: 10.1021/acs.joc.0c02727] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jin-Yao Yong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Wen-Rui Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Xiao-jing Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Guo-Zhu Su
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Mi Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Jian-Pei Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Hong-Li Jia
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, People’s Republic of China
| | - Yu-Huan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Ru-Bing Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Shuang-Gang Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
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13
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Oh J, Xu J, Chong J, Wang D. Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194659. [PMID: 33271312 DOI: 10.1016/j.bbagrm.2020.194659] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022]
Abstract
Transcription elongation by RNA polymerase II (Pol II) is constantly challenged by numerous types of obstacles that lead to transcriptional pausing or stalling. These obstacles include DNA lesions, DNA epigenetic modifications, DNA binding proteins, and non-B form DNA structures. In particular, lesion-induced prolonged transcriptional blockage or stalling leads to genome instability, cellular dysfunction, and cell death. Transcription-coupled nucleotide excision repair (TC-NER) pathway is the first line of defense that detects and repairs these transcription-blocking DNA lesions. In this review, we will first summarize the recent research progress toward understanding the molecular basis of transcriptional pausing and stalling by different kinds of obstacles. We will then discuss new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences; University of California, San Diego, La Jolla, CA 92093, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, United States; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States.
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14
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Deng YH, Chu WD, Shang YH, Yu KY, Jia ZL, Fan CA. P(NMe2)3-Mediated Umpolung Spirocyclopropanation Reaction of p-Quinone Methides: Diastereoselective Synthesis of Spirocyclopropane-Cyclohexadienones. Org Lett 2020; 22:8376-8381. [DOI: 10.1021/acs.orglett.0c02998] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yu-Hua Deng
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, and School of Chemical Science and Technology, Yunnan University, No. 2 Cuihu North Road, Kunming 650091, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, 222 Tianshui Nanlu, Lanzhou 730000, China
| | - Wen-Dao Chu
- College of Chemistry and Chemical Engineering, China West Normal University, No. 1 Shida Road, Nanchong 637002, China
| | - Yun-Han Shang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Research & Development Center for Natural Products, and School of Chemical Science and Technology, Yunnan University, No. 2 Cuihu North Road, Kunming 650091, China
| | - Ke-Yin Yu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, 222 Tianshui Nanlu, Lanzhou 730000, China
| | - Zhi-Long Jia
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, 222 Tianshui Nanlu, Lanzhou 730000, China
| | - Chun-An Fan
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, 222 Tianshui Nanlu, Lanzhou 730000, China
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15
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Outahar F, Moumou M, Hannioui A, Rakib EM, El Ammari L, Saadi M, Akssira M. Synthesis of novel spiro-pyrazole and spiro-isoxazoline derivatives of 9α- and 9β-hydroxyparthenolide. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152409] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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Dai Q, Zhang FL, Du JX, Li ZH, Feng T, Liu JK. Illudane Sesquiterpenoids from Edible Mushroom Agrocybe salicacola and Their Bioactivities. ACS OMEGA 2020; 5:21961-21967. [PMID: 32905428 PMCID: PMC7469647 DOI: 10.1021/acsomega.0c03314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
To comprehensively understand the chemical constituents of the edible mushroom Agrocybe salicacola and their biological functions, a phytochemical separation of the cultural broth of A. salicacola led to the isolation of four new illudane sesquiterpenoids, agrocybins H-K (1-4), along with 10 known analogues (5-14). Compounds 2-4 were racemates of which 2 and 3 were further separated into single enantiomers as 2a/2b and 3a/3b. All new structures with absolute configurations were elucidated on the basis of an extensive spectroscopic analysis and quantum chemistry calculations. Compound 1 possesses a new carbon skeleton that might be derived from the protoilludane backbone. Compounds 1, 5, 8, and 9 show a certain degree of cytotoxicity to five human cancer cell lines. Compound 1 shows a mild inhibitory effect on nitric oxide production with an IC50 value of 31.4 μM. It is concluded that A. salicacola is rich in illudin derivatives with potential bioactivity prospects, which would make A. salicacola a good material of medicine and food homology.
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Affiliation(s)
- Quan Dai
- School
of Pharmaceutical Sciences, South-Central
University for Nationalities, Wuhan 430074, P. R. China
| | - Fa-Lei Zhang
- School
of Pharmaceutical Sciences, South-Central
University for Nationalities, Wuhan 430074, P. R. China
| | - Jiao-Xian Du
- School
of Pharmaceutical Sciences, South-Central
University for Nationalities, Wuhan 430074, P. R. China
| | - Zheng-Hui Li
- School
of Pharmaceutical Sciences, South-Central
University for Nationalities, Wuhan 430074, P. R. China
- The
Modernization Engineering Technology Research Center of Ethnic Minority
Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China
| | - Tao Feng
- School
of Pharmaceutical Sciences, South-Central
University for Nationalities, Wuhan 430074, P. R. China
- The
Modernization Engineering Technology Research Center of Ethnic Minority
Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China
| | - Ji-Kai Liu
- School
of Pharmaceutical Sciences, South-Central
University for Nationalities, Wuhan 430074, P. R. China
- The
Modernization Engineering Technology Research Center of Ethnic Minority
Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, P. R. China
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17
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Zhang M, Li T, Cui C, Song X, Chang J. Stereoselective Sequential Spirocyclopropanation/Cloke-Wilson Rearrangement Reactions for Synthesis of trans-β,γ-Disubstituted γ-Butyrolactones Using Alkylidene Meldrum's Acid and Benzyl Halides. J Org Chem 2020; 85:2266-2276. [PMID: 31920086 DOI: 10.1021/acs.joc.9b02978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The stereoselective sequential spirocyclopropanation/Cloke-Wilson rearrangement reactions have been developed to synthesize γ-butyrolactones using alkylidene Meldrum's acids and benzyl halides. The DBU-promoted spirocyclopropanation was carried out efficiently at room temperature to generate trans-isomeric spirocyclopropyl Meldrum's acid, and the following stereospecific thermal decarboxylative Cloke-Wilson rearrangement afforded trans-γ-butyrolactones. A variety of aromatic and aliphatic Meldrum's acid derived olefins and benzyl halides were tolerated. Various trans-β,γ-disubstituted γ-butyrolactones were produced with moderate to good overall yields from 46 to 96% and excellent diastereoselectivities.
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Affiliation(s)
- Minli Zhang
- College of Chemistry , Zhengzhou University , No. 100 Science Avenue , Zhengzhou 450001 , P. R. China
| | - Tong Li
- College of Chemistry , Zhengzhou University , No. 100 Science Avenue , Zhengzhou 450001 , P. R. China
| | - Chaoxing Cui
- College of Chemistry , Zhengzhou University , No. 100 Science Avenue , Zhengzhou 450001 , P. R. China
| | - Xixi Song
- College of Chemistry , Zhengzhou University , No. 100 Science Avenue , Zhengzhou 450001 , P. R. China
| | - Junbiao Chang
- College of Chemistry , Zhengzhou University , No. 100 Science Avenue , Zhengzhou 450001 , P. R. China
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18
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Le P, Nodwell MB, Eirich J, Sieber SA. A Chemical Proteomic Analysis of Illudin-Interacting Proteins. Chemistry 2019; 25:12644-12651. [PMID: 31310394 PMCID: PMC6900183 DOI: 10.1002/chem.201902919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/15/2019] [Indexed: 01/22/2023]
Abstract
The illudin natural product family are fungal secondary metabolites with a characteristic spirocyclopropyl‐substituted fused 6,5‐bicyclic ring system. They have been extensively studied for their cytotoxicity in various tumor cell types, and semisynthetic derivatives with improved therapeutic characteristics have progressed to clinical trials. Although it is believed that this potent alkylating compound class acts mainly through DNA modification, little is known about its binding to protein sites in a cellular context. To reveal putative protein targets of the illudin family in live cancer cells, we employed a semisynthetic strategy to access a series of illudin‐based probes for activity‐based protein profiling (ABPP). While the probes largely retained potent cytotoxicity, proteomic profiling studies unraveled multiple protein hits, suggesting that illudins exert their mode of action not from addressing a specific protein target but rather from DNA modification and unselective protein binding.
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Affiliation(s)
- Philipp Le
- Department Chemie, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Matthew B Nodwell
- Department Chemie, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.,Current address: Department of Chemistry, Simon Fraser University, Burnaby, Canada
| | - Jürgen Eirich
- Department Chemie, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.,Current address: Institute for Plant Biology and Biotechnology (IBBP), Universität Münster, Münster, Germany
| | - Stephan A Sieber
- Department Chemie, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
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19
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Zhu Y, Zhang M, Li T, Song X. AlCl
3
‐Promoted Stereospecific Cloke‐Wilson Rearrangement of Spirocyclopropyl Barbiturates for the Synthesis of Substituted Dihydrofuro[2,3‐
d
]pyrimidines. ChemistrySelect 2019. [DOI: 10.1002/slct.201903330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yuanyuan Zhu
- College of Chemistry and Molecular EngineeringZhengzhou University No.100 Science Avenue Zhengzhou 450001, P. R. China
| | - Minli Zhang
- College of Chemistry and Molecular EngineeringZhengzhou University No.100 Science Avenue Zhengzhou 450001, P. R. China
| | - Tong Li
- College of Chemistry and Molecular EngineeringZhengzhou University No.100 Science Avenue Zhengzhou 450001, P. R. China
| | - Xixi Song
- College of Chemistry and Molecular EngineeringZhengzhou University No.100 Science Avenue Zhengzhou 450001, P. R. China
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20
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Wilson MR, Jiang Y, Villalta PW, Stornetta A, Boudreau PD, Carrá A, Brennan CA, Chun E, Ngo L, Samson LD, Engelward BP, Garrett WS, Balbo S, Balskus EP. The human gut bacterial genotoxin colibactin alkylates DNA. Science 2019; 363:363/6428/eaar7785. [PMID: 30765538 DOI: 10.1126/science.aar7785] [Citation(s) in RCA: 329] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/16/2018] [Accepted: 12/21/2018] [Indexed: 12/13/2022]
Abstract
Certain Escherichia coli strains residing in the human gut produce colibactin, a small-molecule genotoxin implicated in colorectal cancer pathogenesis. However, colibactin's chemical structure and the molecular mechanism underlying its genotoxic effects have remained unknown for more than a decade. Here we combine an untargeted DNA adductomics approach with chemical synthesis to identify and characterize a covalent DNA modification from human cell lines treated with colibactin-producing E. coli Our data establish that colibactin alkylates DNA with an unusual electrophilic cyclopropane. We show that this metabolite is formed in mice colonized by colibactin-producing E. coli and is likely derived from an initially formed, unstable colibactin-DNA adduct. Our findings reveal a potential biomarker for colibactin exposure and provide mechanistic insights into how a gut microbe may contribute to colorectal carcinogenesis.
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Affiliation(s)
- Matthew R Wilson
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Yindi Jiang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Paul D Boudreau
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Andrea Carrá
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Caitlin A Brennan
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eunyoung Chun
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lizzie Ngo
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | | | - Wendy S Garrett
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Institute, Boston, MA 02115, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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21
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Jiang Y, Stornetta A, Villalta PW, Wilson MR, Boudreau PD, Zha L, Balbo S, Balskus EP. Reactivity of an Unusual Amidase May Explain Colibactin's DNA Cross-Linking Activity. J Am Chem Soc 2019; 141:11489-11496. [PMID: 31251062 PMCID: PMC6728428 DOI: 10.1021/jacs.9b02453] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Certain commensal and pathogenic bacteria produce colibactin, a small-molecule genotoxin that causes interstrand cross-links in host cell DNA. Although colibactin alkylates DNA, the molecular basis for cross-link formation is unclear. Here, we report that the colibactin biosynthetic enzyme ClbL is an amide bond-forming enzyme that links aminoketone and β-keto thioester substrates in vitro and in vivo. The substrate specificity of ClbL strongly supports a role for this enzyme in terminating the colibactin NRPS-PKS assembly line and incorporating two electrophilic cyclopropane warheads into the final natural product scaffold. This proposed transformation was supported by the detection of a colibactin-derived cross-linked DNA adduct. Overall, this work provides a biosynthetic explanation for colibactin's DNA cross-linking activity and paves the way for further study of its chemical structure and biological roles.
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Affiliation(s)
- Yindi Jiang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, United States
| | - Peter W. Villalta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, United States
| | - Matthew R. Wilson
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Paul D. Boudreau
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Li Zha
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, United States
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, United States
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22
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Pourshab M, Asghari S, Tajbakhsh M, Khalilpour A. Diastereoselective Sonochemical Synthesis of Spirocyclopropaneoxindoles and Evaluation of Their Antioxidant and Cytotoxic Activities. Chem Biodivers 2019; 16:e1900087. [PMID: 30994253 DOI: 10.1002/cbdv.201900087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/16/2019] [Indexed: 01/04/2023]
Abstract
An efficient diastereoselective synthesis of spirocyclopropaneoxindoles is reported using three-component reactions of various phenacylidenetriphenylphosphorane, isatins and phenacyl bromide under ultrasonic irradiation. The structures of synthesized spirocyclopropaneoxindoles were characterized by their spectral data. The antioxidant activities of the synthesized compounds were evaluated by 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay. Among the products, those with NH group in their structure exhibited higher antioxidant activities than other derivatives. Also, in vitro cytotoxicity of compounds 4b, 4e, 4j, 4k were examined against heLa cancer cell lines using MTT assay. The results revealed that compound 4j with chlorine substituent on phenyl group displayed higher cytotoxicity activity (IC50 =4.50±0.30 μg/mL) after 48 h.
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Affiliation(s)
- Maryam Pourshab
- Department of Organic Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-95447, Iran
| | - Sakineh Asghari
- Department of Organic Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-95447, Iran.,Nano and Biotechnology Research group, University of Mazandaran, Babolsar, 47416-95447, Iran
| | - Mahmoud Tajbakhsh
- Department of Organic Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-95447, Iran
| | - Asieh Khalilpour
- Department of Environmental health Engineering, Faculty of Paramedical Sciences, Babol University of Medicinal Sciences, Babol, 4717-647745, Iran
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23
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Biological and chemical diversity go hand in hand: Basidiomycota as source of new pharmaceuticals and agrochemicals. Biotechnol Adv 2019; 37:107344. [PMID: 30738916 DOI: 10.1016/j.biotechadv.2019.01.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
The Basidiomycota constitutes the second largest higher taxonomic group of the Fungi after the Ascomycota and comprises over 30.000 species. Mycelial cultures of Basidiomycota have already been studied since the 1950s for production of antibiotics and other beneficial secondary metabolites. Despite the fact that unique and selective compounds like pleuromutilin were obtained early on, it took several decades more until they were subjected to a systematic screening for antimicrobial and anticancer activities. These efforts led to the discovery of the strobilurins and several hundreds of further compounds that mainly constitute terpenoids. In parallel the traditional medicinal mushrooms of Asia were also studied intensively for metabolite production, aimed at finding new therapeutic agents for treatment of various diseases including metabolic disorders and the central nervous system. While the evaluation of this organism group has in general been more tedious as compared to the Ascomycota, the chances to discover new metabolites and to develop them further to candidates for drugs, agrochemicals and other products for the Life Science industry have substantially increased over the past decade. This is owing to the revolutionary developments in -OMICS techniques, bioinformatics, analytical chemistry and biotechnological process technology, which are steadily being developed further. On the other hand, the new developments in polythetic fungal taxonomy now also allow a more concise selection of previously untapped organisms. The current review is dedicated to summarize the state of the art and to give an outlook to further developments.
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Lv X, Hu F, Duan K, Li SS, Liu Q, Xiao J. Aromatization-Driven Cascade [1,5]-Hydride Transfer/Spirocyclization Promoted by Fluorinated Alcohols. J Org Chem 2019; 84:1833-1844. [DOI: 10.1021/acs.joc.8b02754] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xintong Lv
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Fangzhi Hu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Kang Duan
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Shuai-Shuai Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Qing Liu
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266590, China
| | - Jian Xiao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
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Tang Y, Zhao ZZ, Yao JN, Feng T, Li ZH, Chen HP, Liu JK. Irpeksins A-E, 1,10- seco-Eburicane-Type Triterpenoids from the Medicinal Fungus Irpex lacteus and Their Anti-NO Activity. JOURNAL OF NATURAL PRODUCTS 2018; 81:2163-2168. [PMID: 30296083 DOI: 10.1021/acs.jnatprod.7b00845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Five new triterpenoids, irpeksins A-E (1-5), were isolated from fruiting bodies of the medicinal fungus Irpex lacteus. The structures as well as absolute configurations of the new compounds were established via extensive spectroscopic analysis, computational methods, and Cotton effects. Compounds 1-4 are featured by a scaffold of 1,10- seco- and ring B aromatic eburicane (24-methyllanostane), and compound 5 is characterized by a scaffold of 1,10-9,11- diseco- and ring B aromatic eburicane, which represents unprecedented cleavage patterns in the lanostane family. Compounds 1-5 showed significant inhibitory activity against NO production in LPS-activated RAW 264.7 macrophage cells with IC50 values varying from 2.2 to 19.6 μM.
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Affiliation(s)
- Yang Tang
- State Key Laboratory of Phytochemistry and Plant Resources in West China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Zhen-Zhu Zhao
- State Key Laboratory of Phytochemistry and Plant Resources in West China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
| | - Jian-Neng Yao
- State Key Laboratory of Phytochemistry and Plant Resources in West China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Tao Feng
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
| | - Zheng-Hui Li
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
| | - He-Ping Chen
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
| | - Ji-Kai Liu
- School of Pharmaceutical Sciences , South-Central University for Nationalities , Wuhan 430074 , People's Republic of China
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Shao J, Chen W, Zhao M, Shu K, Liu H, Tang P. Substrate-Controlled Synthesis of Spirocyclopropylpyrazolones and Bicyclic 4,5-Dihydropyrazoles from 1,2-Diaza-1,3-dienes with Sulfur Ylides. Org Lett 2018; 20:3992-3995. [DOI: 10.1021/acs.orglett.8b01562] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiaan Shao
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou, 310018, P. R. China
| | - Wenteng Chen
- College of Pharmaceutical Science, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Menghao Zhao
- Innovation Center of Chinese Medicine, China State Institute of Pharmaceutical Industry, Shanghai 201203, P. R. China
| | - Ke Shu
- College of Pharmaceutical Science, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Huan Liu
- College of Pharmaceutical Science, Zhejiang University, Hangzhou, 310058, P. R. China
| | - Pai Tang
- College of Pharmaceutical Science, Zhejiang University, Hangzhou, 310058, P. R. China
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Yang S, Lu D, Zhu Y, Shi M, Luo F, Gong Y. Ethyl 6-Hydroxyfulvene-1-Carboxylate: A Reagent Discriminating Primary Amines from Secondary Amines. J Org Chem 2018; 83:6681-6689. [PMID: 29851346 DOI: 10.1021/acs.joc.8b01046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A highly chemo-selective reaction was observed when ethyl 6-hydroxyfulvene-1-carboxylate 1 was treated with different nucleophiles such as primary amines, secondary amines, alcohols, and thiols. Among them, only primary amines are reactive toward 1 to afford the condensation products 3, which exhibit good stability under both weakly acidic and basic conditions. The condensation process proved to be reversible between different primary amines. On the basis of this observation, the chemical selectivity of typical primary aromatic amines was evaluated quantitatively by determining equilibrium constants of the condensation reactions with aniline as a reference. Moreover, the primary amines of 3 can be readily released upon treatment with aqueous ammonia, making 6-hydroxyfulvene-1-carboxylate 1 a promising protecting reagent for primary amines.
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Affiliation(s)
- Sen Yang
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , China
| | - Dengfu Lu
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , China
| | - Yuequan Zhu
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , China
| | - Mei Shi
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , China
| | - Fan Luo
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , China
| | - Yuefa Gong
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , 1037 Luoyu Road , Wuhan 430074 , China
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Faïs T, Delmas J, Barnich N, Bonnet R, Dalmasso G. Colibactin: More Than a New Bacterial Toxin. Toxins (Basel) 2018; 10:toxins10040151. [PMID: 29642622 PMCID: PMC5923317 DOI: 10.3390/toxins10040151] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 12/16/2022] Open
Abstract
Cyclomodulins are bacterial toxins that interfere with the eukaryotic cell cycle. A new cyclomodulin called colibactin, which is synthetized by the pks genomic island, was discovered in 2006. Despite many efforts, colibactin has not yet been purified, and its structure remains elusive. Interestingly, the pks island is found in members of the family Enterobacteriaceae (mainly Escherichia coli and Klebsiella pneumoniae) isolated from different origins, including from intestinal microbiota, septicaemia, newborn meningitis, and urinary tract infections. Colibactin-producing bacteria induce chromosomal instability and DNA damage in eukaryotic cells, which leads to senescence of epithelial cells and apoptosis of immune cells. The pks island is mainly observed in B2 phylogroup E. coli strains, which include extra-intestinal pathogenic E. coli strains, and pksE. coli are over-represented in biopsies isolated from colorectal cancer. In addition, pksE. coli bacteria increase the number of tumours in diverse colorectal cancer mouse models. Thus, colibactin could have a major impact on human health. In the present review, we will focus on the biological effects of colibactin, the distribution of the pks island, and summarize what is currently known about its synthesis and its structure.
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Affiliation(s)
- Tiphanie Faïs
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-63000 Clermont-Ferrand, France.
- CHU Clermont-Ferrand, Laboratoire de Bactériologie, Centre de Biologie, F-63003 Clermont-Ferrand, France.
| | - Julien Delmas
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-63000 Clermont-Ferrand, France.
- CHU Clermont-Ferrand, Laboratoire de Bactériologie, Centre de Biologie, F-63003 Clermont-Ferrand, France.
| | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-63000 Clermont-Ferrand, France.
| | - Richard Bonnet
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-63000 Clermont-Ferrand, France.
- CHU Clermont-Ferrand, Laboratoire de Bactériologie, Centre de Biologie, F-63003 Clermont-Ferrand, France.
| | - Guillaume Dalmasso
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-63000 Clermont-Ferrand, France.
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Wang X, Li Y, Knecht T, Daniliuc CG, Houk KN, Glorius F. Unprecedented Dearomatized Spirocyclopropane in a Sequential Rhodium(III)‐Catalyzed C−H Activation and Rearrangement Reaction. Angew Chem Int Ed Engl 2018; 57:5520-5524. [DOI: 10.1002/anie.201800803] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/20/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Xiaoming Wang
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Germany
| | - Yingzi Li
- University of California Department of Chemistry and Biochemistry Los Angeles CA 90095 USA
| | - Tobias Knecht
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Germany
| | - Constantin G. Daniliuc
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Germany
| | - K. N. Houk
- University of California Department of Chemistry and Biochemistry Los Angeles CA 90095 USA
| | - Frank Glorius
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Germany
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Abstract
The use of readily accessible ammonium ylides for (asymmetric) transformations, especially cyclization reactions, has received considerable attention over the past two decades. A variety of highly enantioselective protocols to facilitate annulation reactions have recently been introduced as an alternative to other common methods including S-ylide-mediated strategies. It is the intention of this short review to provide an introduction to this field by highlighting the potential of ammonium ylides for (asymmetric) cyclization reactions as well as to present the limitations and challenges of these methods.
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Affiliation(s)
- Lukas Roiser
- Institute of Organic Chemistry, Johannes Kepler University Linz Altenbergerstr. 69 4040 Linz (Austria)
| | - Katharina Zielke
- Institute of Organic Chemistry, Johannes Kepler University Linz Altenbergerstr. 69 4040 Linz (Austria)
| | - Mario Waser
- Institute of Organic Chemistry, Johannes Kepler University Linz Altenbergerstr. 69 4040 Linz (Austria)
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Wang X, Li Y, Knecht T, Daniliuc CG, Houk KN, Glorius F. Beispielloses dearomatisiertes Spirocyclopropan in einer sequenziellen Rhodium(III)‐katalysierten C‐H‐Aktivierung und Umlagerungsreaktion. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xiaoming Wang
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Deutschland
| | - Yingzi Li
- University of California Department of Chemistry and Biochemistry Los Angeles CA 90095 USA
| | - Tobias Knecht
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Deutschland
| | - Constantin G. Daniliuc
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Deutschland
| | - K. N. Houk
- University of California Department of Chemistry and Biochemistry Los Angeles CA 90095 USA
| | - Frank Glorius
- Westfälische Wilhelms-Universität Münster Organisch-Chemisches Institut Corrensstraße 40 48149 Münster Deutschland
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Tang JJ, He QR, Dong S, Guo X, Wang YG, Lei BL, Tian JM, Gao JM. Diversity Modification and Structure-Activity Relationships of Two Natural Products 1β-hydroxy Alantolactone and Ivangustin as Potent Cytotoxic Agents. Sci Rep 2018; 8:1722. [PMID: 29379131 PMCID: PMC5789092 DOI: 10.1038/s41598-018-20192-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/16/2018] [Indexed: 01/31/2023] Open
Abstract
Sesquiterpene lactones (STLs) are a class of plant secondary metabolites widely found in nature with potent antitumor activities. In this work, two isolated STLs 1β-hydroxy alantolactone (1) and ivangustin (2) were derivatized through diversity-oriented strategy, and in vitro cytotoxic activity assessments were conducted against six cell lines including HeLa, PC-3, HEp-2, HepG2, CHO and HUVEC. The cytotoxic structure-activity relationship showed that the double bond between C5 and C6 was beneficial to improve activity; C1-OH oxidized derivatives showed a slight stronger activity, comparable to the positive drug etoposide (VP-16). Yet, C1-OH esterified derivatives decreased the potency which were different from those of 1-O-acetylbritannilactone (ABL) reported previously by us, and C13-methylene reductive and spiro derivatives resulted in almost complete ablation of cytotoxic activity. Mechanistic basis of cytotoxicity of the representative compound 1i was assayed to relate with apoptosis and cell cycle arrest. Furthermore, 1i inhibited TNF-α-induced canonical NF-κB signaling in PC-3 cells. Molecular modeling studies exhibited additional hydrogen bond interaction between 1i and the residue Lys37 of p65, indicating that 1i could form covalent protein adducts with Cys38 on p65.
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Affiliation(s)
- Jiang-Jiang Tang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
| | - Qiu-Rui He
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Shuai Dong
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Xin Guo
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Yu-Gong Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Bei-Lei Lei
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Jun-Mian Tian
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, China.
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Winter M, Gaunersdorfer C, Roiser L, Zielke K, Monkowius U, Waser M. Synthesis of Trifluoroacetyl-Substituted Cyclopropanes Using Onium Ylides. European J Org Chem 2018; 2018:418-421. [PMID: 29491744 PMCID: PMC5817241 DOI: 10.1002/ejoc.201701699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 01/27/2023]
Abstract
The use of carbonyl-stabilized ammonium- and sulfonium ylides allows for the synthesis of highly-functionalized trifluoroacetyl-substituted cyclopropanes. It turned out that the diastereoselectivities strongly depend on the nature of the chosen ylide and the employed base. The products could be obtained in good yields under operationally simple conditions.
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Affiliation(s)
- Michael Winter
- Institute of Organic ChemistryJohannes Kepler University LinzAltenbergerstr. 694040LinzAustria
| | - Christina Gaunersdorfer
- Institute of Organic ChemistryJohannes Kepler University LinzAltenbergerstr. 694040LinzAustria
| | - Lukas Roiser
- Institute of Organic ChemistryJohannes Kepler University LinzAltenbergerstr. 694040LinzAustria
| | - Katharina Zielke
- Institute of Organic ChemistryJohannes Kepler University LinzAltenbergerstr. 694040LinzAustria
| | - Uwe Monkowius
- School of EducationJohannes Kepler University LinzAltenbergerstr. 694040LinzAustria
| | - Mario Waser
- Institute of Organic ChemistryJohannes Kepler University LinzAltenbergerstr. 694040LinzAustria
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Target Identification of Bioactive Covalently Acting Natural Products. Curr Top Microbiol Immunol 2018; 420:351-374. [PMID: 30105423 DOI: 10.1007/82_2018_121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There are countless natural products that have been isolated from microbes, plants, and other living organisms that have been shown to possess therapeutic activities such as antimicrobial, anticancer, or anti-inflammatory effects. However, developing these bioactive natural products into drugs has remained challenging in part because of their difficulty in isolation, synthesis, mechanistic understanding, and off-target effects. Among the large pool of bioactive natural products lies classes of compounds that contain potential reactive electrophilic centers that can covalently react with nucleophilic amino acid hotspots on proteins and other biological molecules to modulate their biological action. Covalently acting natural products are more amenable to rapid target identification and mapping of specific druggable hotspots within proteins using activity-based protein profiling (ABPP)-based chemoproteomic strategies. In addition, the granular biochemical insights afforded by knowing specific sites of protein modifications of covalently acting natural products enable the pharmacological interrogation of these sites with more synthetically tractable covalently acting small molecules whose structures are more easily tuned. Both discovering binding pockets and targets hit by natural products and exploiting druggable modalities targeted by natural products with simpler molecules may overcome some of the challenges faced with translating natural products into drugs.
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Valkute TR, Aratikatla EK, Gupta NA, Ganga S, Santra MK, Bhattacharya AK. Synthesis and anticancer studies of Michael adducts and Heck arylation products of sesquiterpene lactones, zaluzanin D and zaluzanin C from Vernonia arborea. RSC Adv 2018; 8:38289-38304. [PMID: 35559081 PMCID: PMC9089800 DOI: 10.1039/c8ra06238b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/03/2018] [Indexed: 11/13/2022] Open
Abstract
Sesquiterpene lactones containing α-methylene-γ-lactones, zaluzanin D 1 and zaluzanin C 2 were isolated from the leaves of Vernonia arborea. Several diverse Michael adducts (3–22) and Heck arylation analogs (23–34) of 1 have been synthesized by reacting with various amines and aryl iodides, respectively and were assayed for their in vitro anticancer activities against human breast cancer cell lines MCF7 and MDA-MB-231. Among all the synthesized analogs, Michael adducts 9 and 10 showed better anticancer activities as compared to 1. However, among these compounds, only 10 has minimal cytotoxic effect on normal breast epithelial MCF10A cells. Our detailed mechanistic studies reveal that compounds 9 and 10 execute their antiproliferative activity through induction of apoptosis and thereby inhibit the cancer cells proliferation and compound 10 could be a lead compound for designing potential anti-cancer compound. Sesquiterpene lactones containing α-methylene-γ-lactones, zaluzanin D 1 and zaluzanin C 2 were isolated from the leaves of Vernonia arborea.![]()
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Affiliation(s)
- Tushar R. Valkute
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune-41108
- India
| | - Eswar K. Aratikatla
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune-41108
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Neha A. Gupta
- Biology of Cancer and Chronic Diseases
- National Centre for Cell Sciences
- Pune-411 007
- India
| | - S. Ganga
- Biology of Cancer and Chronic Diseases
- National Centre for Cell Sciences
- Pune-411 007
- India
| | - Manas K. Santra
- Biology of Cancer and Chronic Diseases
- National Centre for Cell Sciences
- Pune-411 007
- India
| | - Asish K. Bhattacharya
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune-41108
- India
- Academy of Scientific and Innovative Research (AcSIR)
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Chen L, Zhang JP, Liu X, Tang JJ, Xiang P, Ma XM. Semisynthesis, an Anti-Inflammatory Effect of Derivatives of 1β-Hydroxy Alantolactone from Inula britannica. Molecules 2017; 22:molecules22111835. [PMID: 29077042 PMCID: PMC6150205 DOI: 10.3390/molecules22111835] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 12/30/2022] Open
Abstract
1β-hydroxy alantolactone, a sesquiterpene lactone mainly isolated from Inula genus plants, exhibits potent anti-inflammatory and anticancer activities. In this work, 1β-hydroxy alantolactone was isolated and five derivatives were prepared through different reactions at the C1-OH and C13-methylene motifs. The structure-activity relationships (SAR) of anti-inflammatory effects against NO production in RAW264.7 cells showed that the α-methylene-γ-butyrolactone motif was essential for NO production suppression and that retaining the C1-OH group can remarkably improve this effect. The NF-κB signaling pathway plays a pivotal role in the regulation of NO expression. Moreover, the levels of p65 and p50 phosphorylation were investigated and active compound 1 inhibited phosphorylation of p65 and p50 in TNF-α-induced NF-κB signaling. Further molecular docking suggested that 1 may target the p65 of NF-κB.
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Affiliation(s)
- Lin Chen
- Department of Immunology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China.
- Department of Infectious Disease, the First Hospital of Lanzhou University, Lanzhou 730000, China.
| | - Jian-Ping Zhang
- Department of Pharmacy, the First Hospital of Lanzhou University, Lanzhou 730000, China.
| | - Xin Liu
- Department of Infectious Disease, the First Hospital of Lanzhou University, Lanzhou 730000, China.
| | - Jiang-Jiang Tang
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, China.
| | - Ping Xiang
- College of Plant Protection, Northwest A&F University, Yangling 712100, China.
| | - Xing-Ming Ma
- Department of Immunology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China.
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Cytotoxic protein from the mushroom Coprinus comatus possesses a unique mode for glycan binding and specificity. Proc Natl Acad Sci U S A 2017; 114:8980-8985. [PMID: 28784797 DOI: 10.1073/pnas.1706894114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glycans possess significant chemical diversity; glycan binding proteins (GBPs) recognize specific glycans to translate their structures to functions in various physiological and pathological processes. Therefore, the discovery and characterization of novel GBPs and characterization of glycan-GBP interactions are significant to provide potential targets for therapeutic intervention of many diseases. Here, we report the biochemical, functional, and structural characterization of a 130-amino-acid protein, Y3, from the mushroom Coprinus comatus Biochemical studies of recombinant Y3 from a yeast expression system demonstrated the protein is a unique GBP. Additionally, we show that Y3 exhibits selective and potent cytotoxicity toward human T-cell leukemia Jurkat cells compared with a panel of cancer cell lines via inducing caspase-dependent apoptosis. Screening of a glycan array demonstrated GalNAcβ1-4(Fucα1-3)GlcNAc (LDNF) as a specific Y3-binding ligand. To provide a structural basis for function, the crystal structure was solved to a resolution of 1.2 Å, revealing a single-domain αβα-sandwich motif. Two monomers were dimerized to form a large 10-stranded, antiparallel β-sheet flanked by α-helices on each side, representing a unique oligomerization mode among GBPs. A large glycan binding pocket extends into the dimeric interface, and docking of LDNF identified key residues for glycan interactions. Disruption of residues predicted to be involved in LDNF/Y3 interactions resulted in the significant loss of binding to Jurkat T-cells and severely impaired their cytotoxicity. Collectively, these results demonstrate Y3 to be a GBP with selective cytotoxicity toward human T-cell leukemia cells and indicate its potential use in cancer diagnosis and treatment.
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39
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Zha L, Jiang Y, Henke MT, Wilson MR, Wang JX, Kelleher NL, Balskus EP. Colibactin assembly line enzymes use S-adenosylmethionine to build a cyclopropane ring. Nat Chem Biol 2017; 13:1063-1065. [PMID: 28805802 PMCID: PMC5657534 DOI: 10.1038/nchembio.2448] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 06/23/2017] [Indexed: 01/01/2023]
Abstract
Despite containing an α-amino acid, the versatile cofactor S-adenosylmethionine (SAM) is not a known building block for nonribosomal peptide synthetase (NRPS) assembly lines. Here we report an unusual NRPS module from colibactin biosynthesis that uses SAM for amide bond formation and subsequent cyclopropanation. Our findings showcase a new use for SAM and reveal a novel biosynthetic route to a functional group that likely mediates colibactin's genotoxicity.
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Affiliation(s)
- Li Zha
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Yindi Jiang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Matthew T Henke
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA
| | - Matthew R Wilson
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jennifer X Wang
- Small Molecule Mass Spectrometry Facility, FAS Division of Science, Cambridge, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.,Department of Molecular Biosciences and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
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40
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Unique ring expansion of a 6-3 bicyclic ring system forming a functionalized 7-membered ring accelerated by nitrogen functional groups. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.06.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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Nie BJ, Wu LH, Hu RF, Sun Y, Wu J, He P, Huang NY. Synthesis of cyclopropa[c]indeno[1,2-b]quinolines through a MCR/Staudinger/aza-Wittig sequence. SYNTHETIC COMMUN 2017. [DOI: 10.1080/00397911.2017.1328065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Bing-Jie Nie
- College of Chemical Engineering and Food Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Li-Hui Wu
- College of Chemical Engineering and Food Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Ruo-Fei Hu
- College of Chemical Engineering and Food Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Yang Sun
- College of Chemical Engineering and Food Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Jing Wu
- College of Chemical Engineering and Food Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Ping He
- College of Chemical Engineering and Food Science, Hubei University of Arts and Science, Xiangyang, Hubei, China
| | - Nian-Yu Huang
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, China
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42
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Xue F, Deng H, Xue C, Mohamed DKB, Tang KY, Wu J. Reaction discovery using acetylene gas as the chemical feedstock accelerated by the "stop-flow" micro-tubing reactor system. Chem Sci 2017; 8:3623-3627. [PMID: 30155207 PMCID: PMC6094156 DOI: 10.1039/c7sc00408g] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/27/2017] [Indexed: 11/30/2022] Open
Abstract
A “stop-flow” micro-tubing reactor system was designed for accelerating reaction discovery using flammable acetylene gas as the feedstock.
Acetylene gas has been applied as a feedstock under transition-metal catalysis and photo-redox conditions to produce important chemicals including terminal alkynes, fulvenes, and fluorinated styrene compounds. The reaction discovery process was accelerated through the use of “stop-flow” micro-tubing reactors. This reactor prototype was developed by joining elements from both continuous micro-flow and conventional batch reactors, which was convenient and effective for gas/liquid reaction screening. Notably, the developed transformations were either inefficient or unsuccessful in conventional batch reactors. Its success relies on the unique advantages provided by this “stop-flow” micro-tubing reactor system.
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Affiliation(s)
- Fei Xue
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543 .
| | - Hongping Deng
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543 .
| | - Chengwen Xue
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543 .
| | | | - Karen Yuanting Tang
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543 .
| | - Jie Wu
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543 .
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43
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Abstract
The use of Cinchona alkaloid-based chiral ammonium ylides allows for the first highly enantioselective and broadly applicable spirocyclopropanation reactions of para-quinone methides. This strategy provides a straightforward protocol toward the chiral spiro[2.5]octa-4,7-dien-6-one skeleton, which is a frequently found structural motif in important biologically active molecules.
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Affiliation(s)
- Lukas Roiser
- Institute of Organic Chemistry, Johannes Kepler University Linz , Altenbergerstr. 69, 4040 Linz, Austria
| | - Mario Waser
- Institute of Organic Chemistry, Johannes Kepler University Linz , Altenbergerstr. 69, 4040 Linz, Austria
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44
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Abstract
Human-associated microorganisms have the potential to biosynthesize numerous secondary metabolites that may mediate important host-microbe and microbe-microbe interactions. However, there is currently a limited understanding of microbiome-derived natural products. A variety of complementary discovery approaches have begun to illuminate this microbial "dark matter," which will in turn allow detailed mechanistic studies of the effects of these molecules on microbiome and host. Herein, we review recent efforts to uncover microbiome-derived natural products, describe the key approaches that were used to identify and characterize these metabolites, discuss potential functional roles of these molecules, and highlight challenges related to this emerging research area.
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Affiliation(s)
- Matthew R Wilson
- From the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Li Zha
- From the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Emily P Balskus
- From the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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45
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Le Bideau F, Kousara M, Chen L, Wei L, Dumas F. Tricyclic Sesquiterpenes from Marine Origin. Chem Rev 2017; 117:6110-6159. [DOI: 10.1021/acs.chemrev.6b00502] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Franck Le Bideau
- BioCIS,
Faculty of Pharmacy, Université Paris-Sud, CNRS, Université Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Mohammad Kousara
- BioCIS,
Faculty of Pharmacy, Université Paris-Sud, CNRS, Université Paris-Saclay, 92290, Châtenay-Malabry, France
- Faculty
of Pharmacy, Al Andalus University, P.O. Box 101, Tartus, Al Qadmus, Syria
| | - Li Chen
- BioCIS,
Faculty of Pharmacy, Université Paris-Sud, CNRS, Université Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Lai Wei
- BioCIS,
Faculty of Pharmacy, Université Paris-Sud, CNRS, Université Paris-Saclay, 92290, Châtenay-Malabry, France
| | - Françoise Dumas
- BioCIS,
Faculty of Pharmacy, Université Paris-Sud, CNRS, Université Paris-Saclay, 92290, Châtenay-Malabry, France
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46
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Diastereoselective Synthesis of Spirocyclopropanes under Mild Conditions via Formal [2 + 1] Cycloadditions Using 2,3-Dioxo-4-benzylidene-pyrrolidines. Molecules 2017; 22:molecules22020328. [PMID: 28241452 PMCID: PMC6155796 DOI: 10.3390/molecules22020328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 12/28/2022] Open
Abstract
A highly diastereoselective cyclopropanation of cyclic enones with sulfur ylides was developed under catalyst-free conditions, producing multifunctional spirocyclopropanes in generally excellent yields (up to 99% yield and >99:1 d.r.). The asymmetric version of this method was realized by using an easily available chiral sulfur ylide, affording products with moderate to good stereoselectivity.
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47
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Otto C, Spivak G, Aloisi CMN, Menigatti M, Naegeli H, Hanawalt PC, Tanasova M, Sturla SJ. Modulation of Cytotoxicity by Transcription-Coupled Nucleotide Excision Repair Is Independent of the Requirement for Bioactivation of Acylfulvene. Chem Res Toxicol 2017; 30:769-776. [PMID: 28076683 DOI: 10.1021/acs.chemrestox.6b00240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioactivation as well as DNA repair affects the susceptibility of cancer cells to the action of DNA-alkylating chemotherapeutic drugs. However, information is limited with regard to the relative contributions of these processes to the biological outcome of metabolically activated DNA alkylating agents. We evaluated the influence of cellular bioactivation capacity and DNA repair on cytotoxicity of the DNA alkylating agent acylfulvene (AF). We compared the cytotoxicity and RNA synthesis inhibition by AF and its synthetic activated analogue iso-M0 in a panel of fibroblast cell lines with deficiencies in transcription-coupled (TC-NER) or global genome nucleotide excision repair (GG-NER). We related these data to the inherent bioactivation capacity of each cell type on the basis of mRNA levels. We demonstrated that specific inactivation of TC-NER by siRNA had the largest positive impact on AF activity in a cancer cell line. These findings establish that transcription-coupled DNA repair reduces cellular sensitivity to AF, independent of the requirement for bioactivation.
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Affiliation(s)
- Claudia Otto
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
| | - Graciela Spivak
- Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich , 8057 Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , 8057 Zurich, Switzerland
| | - Philip C Hanawalt
- Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Marina Tanasova
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland.,Department of Chemistry, Michigan Technological University , Houghton, Michigan 49932, United States
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
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48
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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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49
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Stornetta A, Zimmermann M, Cimino GD, Henderson PT, Sturla SJ. DNA Adducts from Anticancer Drugs as Candidate Predictive Markers for Precision Medicine. Chem Res Toxicol 2017; 30:388-409. [PMID: 27936622 PMCID: PMC5379252 DOI: 10.1021/acs.chemrestox.6b00380] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 01/23/2023]
Abstract
Biomarker-driven drug selection plays a central role in cancer drug discovery and development, and in diagnostic strategies to improve the use of traditional chemotherapeutic drugs. DNA-modifying anticancer drugs are still used as first line medication, but drawbacks such as resistance and side effects remain an issue. Monitoring the formation and level of DNA modifications induced by anticancer drugs is a potential strategy for stratifying patients and predicting drug efficacy. In this perspective, preclinical and clinical data concerning the relationship between drug-induced DNA adducts and biological response for platinum drugs and combination therapies, nitrogen mustards and half-mustards, hypoxia-activated drugs, reductase-activated drugs, and minor groove binding agents are presented and discussed. Aspects including measurement strategies, identification of adducts, and biological factors that influence the predictive relationship between DNA modification and biological response are addressed. A positive correlation between DNA adduct levels and response was observed for the majority of the studies, demonstrating the high potential of using DNA adducts from anticancer drugs as mechanism-based biomarkers of susceptibility, especially as bioanalysis approaches with higher sensitivity and throughput emerge.
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Affiliation(s)
- Alessia Stornetta
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Maike Zimmermann
- Department
of Internal Medicine, Division of Hematology and Oncology and the
UC Davis Comprehensive Cancer Center, University
of California Davis, 4501 X Street, Sacramento, California 95655, United States
- Accelerated
Medical Diagnostics, Inc., 2121 Second Street, B101, Davis, California 95618, United States
| | - George D. Cimino
- Accelerated
Medical Diagnostics, Inc., 2121 Second Street, B101, Davis, California 95618, United States
| | - Paul T. Henderson
- Department
of Internal Medicine, Division of Hematology and Oncology and the
UC Davis Comprehensive Cancer Center, University
of California Davis, 4501 X Street, Sacramento, California 95655, United States
- Accelerated
Medical Diagnostics, Inc., 2121 Second Street, B101, Davis, California 95618, United States
| | - Shana J. Sturla
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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50
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Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels. Appl Microbiol Biotechnol 2017; 101:2603-2618. [PMID: 28078400 DOI: 10.1007/s00253-017-8091-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
Abstract
Recently, several endophytic fungi have been demonstrated to produce volatile organic compounds (VOCs) with properties similar to fossil fuels, called "mycodiesel," while growing on lignocellulosic plant and agricultural residues. The fact that endophytes are plant symbionts suggests that some may be able to produce lignocellulolytic enzymes, making them capable of both deconstructing lignocellulose and converting it into mycodiesel, two properties that indicate that these strains may be useful consolidated bioprocessing (CBP) hosts for the biofuel production. In this study, four endophytes Hypoxylon sp. CI4A, Hypoxylon sp. EC38, Hypoxylon sp. CO27, and Daldinia eschscholzii EC12 were selected and evaluated for their CBP potential. Analysis of their genomes indicates that these endophytes have a rich reservoir of biomass-deconstructing carbohydrate-active enzymes (CAZys), which includes enzymes active on both polysaccharides and lignin, as well as terpene synthases (TPSs), enzymes that may produce fuel-like molecules, suggesting that they do indeed have CBP potential. GC-MS analyses of their VOCs when grown on four representative lignocellulosic feedstocks revealed that these endophytes produce a wide spectrum of hydrocarbons, the majority of which are monoterpenes and sesquiterpenes, including some known biofuel candidates. Analysis of their cellulase activity when grown under the same conditions revealed that these endophytes actively produce endoglucanases, exoglucanases, and β-glucosidases. The richness of CAZymes as well as terpene synthases identified in these four endophytic fungi suggests that they are great candidates to pursue for development into platform CBP organisms.
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