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Han EJ, Lee SR, Townsend CA, Seyedsayamdost MR. Targeted Discovery of Cryptic Enediyne Natural Products via FRET-Coupled High-Throughput Elicitor Screening. ACS Chem Biol 2023; 18:1854-1862. [PMID: 37463302 PMCID: PMC11062413 DOI: 10.1021/acschembio.3c00281] [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] [Indexed: 07/20/2023]
Abstract
Enediyne antibiotics are a striking family of DNA-cleaving natural products with high degrees of cytotoxicity and structural complexity. Microbial genome sequences, which have recently accumulated, point to an untapped trove of "cryptic" enediynes. Most of the cognate biosynthetic gene clusters (BGCs) are sparingly expressed under standard growth conditions, making it difficult to characterize their products. Herein, we report a fluorescence-based DNA cleavage assay coupled with high-throughput elicitor screening for the rapid, targeted discovery of cryptic enediyne metabolites. We applied the approach to Streptomyces clavuligerus, which harbors two such BGCs with unknown products, identified steroids as effective elicitors, and characterized 10 cryptic enediyne-derived natural products, termed clavulynes A-J with unusual carbonate and terminal olefin functionalities, with one of these congeners matching the recently reported jejucarboside. Our results contribute to the growing repertoire of enediynes and provide a blueprint for identifying additional ones in the future.
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Affiliation(s)
- Esther J Han
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Seoung Rak Lee
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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2
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Zhang H, Li R, Ba S, Lu Z, Pitsinos EN, Li T, Nicolaou KC. DNA Binding and Cleavage Modes of Shishijimicin A. J Am Chem Soc 2019; 141:7842-7852. [DOI: 10.1021/jacs.9b01800] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hao Zhang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Ruofan Li
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Sai Ba
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - Zhaoyong Lu
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Emmanuel N. Pitsinos
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Laboratory of Natural Products Synthesis & Bioorganic Chemistry, Institute of Nanoscience and Nanotechnology, National Centre for Scientific Research “Demokritos”, 153 10 Agia Paraskevi, Greece
| | - Tianhu Li
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
| | - K. C. Nicolaou
- Department of Chemistry, BioScience Research Collaborative, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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Majumdar S, Hossain J, Natarajan R, Banerjee AK, Maiti DK. Phthalate tethered strategy: carbohydrate nitrile oxide cycloaddition to 12–15 member chiral macrocycles with alkenyl chain length controlled orientation of bridged isoxazolines. RSC Adv 2015. [DOI: 10.1039/c5ra22436e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The highly selective synthesis of phthalate templated bridged sugar-based isoxazoline macrocyclic lactones is demonstrated through INOC with alkene.
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Affiliation(s)
- Swapan Majumdar
- Department of Chemistry
- Tripura University
- Suryamaninagar 799 022
- India
| | - Jewel Hossain
- Department of Chemistry
- Tripura University
- Suryamaninagar 799 022
- India
| | | | | | - Dilip K. Maiti
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
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Gerber HP, Koehn FE, Abraham RT. The antibody-drug conjugate: an enabling modality for natural product-based cancer therapeutics. Nat Prod Rep 2013; 30:625-39. [PMID: 23525375 DOI: 10.1039/c3np20113a] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Antibody Drug Conjugate (ADC) is a therapeutic modality consisting of a monoclonal antibody attached to a cytotoxic, small-molecule payload. The antibody portion of the ADC serves as a transport vehicle that recognizes and binds to a protein antigen expressed in tumor tissues. The localized delivery and release of the payload within or near malignant cells allows for targeted delivery of a potent cytotoxic agent to diseased tissue, while reducing damage to antigen-negative, normal tissues. Recent years have witnessed an explosive increase in ADC-based therapies, due mainly to clinical reports of activity in both hematologic and epithelial cancers. Accompanying this upsurge in ADC development is a renewed interest in natural product cytotoxins, which are typically highly potent cell-killing agents, but suffer from poor drug-like properties and narrow safety margins when systemically administered as conventional chemotherapeutics. In this review, we discuss recent advances related to the construction of ADCs, the optimization of ADC safety and efficacy, and the increasingly pivotal roles of natural product payloads in the current and future landscape of ADC therapy.
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Affiliation(s)
- Hans-Peter Gerber
- Pfizer Worldwide Research and Development, Oncology Research Unit, 401 Middletown Road, Pearl River, NY, USA.
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5
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Ellestad GA. Structural and conformational features relevant to the anti-tumor activity of calicheamicin γ 1I. Chirality 2011; 23:660-71. [DOI: 10.1002/chir.20990] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Biggins JB, Onwueme KC, Thorson JS. Resistance to enediyne antitumor antibiotics by CalC self-sacrifice. Science 2003; 301:1537-41. [PMID: 12970566 DOI: 10.1126/science.1086695] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Antibiotic self-resistance mechanisms, which include drug elimination, drug modification, target modification, and drug sequestration, contribute substantially to the growing problem of antibiotic resistance among pathogenic bacteria. Enediynes are among the most potent naturally occurring antibiotics, yet the mechanism of resistance to these toxins has remained a mystery. We characterize an enediyne self-resistance protein that reveals a self-sacrificing paradigm for resistance to highly reactive antibiotics, and thus another opportunity for nonpathogenic or pathogenic bacteria to evade extremely potent small molecules.
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Affiliation(s)
- John B Biggins
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Wu M, Stoermer D, Tullius TD, Townsend CA. Calicheamicin−Homeodomain Conjugate as an Efficient, Sequence-Specific DNA Cleavage and Mapping Tool. J Am Chem Soc 2000. [DOI: 10.1021/ja002280o] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Minwan Wu
- Department of Chemistry, The Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218 Department of Chemistry, Boston University 590 Commonwealth Ave., Boston, Massachusetts 02215
| | - Doris Stoermer
- Department of Chemistry, The Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218 Department of Chemistry, Boston University 590 Commonwealth Ave., Boston, Massachusetts 02215
| | - Thomas D. Tullius
- Department of Chemistry, The Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218 Department of Chemistry, Boston University 590 Commonwealth Ave., Boston, Massachusetts 02215
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218 Department of Chemistry, Boston University 590 Commonwealth Ave., Boston, Massachusetts 02215
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Biggins JB, Prudent JR, Marshall DJ, Ruppen M, Thorson JS. A continuous assay for DNA cleavage: the application of "break lights" to enediynes, iron-dependent agents, and nucleases. Proc Natl Acad Sci U S A 2000; 97:13537-42. [PMID: 11095715 PMCID: PMC17611 DOI: 10.1073/pnas.240460997] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Although extensive effort has been applied toward understanding the mechanism by which enediynes cleave DNA, a continuous assay for this phenomenon is still lacking. In fact, with the exception of assays for DNase, continuous assays for most DNA cleavage events are unavailable. This article describes the application of "molecular break lights" (a single-stranded oligonucleotide that adopts a stem-and-loop structure and carries a 5'-fluorescent moiety, a 3'-nonfluorescent quenching moiety, and an appropriate cleavage site within the stem) to develop the first continuous assay for cleavage of DNA by enediynes. Furthermore, the generality of this approach is demonstrated by using the described assay to directly compare the DNA cleavage by naturally occurring enediynes [calicheamicin and esperamicin), non-enediyne small molecule agents (bleomycin, methidiumpropyl-EDTA-Fe(II), and EDTA-Fe(II]), as well as the restriction endonuclease BamHI. Given the simplicity, speed, and sensitivity of this approach, the described methodology could easily be extended to a high throughput format and become a new method of choice in modern drug discovery to screen for novel protein-based or small molecule-derived DNA cleavage agents.
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Affiliation(s)
- J B Biggins
- Laboratory for Biosynthetic Chemistry, Memorial Sloan-Kettering Cancer Center and the Sloan-Kettering Division, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY, USA
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Nicolaou KC, Baran PS, Zhong YL, Vega JA. Novel IBX-Mediated Processes for the Synthesis of Amino Sugars and Libraries Thereof. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/1521-3757(20000717)112:14<2625::aid-ange2625>3.0.co;2-q] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bailly C, Qu X, Graves DE, Prudhomme M, Chaires JB. Calories from carbohydrates: energetic contribution of the carbohydrate moiety of rebeccamycin to DNA binding and the effect of its orientation on topoisomerase I inhibition. CHEMISTRY & BIOLOGY 1999; 6:277-86. [PMID: 10322124 DOI: 10.1016/s1074-5521(99)80073-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Only a few antitumor drugs inhibit the DNA breakage-reunion reaction catalyzed by topoisomerase. One is the camptothecin derivative topotecan that has recently been used clinically. Others are the glycosylated antibiotic rebeccamycin and its synthetic analog NB-506, which is presently in phase I of clinical trials. Unlike the camptothecins, rebeccamycin-type compounds bind to DNA. We set out to elucidate the molecular basis of their interaction with duplex DNA, with particular emphasis on the role of the carbohydrate residue. RESULTS We compared the DNA-binding and topoisomerase-I-inhibition activities of two isomers of rebeccamycin that contain a galactose residue attached to the indolocarbazole chromophore via an alpha (axial) or a beta (equatorial) glycosidic linkage. The modification of the stereochemistry of the chromophore-sugar linkage results in a marked change of the DNA-binding and topoisomerase-I- poisoning activities. The inverted configuration at the C-1' of the carbohydrate residue abolishes intercalative binding of the drug to DNA thereby drastically reducing the binding affinity. Consequently, the alpha isomer has lost the capacity to induce topoisomerase-I-mediated cleavage of DNA. Comparison with the aglycone allowed us to determine the energetic contribution of the sugar residue. CONCLUSIONS The optimal interaction of rebeccamycin analogs with DNA is controlled to a large extent by the stereochemistry of the sugar residue. The results clarify the role of carbohydrates in stereospecific drug-DNA interactions and provide valuable information for the rational design of new rebeccamycin-type antitumor agents.
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Affiliation(s)
- C Bailly
- Centre Oscar Lambret et INSERM U-524 Lille, 59045, France.
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12
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Clive DLJ, Bo Y, Tao Y, Daigneault S, Wu YJ, Meignan G. Synthesis of (±)-Calicheamicinone by Two Methods. J Am Chem Soc 1998. [DOI: 10.1021/ja980292s] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Derrick L. J. Clive
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Yunxin Bo
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Yong Tao
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Sylvain Daigneault
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Yong-Jin Wu
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Gérard Meignan
- Contribution from the Chemistry Department, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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13
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Chatterji T, Gates KS. DNA cleavage by 7-methylbenzopentathiepin: a simple analog of the antitumor antibiotic varacin. Bioorg Med Chem Lett 1998; 8:535-8. [PMID: 9871613 DOI: 10.1016/s0960-894x(98)00066-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The compound 7-methylbenzopentathiepin, a simple analog of the benzopentathiepin antitumor antibiotic varacin, was shown to be a potent thiol-dependent DNA-cleaving agent. Biological experiments previously suggested that DNA cleavage might play a role in the cytotoxicity of varacin; however, this is the first direct evidence that benzopentathiepins can cause DNA strand breaks under physiologically relevant conditions.
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Affiliation(s)
- T Chatterji
- Department of Chemistry, University of Missouri-Columbia 65211, USA
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LaMarr WA, Yu L, Nicolaou KC, Dedon PC. Supercoiling affects the accessibility of glutathione to DNA-bound molecules: positive supercoiling inhibits calicheamicin-induced DNA damage. Proc Natl Acad Sci U S A 1998; 95:102-7. [PMID: 9419336 PMCID: PMC18140 DOI: 10.1073/pnas.95.1.102] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
DNA superhelical tension, an important feature of genomic organization, is known to affect the interactions of intercalating molecules with DNA. However, the effect of torsional tension on nonintercalative DNA-binding chemicals has received less attention. We demonstrate here that the enediyne calicheamicin gamma1I, a strand-breaking agent specific to the minor groove, causes approximately 50% more damage in negatively supercoiled plasmid DNA than in DNA with positive superhelicity. Furthermore, we show that the decrease in damage in positively supercoiled DNA is controlled at the level of thiol activation of the drug. Our results suggest that supercoiling may affect both the activity of nonintercalating genotoxins in vivo and the accessibility of glutathione and other small physiologic molecules to DNA-bound chemicals or reactions occurring in the grooves of DNA.
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Affiliation(s)
- W A LaMarr
- Division of Toxicology, 56-787, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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15
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Mulhearn DC, Bachrach SM. Selective Nucleophilic Attack of Trisulfides. An ab Initio Study. J Am Chem Soc 1996. [DOI: 10.1021/ja9620090] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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