title: Structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin A.
abstract: (-)-Lomaiviticin A (1) is a complex antiproliferative metabolite that inhibits the growth of many cultured cancer cell lines at low nanomolar-picomolar concentrations. (-)-Lomaiviticin A (1) possesses a C2-symmetric structure that contains two unusual diazotetrahydrobenzo[b]fluorene (diazofluorene) functional groups. Nucleophilic activation of each diazofluorene within 1 produces vinyl radical intermediates that affect hydrogen atom abstraction from DNA, leading to the formation of DNA double-strand breaks (DSBs). Certain DNA DSB repair-deficient cell lines are sensitized toward 1, and 1 is under evaluation in preclinical models of these tumor types. However, the mode of binding of 1 to DNA had not been determined. Here we elucidate the structure of a 1:1 complex between 1 and the duplex d(GCTATAGC)2 by NMR spectroscopy and computational modeling. Unexpectedly, we show that both diazofluorene residues of 1 penetrate the duplex. This binding disrupts base pairing leading to ejection of the central AT bases, while placing the proreactive centers of 1 in close proximity to each strand. DNA binding may also enhance the reactivity of 1 toward nucleophilic activation through steric compression and conformational restriction (an example of shape-dependent catalysis). This study provides a structural basis for the DNA cleavage activity of 1, will guide the design of synthetic DNA-activated DNA cleavage agents, and underscores the utility of natural products to reveal novel modes of small molecule-DNA association.
authors.affiliation: Department of Chemistry, Yale University, New Haven, CT 06520;
authors.forename: Christina M
authors.initials: CM
authors.lastname: Woo
authors.affiliation: Department of Chemistry, Yale University, New Haven, CT 06520;
authors.forename: Zhenwu
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Chemistry, Yale University, New Haven, CT 06520;
authors.forename: Eric K
authors.identifier: http://orcid.org/0000-0002-4612-3634
authors.initials: EK
authors.lastname: Paulson
authors.affiliation: Department of Chemistry, Yale University, New Haven, CT 06520; Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520 seth.herzon@yale.edu.
authors.forename: Seth B
authors.initials: SB
authors.lastname: Herzon
mesh_terms: D000903:Antibiotics, Antineoplastic / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D053837:DNA Cleavage; D005449:Fluorenes / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology; D005453:Fluorescence; D009682:Magnetic Resonance Spectroscopy; D008837:Micrococcus / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes; D000095602:Angucyclines and Angucyclinones
chemical_list: D000903:Antibiotics, Antineoplastic; D004247:DNA; D005449:Fluorenes; D009692:Nucleic Acid Heteroduplexes; C433842:lomaiviticin A; D000095602:Angucyclines and Angucyclinones; C427203:calf thymus DNA
keywords: DNA; NMR; double-strand break; natural product