Solution structure of the calicheamicin γ1-DNA complex

Kumar, Rupesh; Ikemoto, Norihiro; Patel, Dinshaw J.

doi:10.1006/jmbi.1996.0718

Cited by 80 publications

(74 citation statements)

References 34 publications

(77 reference statements)

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“…With the vast majority of DNA-binding small molecules equipped with carbohydrate groups, the sugar moiety nestles within the minor groove of the helix and participates positively in the DNA recognition process. This is the case for the well known anthracycline antibiotics (e.g., adriamycin) (Chaires, 1996) as well as the enediyne antibiotics (e.g., calicheamicin) (Kumar et al, 1997) and many other antitumor agents, such as mithramycin and chromomycin (Keniry et al, 1993). Moreover, the fact that addition, deletion, or relocation of the 2-amino group of guanine residues affects the sequence-selective binding of R-3 to DNA indicates that the drug must somehow sense the presence of a substituent on the edges of the bases in the minor groove.…”

Section: Discussionmentioning

confidence: 97%

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

et al. 1998

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We investigated the interaction with DNA of two synthetic derivatives of the antitumor antibiotic rebeccamycin: R-3, which is a potent topoisomerase I inhibitor and contains a methoxyglucose moiety appended to the indolocarbazole chromophore, and its aglycone, R-4. Spectroscopic measurements indicate that R-3 intercalates into DNA and that its carbohydrate domain contributes significantly to reinforce the affinity for DNA. Two complementary ligation assays concur that R-3, but not its aglycone counterpart, exerts a significant effect on the curvature and/or the flexibility of DNA. The sugar moiety may be responsible for preferential binding of R-3 to circular (or bent) DNA molecules as opposed to linear DNA fragments. The sequence selectivity of binding to DNA has been studied thoroughly by footprinting with DNase I and two other nucleases. The glycosylated compound is highly selective for nucleotide sequences containing GpT (ApC) and TpG (CpA) steps. The derivative lacking the sugar moiety on the indolocarbazole chromophore binds at essentially identical sites but with considerably lower affinity, so it seems that the chromophore rather than the carbohydrate is responsible for the preferential binding to sequences surrounding GpT and TpG steps. The influence of the exocyclic substituents present on the bases at the recognition sites (i.e., the 2-amino group of guanine and the 5-methyl group of thymine) was evaluated using two series of modified DNA molecules prepared by polymerase chain reaction containing inosine and/or 2,6-diaminopurine and uridine and/or 5-methylcytosine residues. The introduction of the amino group onto purine residues or the addition of a methyl group to pyrimidine residues suffices to create new drug binding sites. Therefore, unlike most DNA-binding small molecules, the rebeccamycin analogue seems to be highly sensitive to any modification of the exocyclic substituents on the bases in both the major and minor grooves of the double helix. The footprinting profiles with the different DNA fragments bear a remarkable resemblance to those determined for nogalamycin and bisnaphthalimide compounds known to recognize their preferred GpT and TpG sites via intercalation from the major groove. The unique DNA binding characteristics of the rebeccamycin analogue correlate well with its inhibitory effects on topoisomerase I .The camptothecin derivatives irinotecan (CPT-11) and topotecan recently introduced in cancer chemotherapy are arguably the best characterized topoisomerase I poisons (Pommier and Tanizawa, 1993). These drugs interfere with the breakage-rejoining reaction by stabilizing a covalent topoisomerase I/DNA intermediate (usually referred to as cleavable complex), which can be detected by the appearance of DNA strand breaks on denaturation of the protein with a detergent. So far, relatively few other drugs have been shown to promote topoisomerase I-mediated DNA cleavage. Intoplicine, saintopins, and related naphthacene-dione antibiotics as well as alkaloids such as bulgarein and cor...

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Section: Discussionmentioning

confidence: 97%

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

et al. 1998

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“…It is difficult to explain a specificity for both A͞T-or G͞C-rich sequences because they are substantially different in shape and hydrogen-bonding array. Because the carbohydrate tail of calicheamicin seems to be a rigid structure (40), binding the drug should induce steric pressure on DNA, suggesting a definition of ''sequence specificity'' as an ability to make the necessary adjustment for the best fit at the lowest energy cost (38,(41)(42)(43)(44).…”

Section: Discussionmentioning

confidence: 99%

Interaction of calicheamicin γ ₁ ^I and its related carbohydrates with DNA–protein complexes

Sissi

Aiyar²,

Boyer³

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

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We report studies of the contribution of DNA structure, holding the sequence constant, to the affinity of calicheamicin ␥ 1 I and its aryltetrasaccharide moiety for DNA. We used polynucleotide chains as models of known proteinbinding sequences [the catabolite activator protein (CAP) consensus sequence, AP-1 and cAMP response element (CRE) sites] in their free and protein-bound forms. The proteins were selected to provide examples in which the minor-groove binding site for the carbohydrate is (CAP) or is not (GCN4) covered by the protein. Additionally, peptides related to the GCN4 and CREB families, which have different bending effects on their DNA-binding sites, were used. We observe that proteins of the CREB class, which induce a tendency to bend toward the minor groove at the center of the site, inhibit drug-cleavage sites located at the center of the free AP-1 or CRE DNA sites. In the case of GCN4, which does not induce DNA bending, there is no effect on calicheamicin cleavage of the CRE site, but we observe a GCN4-induced rearrangement of the cutting pattern in the AP-1 site. This effect may arise from either a subtle local conformational rearrangement not accompanied by bending or a localized reduction in DNA f lexibility. Whereas GCN4 binding is not inhibited by the calicheamicin aryltetrasaccharide, binding of CAP to its DNA target is significantly inhibited, and calicheamicin cutting of DNA at the center of the CAP-DNA complex site is strongly reduced by protein binding. This result probably ref lects steric inhibition of drug binding by the protein.

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“…A prominent member of the enediyne family, 1 is a premiere example of nature's ingenuity (1)(2)(3)(4)(5)(6). Of the two distinct structural regions within 1 (7,8), the aryltetrasaccharide is composed of a unique set of carbohydrate and aromatic units that site-specifically deliver the metabolite into the minor groove of DNA (9), whereas the aglycone, or ''warhead,'' consists of a highly functionalized bicyclo [7.3.1]tridecadiynene core structure with an allylic trisulfide serving as the triggering mechanism. Aromatization of the bicyclo [7.3.1]tridecadiynene core structure, via a 1,4-dehydrobenzene-diradical, results in the sitespecific oxidative double-strand scission of the targeted DNA, and this extraordinary reactivity has sparked considerable interest in the pharmaceutical industry (10,11).…”

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confidence: 99%

A continuous assay for DNA cleavage: The application of “break lights” to enediynes, iron-dependent agents, and nucleases

Biggins

Prudent²,

Marshall³

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

110

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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 stemand-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.calicheamicin ͉ esperamicin ͉ assay ͉ molecular beacon ͉ bleomycin

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Solution structure of the calicheamicin γ1-DNA complex

Cited by 80 publications

References 34 publications

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

Interaction of calicheamicin γ ₁ ^I and its related carbohydrates with DNA–protein complexes

A continuous assay for DNA cleavage: The application of “break lights” to enediynes, iron-dependent agents, and nucleases

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Solution structure of the calicheamicin γ1-DNA complex

Cited by 80 publications

References 34 publications

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

Recognition of Specific Sequences in DNA by a Topoisomerase I Inhibitor Derived from the Antitumor Drug Rebeccamycin

Interaction of calicheamicin γ 1 I and its related carbohydrates with DNA–protein complexes

A continuous assay for DNA cleavage: The application of “break lights” to enediynes, iron-dependent agents, and nucleases

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Interaction of calicheamicin γ ₁ ^I and its related carbohydrates with DNA–protein complexes