Coupled kinetic analysis of cleavage of DNA by esperamicin and calicheamicin

Kishikawa, Hiroko; Jiang, Ying; Goodisman, Jerry; Dabrowiak, James C.

doi:10.1021/ja00014a040

Cited by 70 publications

(53 citation statements)

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“…1B), the absence of an independent pathway for double-strand cleavage is proposed: linearization would be produced by accumulation of single strand breaks at close positions in the opposite strands. In order to confirm this point, a coupled kinetic analysis of the cleavage by dq2pyp was conducted, using the model and equations put forward by Kishikawa et al [10]. Fig.…”

Section: Resultsmentioning

confidence: 95%

“…Fig. 2 reflects the amount of cleavage as a function of both drug concentration and time, together with the best fits of the single-strand cleavage model [10] to the experimental data. From the analysis, a k>~]l/kn_,ni ratio of kinetic constants of about 25 results, indicating that linearization occurs more probably by accumulation of single-strand breaks.…”

Section: Resultsmentioning

confidence: 99%

“…From the analysis, a k>~]l/kn_,ni ratio of kinetic constants of about 25 results, indicating that linearization occurs more probably by accumulation of single-strand breaks. Moreover, attempts to fit a doublestrand cleavage model [10] to the experimental data resulted in unacceptable results. Thus, dq2pyp seems to photocleave DNA essentially by producing randomly distributed single-strand breaks.…”

Section: Resultsmentioning

confidence: 99%

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DNA photocleavage by novel intercalating 6‐(2‐pyridinium)phenanthridinium viologens

1995

FEBS Letters

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A new type of DNA-intercalating viologen dications, derived from the N,N'-dialkyl-6-(2-pyridyl)phenanthridine structure (in which dialkyl is -CH2CH2-, -CH2CH2CH2-, or (-CH3)2, abbreviated dq2pyp, dq3pyp, and Me2pyp, respectively), are able to produce frank strand breaks in supercoiled plasmid DNA upon irradiation with visible light. The amount of photocleavage is similar for the three drugs. The observed DNA photosensitization appears to follow a single-strand cleavage model, as shown by a kinetic analysis of the reaction with dq2pyp. The photodynamic action of the drugs seems to be initiated by a light-induced electron transfer reaction from the nucleobases, given the singlet excited-state redox potentials (ca. + 2.1 V vs. SHE) and the low quantum yields of singlet molecular oxygen production of the drugs (0.1-0.2 in aerated D20). Key words. Intercalating viologen; DNA photocleavage;Photoinduced electron transfer reaction of Io 2 with guanine; (b) direct or OH'-mediated hydrogen abstraction from the deoxyribose moiety; (c) oxidation of guanine by the photoexcited drug. It is not uncommon to find the simultaneous participation of two of such processes in the sensitized photooxidation of nucleosides [4].In a recent paper [5], we have reported the intercalative interaction with DNA of a novel family of photoactive organic compounds, namely dialkylated 6-(2-pyridyl)phenanthridine (pyp) viologens (Scheme 1). The possibility of photochemistry with DNA was then suggested, based on their singlet excited state redox potentials and the efficient fluorescence quenching observed with GMP and AMP (kq = 1.2 x 10 l° and 6.8 x l09 M ~. s ], respectively). The goal of the present paper is to report the capability of dq2pyp, dq3pyp, and Me2pyp, to photosensitize DNA cleavage, as well as to obtain evidences about the possible mechanism responsible for their photodynamic activity.

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Section: Resultsmentioning

confidence: 95%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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DNA photocleavage by novel intercalating 6‐(2‐pyridinium)phenanthridinium viologens

1995

FEBS Letters

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“…A plot of the optical density data derived from agarose gel experiments with pM2 DNA as a function of increasing chromophore concentrations showed that, at low concentrations, single-strand breaks accumulate on average four times more rapidly than double-strand breaks, consistent with a single-strand cutting behavior (24). The electrophoretic mobilities of the cleavage products obtained in the 5'-and 3'-end-labeled studies seem to suggest 4' hydrogen atom abstraction along with a small portion of 5' hydrogen abstraction from the targeted DNA deoxyribose sugars (4,(12)(13)(14)(15)(16)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34).…”

Section: Discussionmentioning

confidence: 93%

Kedarcidin chromophore: an enediyne that cleaves DNA in a sequence-specific manner.

Zein

Colson

Leet

et al. 1993

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

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Kedarcidin chromophore is a 9-membered enediyne, recentiy isolated from an actinomycete strain. In vivo studies show this molecule to be extremely active against P388 leukemia and B16 melanoma. Cytotoxicity assays on the HCT116 colon carcinoma cell line result in an IC50 value of 1 nM. In vitro experiments with 4X174, pM2 DNA, and 32p-end-labeled restriction fragments demonstrate that this chromophore binds and cleaves duplex DNA with a remarkable sequence selectivity producing single-strand breaks. The DNA binding and cleavage properties of the potent enediyne antitumor antibiotics have been the focus of intense study by a number of groups for the past several years. Kedarcidin chromoprotein is a recently identified member of this unusual family of microbial metabolites (1-3, t). In vitro cytotoxicity assays using the HCT116 colon carcinoma cell line showed the chromophore to possess potent cytotoxicity (IC50, 1 nM) similar to that of Adriamycin (W.S. and N.Z., unpublished data). Moreover, the chromophore exhibited superior antitumor activity against murine P388 leukemia and B16 melanoma models (W. C. Rose, personal communication). As with neocarzinostatin (4-7), kedarcidin chromophore, a labile 9-membered enediyne, occurs as a component of a highly acidic chromoprotein (1-3). This is in contrast to esperamicin, calicheamicin, and dynemicin, agents that contain 10-membered enediyne rings and, to date, have been isolated without associated apoproteins (8-11). In this paper, we report that the kedarcidin chromophore interacts with duplex DNA and produces specific single-strand cuts. The cleavage chemistry requires reducing agents and oxygen similar to the other naturally occurring enediynes (4)(5)(6)(7)(12)(13)(14)(15)(16)(17)(18)(19)(20) Tris'HCl, pH 7.5, 10:90 (vol/vol), (DMSO/Tris) at 370C for various lengths of time, in a total reaction volume of 10 ,ul. When required, hydrazine and putrescine were added, each to 100 mM (final concentration), and the reaction mixture was incubated at 37°C for an additional hour (21). The different forms of DNA were separated on a 0.9% agarose gel after a 15-h electrophoresis at 30 V with subsequent ethidium bromide staining. The stained gels were photographed and the intensity of the DNA bands was assessed by linear scanning microdensitometry (22).Comparison of the Cleavage of Different 4X174 Forms by the Chromophore. All four forms (+ strand, RFI, RFII, and RFIII) of 4X174 DNA were incubated overnight with the chromophore as described above.Preparation and Labeling of Restriction Fragments. Five restriction fragments were isolated and 5'-end-labeled by using [y-32P]dATP and polynucleotide kinase. The fragments were a 275-bp pBR322 Sal I-BamHI fragment, a 159-bp pBR322 HindIII-EcoRV fragment, a 159-bp pBR322 EcoRVAbbreviations: RF, replicative form; DMSO, dimethyl sulfoxide. tTo whom reprint requests should be addressed.

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“…[1- 4,15,16] This was first demonstrated by Zein and co-workers [17] through the ability of 1 to cause in vitro double-strand scission when in the presence of thiols. Furthermore, the sequence specificity of the cut site of 1 was found to be well defined.…”

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confidence: 99%

The Reactivity of Calicheamicin γ₁^I in the Minor Groove of DNA: The Decisive Role of the Environment

Kraka

Tuttle

2007

Chemistry A European J

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Triggering and Bergman cyclization of calicheamicin gamma(1) (I) outside and inside the minor groove of the duplex 9mer-B-DNA sequence d(CACTCCTGG).d(CCAGGAGTG) were investigated by using density functional theory and molecular mechanics (DFT and MM) descriptions in which the ligand is completely described at the DFT and the receptor at the MM level. The calculated docking energy of calicheamicin gamma(1) (I) (-12.5 kcal mol(-1)) is close to the measured value of -9.7 kcal mol(-1) and the site specificity is in line with experimental observations. Calicheamicin is triggered in the minor groove in such a way that out of a cyclohexenone by Michael addition an E rather than a Z form of a cyclohexanone is formed, which in turn adopts a chair rather than a twistboat form. Decisive for the stereochemistry of the Michael addition is the orientation of the carbamate substituent at the headgroup of calicheamicin. Triggered calicheamicin can undergo the Bergman cyclization at body temperature only if present in its E chair form (activation enthalpy 16.4 kcal mol(-1)). An intermediate biradical is formed (docking energy -13.6 kcal mol(-1)), which has a sufficient lifetime to abstract two hydrogen atoms. Hydrogen abstraction is a two- rather than one-step process and involves the C5(H5') atom first and then the T22(H4') atom in line with experimental observations. The decisive role of using a DFT rather than an MM description for the ligand is documented.

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Coupled kinetic analysis of cleavage of DNA by esperamicin and calicheamicin

Cited by 70 publications

References 0 publications

DNA photocleavage by novel intercalating 6‐(2‐pyridinium)phenanthridinium viologens

DNA photocleavage by novel intercalating 6‐(2‐pyridinium)phenanthridinium viologens

Kedarcidin chromophore: an enediyne that cleaves DNA in a sequence-specific manner.

The Reactivity of Calicheamicin γ₁^I in the Minor Groove of DNA: The Decisive Role of the Environment

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Coupled kinetic analysis of cleavage of DNA by esperamicin and calicheamicin

Cited by 70 publications

References 0 publications

DNA photocleavage by novel intercalating 6‐(2‐pyridinium)phenanthridinium viologens

DNA photocleavage by novel intercalating 6‐(2‐pyridinium)phenanthridinium viologens

Kedarcidin chromophore: an enediyne that cleaves DNA in a sequence-specific manner.

The Reactivity of Calicheamicin γ1I in the Minor Groove of DNA: The Decisive Role of the Environment

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The Reactivity of Calicheamicin γ₁^I in the Minor Groove of DNA: The Decisive Role of the Environment