The reactivity of calicheamicin γ1i in the minor groove of DNA: the decisive role of the environment

Elfi Kraka, Tell Tuttle, Dieter Cremer

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Triggering and Bergman cyclization of calicheamicin γ 1I 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 y1I (-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.

LanguageEnglish
Pages9256-9269
Number of pages14
JournalChemistry - A European Journal
Volume13
Issue number33
Early online date8 Nov 2007
DOIs
Publication statusPublished - 16 Nov 2007

Fingerprint

DNA
Cyclization
Discrete Fourier transforms
Atoms
Hydrogen
Ligands
B-Form DNA
Stereochemistry
Molecular mechanics
Carbamates
DNA sequences
Density functional theory
Enthalpy
Chemical activation
Temperature
cyclohexanone

Keywords

  • ab initio calculations
  • calicheamicin
  • DNA damage
  • environmental effects
  • reaction mechanisms

Cite this

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abstract = "Triggering and Bergman cyclization of calicheamicin γ 1I 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 y1I (-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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The reactivity of calicheamicin γ1i in the minor groove of DNA : the decisive role of the environment. / Kraka, Elfi; Tuttle, Tell; Cremer, Dieter.

In: Chemistry - A European Journal , Vol. 13, No. 33, 16.11.2007, p. 9256-9269.

Research output: Contribution to journalArticle

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