ArticleNucleic acids research2013
Role of the protein in the DNA sequence specificity of the cleavage site stabilized by the camptothecin topoisomerase IB inhibitor: a metadynamics study.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 28 citations in OpenAlex.
- Insight on the Interaction between the Camptothecin Derivative and DNA Oligomer Mimicking the Target of Topo I Inhibitors.Molecules (Basel, Switzerland) · 2022Article
- The Mode of SN38 Derivatives Interacting with Nicked DNA Mimics Biological Targeting of Topo I Poisons.International journal of molecular sciences · 2021Article
- Natural Compounds as Therapeutic Agents: The Case of Human Topoisomerase IB.International journal of molecular sciences · 2021Review
- Topoisomerase IB: a relaxing enzyme for stressed DNA.Cancer drug resistance (Alhambra, Calif.) · 2020Review
- Article
- Mechanistic insight into ligand binding to G-quadruplex DNA.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Camptothecin (CPT) is a topoisomerase IB (TopIB) selective inhibitor whose derivatives are currently used in cancer therapy. TopIB cleaves DNA at any sequence, but in the presence of CPT the only stabilized protein-DNA covalent complex is the one having a thymine in position -1 with respect to the cleavage site. A metadynamics simulation of two TopIB-DNA-CPT ternary complexes differing for the presence of a thymine or a cytosine in position -1 indicates the occurrence of two different drug's unbinding pathways. The free-energy difference between the bound state and the transition state is large when a thymine is present in position -1 and is strongly reduced in presence of a cytosine, in line with the different drug stabilization properties of the two systems. Such a difference is strictly related to the changes in the hydrogen bond network between the protein, the DNA and the drug in the two systems, indicating a direct role of the protein in determining the specificity of the cleavage site sequence stabilized by the CPT. Calculations carried out in presence of one compound of the indenoisoquinoline family (NSC314622) indicate a comparable energy difference between the bound and the transition state independently of the presence of a thymine or a cytosine in position -1, in line with the experimental results.
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