ArticleBiophysical journal2008
Sliding of alkylating anticancer drugs along the minor groove of DNA: new insights on sequence selectivity.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 25 citations in OpenAlex.
- How Can Interleukin-1 Receptor Antagonist Modulate Distinct Cell Death Pathways?Journal of chemical information and modeling · 2019Article
- DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates.PLoS computational biology · 2015Article
- Molecular recognition of DNA by ligands: roughness and complexity of the free energy profile.The Journal of chemical physics · 2013Article
- Molecular motions in drug design: the coming age of the metadynamics method.Journal of computer-aided molecular design · 2011Article
- Dissociation of minor groove binders from DNA: insights from metadynamics simulations.Nucleic acids research · 2008Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Currently, little is known about the molecular recognition pathways between DNA-alkylating anticancer drugs and their targets despite their pharmacological relevance. In the framework of classical molecular dynamics simulations, here we use umbrella sampling to map the potential of mean force (PMF) associated with sliding along the DNA minor groove of two of these compounds. These are an indole derivative of duocarmycin (DSI) and the putative reactive form of anthramycin (anhydro-anthramycin, IMI). Twenty-three configurations were considered for each drug/DNA complex, corresponding to a movement along approximately 3 basepairs. The alkylation site turns out to be the most favorable for DSI, while a barrier of approximately 6 kcal/mol separates the reactive configuration of IMI.DNA from the absolute minimum. An analysis of various contributions to the PMF reveals that solvent effects play an important role for the largest and more flexible drug DSI. Instead, the PMF of IMI.DNA overall correlates with changes in the binding enthalpy. Implications of these results on the sequence selectivity of the two drugs are discussed.
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