In Silico Footprinting of Ligands Binding to the Minor Groove of DNA

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Anthony, Nahoum Guillaume Hsuan and Huchet, Guillaume and Johnston, Blair and Parkinson, John and Suckling, Colin and Waigh, Roger and MacKay, Simon (2005) In Silico Footprinting of Ligands Binding to the Minor Groove of DNA. Journal of Chemical Information and Modeling, 45 (6). pp. 1896-1907. ISSN 1549-9596 (https://doi.org/10.1021/ci050153b)

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Abstract

The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by 'in silico footprinting'. Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting.

ORCID iDs

Anthony, Nahoum Guillaume Hsuan ORCID logoORCID: https://orcid.org/0000-0002-2026-8763, Huchet, Guillaume, Johnston, Blair ORCID logoORCID: https://orcid.org/0000-0001-9785-6822, Parkinson, John ORCID logoORCID: https://orcid.org/0000-0003-4270-6135, Suckling, Colin, Waigh, Roger and MacKay, Simon ORCID logoORCID: https://orcid.org/0000-0001-8000-6557;
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