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Peptide-Ligand Binding Modeling of siRNA with Cell-Penetrating Peptides
Stockholm University, Faculty of Science, Department of Neurochemistry. University of Tartu, Estonia.ORCID iD: 0000-0001-6107-0844
2014 (English)In: BioMed Research International, ISSN 2314-6133, E-ISSN 2314-6141, 257040- p.Article in journal (Refereed) Published
Abstract [en]

The binding affinity of a series of cell-penetrating peptides (CPP) was modeled through docking and making use of the number of intermolecular hydrogen bonds, lipophilic contacts, and the number of sp3 molecular orbital hybridization carbons. The new ranking of the peptides is consistent with the experimentally determined efficiency in the downregulation of luciferase activity, which includes the peptides' ability to bind and deliver the siRNA into the cell. The predicted structures of the complexes of peptides to siRNA were stable throughout 10 ns long, explicit water molecular dynamics simulations. The stability and binding affinity of peptide-siRNA complexes was related to the sidechains and modifications of the CPPs, with the stearyl and quinoline groups improving affinity and stability. The reranking of the peptides docked to siRNA, together with explicit water molecular dynamics simulations, appears to be well suited to describe and predict the interaction of CPPs with siRNA.

Place, publisher, year, edition, pages
2014. 257040- p.
National Category
Chemical Sciences
URN: urn:nbn:se:su:diva-107198DOI: 10.1155/2014/257040ISI: 000340124300001OAI: diva2:744248


Available from: 2014-09-08 Created: 2014-09-05 Last updated: 2015-04-21Bibliographically approved

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Langel, Ülo
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