Document Type
Article
Version Deposited
Published Version
Publication Date
10-9-2013
Publication Title
Journal of The Serbian Chemical Society
DOI
10.2298/JSC130929104A
Abstract
Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD) simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT) potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.
Recommended Citation
Abramyan, Ara M. et al. “An ab-initio study of pyrrole and imidazole arylamides.” Journal of The Serbian Chemical Society 78 (2013): 1789-1795.
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Comments
JSCS is an Open Access journal with no Article Processing Charge.