Reprint of: fRMSDchiral: a novel algorithm to represent differences between positions of stereoisomers in complex with dissymmetric binding site

Rafal D Urniaz; Ewelina E Rutkowska; Anita Plazinska; Krzysztof Jozwiak

doi:10.1016/j.jchromb.2014.05.012

Reprint of: fRMSDchiral: a novel algorithm to represent differences between positions of stereoisomers in complex with dissymmetric binding site

J Chromatogr B Analyt Technol Biomed Life Sci. 2014 Oct 1:968:26-31. doi: 10.1016/j.jchromb.2014.05.012. Epub 2014 May 15.

Authors

Rafal D Urniaz¹, Ewelina E Rutkowska¹, Anita Plazinska¹, Krzysztof Jozwiak²

Affiliations

¹ Medical University of Lublin, Laboratory of Medicinal Chemistry and Neuroengineering, Lublin, Poland.
² Medical University of Lublin, Laboratory of Medicinal Chemistry and Neuroengineering, Lublin, Poland. Electronic address: krzysztof.jozwiak@umlub.pl.

PMID: 24929899
DOI: 10.1016/j.jchromb.2014.05.012

Abstract

The ability of molecules to distinguish between optical isomers is crucial for living systems. The change of position of one enantiomer in respect to the position of the second enantiomer within an asymmetric binding site may be analyzed on different levels. Root Mean Square Deviation (RMSD) may be used for such analyses with low precision. Additional fragment level variants of RMSD allow for more precise definition of differences in location of the main molecular features responsible for recognition of stereoisomers by a selector. Three fRMSDchiral parameters appear to be very useful to precisely quantify the change in orientations of stereoisomers. Proposed calculation emerges as interesting assistance in interpretation of consequences of formation differential interaction(s) responsible for a chiral recognition process.

Keywords: Chiral recognition; Docking; Fragment RMSD; Molecular dynamics; Molecular modeling.