Efficient stacking on protein amide fragments.

Abstract:

:The less polar π-surface of protein amide groups is exposed in many receptor binding sites, either as part of the backbone or in Gln/Asn side chains. Using quantum chemical calculations and Protein Data Bank (PDB) searches on model systems, we investigate the energetics and geometric preferences for the stacking on amide groups of a large number of heteroarenes that are relevant to medicinal chemistry. From this study, we discern that the stacking energy of an aromatic ligand substituent can be improved by: 1) orienting the fragment dipole vector such that it is aligned in an antiparallel fashion with the dipole of the interacting protein amide group, 2) increasing its dipole moment, and 3) decreasing its π-electron density. These guidelines should be helpful to more rationally exploit this interaction type in future structure-based drug design.

journal_name

ChemMedChem

journal_title

ChemMedChem

authors

Harder M,Kuhn B,Diederich F

doi

10.1002/cmdc.201200512

subject

Has Abstract

pub_date

2013-03-01 00:00:00

pages

397-404

issue

3

eissn

1860-7179

issn

1860-7187

journal_volume

8

pub_type

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