Using Surface Scans for the Evaluation of Halogen Bonds toward the Side Chains of Aspartate, Asparagine, Glutamate, and Glutamine

J Chem Inf Model. 2016 Jul 25;56(7):1373-83. doi: 10.1021/acs.jcim.6b00075. Epub 2016 Jul 15.

Abstract

Using halogen-specific Connolly type molecular surfaces, we herein invented a new type of surface-based interaction analysis employed for the study of halogen bonding toward model systems of biologically relevant carboxylates (ASP/GLU) and carboxamides (ASN/GLN). Database mining and statistical assessment of the PDB revealed that such interactions are widely underrepresented at the moment. We observed important distance-dependent adaptions of the binding modes of halobenzenes from a preferential oxygen-directed to a bifurcated interaction geometry of the carboxylate. In addition, halogen···π contacts perpendicular to the nitrogen atom of the carboxamide become increasingly important for the lighter halogens. Our analysis on a MP2/TZVPP level of theory is backed by CCSD(T)/CBS reference calculations. To put the vast interaction energies into perspective, we also performed COSMO-RS calculations of the solvation free energy. Facilitating the visualization of our results mapped onto any binding site of choice, we aim to inspire more design studies showcasing these underrepresented interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides / chemistry
  • Amino Acids / chemistry*
  • Asparagine / chemistry
  • Aspartic Acid / chemistry
  • Carboxylic Acids / chemistry
  • Crystallography, X-Ray
  • Drug Design
  • Glutamic Acid / chemistry
  • Glutamine / chemistry
  • Halogens / chemistry*
  • Models, Molecular
  • Molecular Conformation
  • Solvents / chemistry

Substances

  • Amides
  • Amino Acids
  • Carboxylic Acids
  • Halogens
  • Solvents
  • Glutamine
  • Aspartic Acid
  • Glutamic Acid
  • Asparagine