Fluorine interactions at the thrombin active site: Protein backbone fragments H-Cα-C=O comprise a favorable C-F environment and interactions of C-F with electrophiles

Abstract

In a systematic fluorine scan of a rigid inhibitor to map the fluorophilicity/fluorophobicity of the active site in thrombin, one or more F substituents were introduced into the benzyl ring reaching into the D pocket The 4-fluorobenzyl inhibitor showed a five to tenfold higher affinity than ligands with other fluorination patterns. X-ray crystal-structure analysis of the protein-ligand complex revealed favorable C-F⋯H-Cα-C=O and C-F⋯C=O interactions of the 4-F substituent of the inhibitor with the backbone H-Cα-C=O unit of Asn98. The importance of these interactions was further corroborated by the analysis of small-molecule X-ray crystal-structure searches in the Protein Data Base (PDB) and the Cambridge Structural Database (CSD). In the C-F⋯C=O interactions that are observed for both aromatic and aliphatic C-F units and a variety of carbonyl and carboxyl derivatives, the F atom approaches the C=O C atom preferentially along the pseudotrigonal axis of the carbonyl system. Similar orientational preferences are also seen in the dipolar interactions C-F⋯C=N, C-F⋯C-F, and C-F⋯NO2, in which the F atoms interact at sub-van der Waals distances with the electrophilic centers.