Molecular Recognition at the Active Site of Factor Xa: Cation-Pi Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water.

(2012) Chemistry 18: 213

• PubMed: 22162109 Search on PubMed
• DOI: https://doi.org/10.1002/chem.201102571
• Primary Citation of Related Structures:  
  2Y5F,2Y5G,2Y5H


• PubMed Abstract: 
  

  Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i)=2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.

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Organizational Affiliation: 
• Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland.