title: New inhibitors of thrombin and other trypsin-like proteases: hydrogen bonding of an aromatic cyano group with a backbone amide of the P1 binding site replaces binding of a basic side chain.
abstract: Highly effective thrombin inhibitors have been obtained by preparing boronic acid analogues of m-cyano-substituted phenylalanine and its incorporation into peptides. The cyano group enhances binding by several orders of magnitude. For example, Ac-(D)Phe-Pro-boroPheOH binds to thrombin with a Ki of 320 nM and the Ki of Ac-(D)Phe-Pro-boroPhe(m-CN)-OH is 0.79 nM. Protein crystal structure determination of trypsin complexed to H-(D)Phe-Pro-boroPhe(m-CN)-OH indicates that the aromatic side chain is bound in the P1 binding site and that the cyano group can act as a H-bond acceptor for the amide proton of Gly219. Enhanced binding for inhibitors containing the m-cyano group was observed for coagulation factor Xa and for the factor VIIa.tissue factor complex [Ki values of Ac-(D)Phe-Pro-boroPhe(mCN)-OH are 760 and 3.3 nM, respectively]. This result is consistent with the sequence homology of these two enzymes in the P1 binding site. Two enzymes lacking the strict homology in the P1 binding site, pancreatic kallikrein and chymotrypsin, did not exhibit significantly enhanced binding.
authors.affiliation: Chemical and Physical Sciences, DuPont Merck Pharmaceutical Company, P. O. Box 80500, Wilmington, Delaware 19880-0500, USA.
authors.forename: S L
authors.initials: SL
authors.lastname: Lee
authors.forename: R S
authors.initials: RS
authors.lastname: Alexander
authors.forename: A
authors.initials: A
authors.lastname: Smallwood
authors.forename: R
authors.initials: R
authors.lastname: Trievel
authors.forename: L
authors.initials: L
authors.lastname: Mersinger
authors.forename: P C
authors.initials: PC
authors.lastname: Weber
authors.forename: C
authors.initials: C
authors.lastname: Kettner
mesh_terms: D000577:Amides; D001665:Binding Sites; D001897:Boronic Acids / Q000378:metabolism; D018360:Crystallography, X-Ray; D003486:Cyanides / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D009842:Oligopeptides / Q000138:chemical synthesis / Q000494:pharmacology; D010649:Phenylalanine / Q000031:analogs & derivatives / Q000378:metabolism; D011392:Proline / Q000378:metabolism; D011485:Protein Binding; D012697:Serine Endopeptidases / Q000378:metabolism; D013917:Thrombin / Q000037:antagonists & inhibitors* / Q000378:metabolism; D014361:Trypsin Inhibitors / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000577:Amides; D001897:Boronic Acids; D003486:Cyanides; D046911:Macromolecular Substances; D009842:Oligopeptides; D014361:Trypsin Inhibitors; D010649:Phenylalanine; D011392:Proline; D012697:Serine Endopeptidases; D013917:Thrombin