| Abstract
| - Novel aryl derivatives of benzamidine were synthesized and tested for their inhibitory potencyagainst bovine trypsin, rat skin tryptase, human recombinant granzyme A, human thrombin, and humanplasma kallikrein. All compounds show competitive inhibition against these proteases with Ki values inthe micromolar range. X-ray structures were determined to 1.8 Å resolution for trypsin complexed withtwo of the para-substituted benzamidine derivatives, 1-(4-amidinophenyl)-3-(4-chlorophenyl)urea (ACPU)and 1-(4-amidinophenyl)-3-(4-phenoxyphenyl)urea (APPU). Although the inhibitors do not engage indirect and specific interactions outside the S1 pocket, they do form intimate indirect contacts with theactive site of trypsin. The inhibitors are linked to the enzyme by a sulfate ion that forms an intricatenetwork of three-centered hydrogen bonds. Comparison of these structures with other serine proteasestructures with noncovalently bound oxyanions reveals a pair of highly conserved oxyanion-binding sitesin the active site. The positions of noncovalently bound oxyanions, such as the oxygen atoms of sulfate,are distinct from the positions of covalent oxyanions of tetrahedral intermediates. Noncovalent oxyanionpositions are outside the “oxyanion hole.” Kinetics data suggest that protonation stabilizes the ternaryinhibitor/oxyanion/protease complex. In sum, both cations and anions can mediate Ki. Cation mediationof potency of competitive inhibitors of serine proteases was previously reported by Stroud and co-workers[Katz, B. A., Clark, J. M., Finer-Moore, J. S., Jenkins, T. E., Johnson, C. R., Ross, M. J., Luong, C.,Moore, W. R., and Stroud, R. M. (1998) Nature 391, 608−612].
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