Structure-based design of potent, amidine-derived inhibitors of factor Xa:Evaluation of selectivity, anticoagulant activity, and antithrombotic activity

To enhance the potency of 1,2-dibenzamidobenzene-derived inhibitors of fact or Xa (fXa), an amidine substituent was incorporated on one of the benzoyl side chains to interact with Asp189 in the S1 specificity pocket. Lead mole cule 1 was docked into the active site of Ma to facilitate inhibitor design . Subsequently, iterative SAR studies and molecular modeling led to a 1000- fold increase in Ma affinity and a refined model of the new inhibitors in t he Ma active site. Strong support for the computational model was achieved through the acquisition of an X-ray crystal structure using thrombin as a s urrogate protein. The amidines in this series show high levels of selectivi ty for the inhibition of Ma relative to other trypsin-like serine proteases . Furthermore, the Ma affinity of compounds in this series (K-ass = 50-500 x 10(6) L/mol) translates effectively into both anticoagulant activity in v itro and antithrombotic activity in vivo.