Recent advances in the design of mechanism-based (or suicide) and transition state inhibitors for serine proteases, along with the resolution of the crystal structure of thrombin, now makes it possible to pioneer a new generation of clinically useful antithrombotic agents. The long term goal of this research is the design, synthesis, and testing of potent new low molecular weight antithrombotic agents suitable for clinical use in humans in situations where heparin and aspirin are ineffective. Although there are several classes of antithrombotic drugs currently in use, none prevent reocclusion of some diseased arteries cleared by thrombolysis or the occlusive complications associated with surgical management of patients with vascular diseases. Clearly there is a need for more effective antithrombotic drugs. Thrombin and the enzymes which produce thrombin are serine proteases with trypsin-like specificity. Thrombin has a critical role in the activation of platelets during the formation of arterial thrombus in addition to mediating fibrin-rich thrombus formation. Small molecular weight thrombin inhibitors will abolish the formation of arterial thrombi, a process that is resistant to heparin. Thus, mechanism-based and transition-state inhibitors for thrombin or the enzymes which generate thrombin are likely to be clinically useful anticoagulants. Mechanism-based and transition state inhibitors have the advantage of being potent, specific for the target enzyme, unreactive with other proteins and thus non-toxic. The recent resolution of the x-ray structure of thrombin presents the opportunity for solving the structures of thrombin-inhibitor complexes and using computer-aided molecular modeling in the design of new more potent inhibitor structures for thrombin. The inhibitors synthesized in this research will be tested for 1) in vitro potency and specificity using purified coagulation serine proteases, 2) stability in plasma, 3) ability to inhibit complexes of coagulation proteases with their natural cofactors, and 4) efficacy in small animal models. The inhibitors produced in this research will be potentially useful for therapy and their study by kinetic analysis, x-ray diffraction analysis, in vitro coagulation tests, and in vivo testing will provide important new insights into thrombogenesis and the hemostatic mechanism.