Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics

J Med Chem. 2020 Nov 12;63(21):12574-12594. doi: 10.1021/acs.jmedchem.0c01035. Epub 2020 Oct 27.


Despite extensive research on small molecule thrombin inhibitors for oral application in the past decades, only a single double prodrug with very modest oral bioavailability has reached human therapy as a marketed drug. We have undertaken major efforts to identify neutral, non-prodrug inhibitors. Using a holistic analysis of all available internal data, we were able to build computational models and apply these for the selection of a lead series with the highest possibility of achieving oral bioavailability. In our design, we relied on protein structure knowledge to address potency and identified a small window of favorable physicochemical properties to balance absorption and metabolic stability. Protein structure information on the pregnane X receptor helped in overcoming a persistent cytochrome P450 3A4 induction problem. The selected compound series was optimized to a highly potent, neutral, non-prodrug thrombin inhibitor by designing, synthesizing, and testing derivatives. The resulting optimized compound, BAY1217224, has reached first clinical trials, which have confirmed the desired pharmacokinetic properties.

MeSH terms

  • Administration, Oral
  • Animals
  • Anticoagulants / chemical synthesis*
  • Anticoagulants / chemistry
  • Anticoagulants / pharmacokinetics
  • Anticoagulants / pharmacology
  • Benzoxazoles / chemistry
  • Benzoxazoles / metabolism
  • Benzoxazoles / pharmacology
  • Binding Sites
  • Cytochrome P-450 CYP3A / genetics
  • Cytochrome P-450 CYP3A / metabolism
  • Drug Design*
  • Half-Life
  • Humans
  • Imidazoles / chemistry
  • Imidazoles / metabolism
  • Imidazoles / pharmacology
  • Inhibitory Concentration 50
  • Male
  • Molecular Docking Simulation
  • Oxazolidinones / chemistry
  • Oxazolidinones / metabolism
  • Oxazolidinones / pharmacology
  • Pregnane X Receptor / genetics
  • Pregnane X Receptor / metabolism
  • Rats
  • Rats, Wistar
  • Structure-Activity Relationship
  • Thrombin / antagonists & inhibitors*
  • Thrombin / metabolism
  • Transcriptional Activation / drug effects


  • Anticoagulants
  • Benzoxazoles
  • Imidazoles
  • Oxazolidinones
  • Pregnane X Receptor
  • Cytochrome P-450 CYP3A
  • Thrombin