Design, synthesis, and biological activity of potent and selective inhibitors of blood coagulation factor Xa
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Updated: Aug 23, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
J Adam Willardsen1, Danette A Dudley, Wayne L Cody
1Department of Chemistry, Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, Michigan 48105, USA.
Abstract:
Factor Xa (FXa) has materialized as a key enzyme for the intervention of the blood coagulation cascade and for the development of new antithrombotic agents. FXa is the lone enzyme responsible for the production of thrombin and therefore is an attractive target for the control of thrombus formation. We have designed and synthesized a unique series of quinoxalinone FXa inhibitors. This series resulted in 3-[4-[5-((2S,6R)-2,6-dimethylpiperidin-1-yl)pentyl]-3-oxo-3,4-dihydroquinoxolin-2-yl]benzamidine (35) with 0.83 nM activity against FXa and excellent selectivity over similar serine proteases. An X-ray crystal structure of compound 35 bound to trypsin along with molecular modeling has led to a predicted binding conformation of compound 35 in FXa. Compound 35 has also been proven to be efficacious in vivo in both the rabbit veno-venous shunt and dog electrolytic injury models. In addition, it was shown that compound 35 did not significantly increase bleeding times in a rabbit model except at the highest doses and plasma concentrations were elevated in a dose dependent manner following a bolus dose and continuous intravenous infusion.
Insights
Researchers developed novel quinoxalinone inhibitors targeting Factor Xa (FXa), a key enzyme in blood clotting. Compound 35 demonstrated potent FXa inhibition and efficacy in vivo with a favorable bleeding profile, showing promise as an antithrombotic agent.
Area of Science:
- Biochemistry
- Pharmacology
- Medicinal Chemistry
Background:
- Factor Xa (FXa) is a critical enzyme in the blood coagulation cascade.
- FXa's role in thrombin generation makes it a significant target for antithrombotic drug development.
Purpose of the Study:
- To design and synthesize novel quinoxalinone-based inhibitors of FXa.
- To evaluate the potency, selectivity, and in vivo efficacy of a lead compound.
Main Methods:
- Chemical synthesis of quinoxalinone derivatives.
- Enzyme inhibition assays to determine potency and selectivity.
- X-ray crystallography and molecular modeling for structural insights.
- In vivo efficacy studies in rabbit and dog models.
- Pharmacokinetic and bleeding time assessments.
Main Results:
- A novel series of quinoxalinone FXa inhibitors was synthesized.
- Compound 35 exhibited potent FXa inhibition (0.83 nM) and high selectivity.
- Structural analysis predicted compound 35's binding conformation in FXa.
- Compound 35 demonstrated in vivo efficacy in thrombosis models.
- Compound 35 showed a dose-dependent increase in plasma concentration and minimal impact on bleeding times at therapeutic doses.
Conclusions:
- The synthesized quinoxalinone derivatives represent a promising class of FXa inhibitors.
- Compound 35 is a potent and selective FXa inhibitor with demonstrated in vivo efficacy and a potentially manageable safety profile for antithrombotic therapy.
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