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Published on: August 4, 2009
Nonstandard Factor VIIa Binding Mode Reveals S1 Pocket Plasticity in Trypsin-Like Proteases
Laura Tesmer1,2, Hans Matter2, Otmar Klingler3
1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
Abstract:
Factor VIIa (FVIIa) catalyzes the first step of the blood coagulation cascade. The expected wide therapeutic window between antithrombotic efficacy and bleeding risk makes FVIIa an attractive drug target. However, no FVIIa inhibitors have reached the market so far, mostly due to poor oral bioavailability. To date, in all ligand-bound X-ray crystal structures of FVIIa, the binding pocket of FVIIa is in an active, open form. Here, we present an X-ray crystal structure of the FVIIa-tissue factor complex with a bound oxazole-based inhibitor at 1.9 Å resolution, with an extensively remodeled active site and a collapsed S1 pocket. Using collectively 0.17 ms of atomistic molecular dynamics simulations, we observed conformational transitions between the collapsed and open forms of the S1 pockets of FVIIa and 12 other serine peptidases out of 16 studied, indicating an equilibrium of open and collapsed states of the S1 pocket in FVIIa and the majority of the serine proteases studied. Therefore, our results point to a general S1 pocket plasticity, which provides the basis for a completely new way of inhibiting FVIIa and other serine proteases.
Insights
Factor VIIa (FVIIa) inhibitors are sought for antithrombotic therapy. A new crystal structure reveals a remodeled active site and collapsed S1 pocket, suggesting a novel inhibition strategy for FVIIa and related serine proteases.
Area of Science:
- Biochemistry
- Structural Biology
- Pharmacology
Background:
- Factor VIIa (FVIIa) is a key enzyme in blood coagulation.
- FVIIa inhibitors are attractive drug targets due to a potential wide therapeutic window.
- Existing FVIIa inhibitors face challenges, primarily poor oral bioavailability.
Purpose of the Study:
- To present a novel X-ray crystal structure of the FVIIa-tissue factor complex with a bound inhibitor.
- To investigate the structural plasticity of the FVIIa active site, particularly the S1 pocket.
- To explore new strategies for inhibiting FVIIa and other serine proteases.
Main Methods:
- X-ray crystallography of the FVIIa-tissue factor complex with an oxazole-based inhibitor at 1.9 Å resolution.
- Atomistic molecular dynamics simulations (0.17 ms total).
- Analysis of conformational transitions in the S1 pocket of FVIIa and other serine peptidases.
Main Results:
- The crystal structure revealed an extensively remodeled active site and a collapsed S1 pocket upon inhibitor binding.
- Molecular dynamics simulations showed conformational transitions between open and collapsed S1 pocket states in FVIIa.
- Similar S1 pocket plasticity was observed in 12 out of 16 studied serine peptidases.
Conclusions:
- FVIIa exhibits S1 pocket plasticity, existing in an equilibrium between open and collapsed states.
- This plasticity offers a basis for developing novel FVIIa inhibitors.
- The findings suggest a generalizable approach for inhibiting other serine proteases.
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