Mechanism of the Anticoagulant Activity of Thrombin Mutant W215A/E217A

The thrombin mutant W215A/E217A (WE) is a potent anticoagulant both in vitro and in vivo. Previous x-ray structural studies have shown that WE assumes a partially collapsed conformation that is similar to the inactive E* form, which explains its drastically reduced activity toward substrate. Whether this collapsed conformation is genuine, rather than the result of crystal packing or the mutation introduced in the critical 215–217 β-strand, and whether binding of thrombomodulin to exosite I can allosterically shift the E* form to the active E form to restore activity toward protein C are issues of considerable mechanistic importance to improve the design of an anticoagulant thrombin mutant for therapeutic applications. Here we present four crystal structures of WE in the human and murine forms that confirm the collapsed conformation reported previously under different experimental conditions and crystal packing. We also present structures of human and murine WE bound to exosite I with a fragment of the platelet receptor PAR1, which is unable to shift WE to the E form. These structural findings, along with kinetic and calorimetry data, indicate that WE is strongly stabilized in the E* form and explain why binding of ligands to exosite I has only a modest effect on the E*-E equilibrium for this mutant. The E* → E transition requires the combined binding of thrombomodulin and protein C and restores activity of the mutant WE in the anticoagulant pathway.Thrombin is the pivotal protease of blood coagulation and is endowed with both procoagulant and anticoagulant roles in vivo (1). Thrombin acts as a procoagulant when it converts fibrinogen into an insoluble fibrin clot, activates clotting factors V, VIII, XI, and XIII, and cleaves PAR1² and PAR4 on the surface of human platelets thereby promoting platelet aggregation (2). Upon binding to thrombomodulin, a receptor present on the membrane of endothelial cells, thrombin becomes unable to interact with fibrinogen and PAR1 but increases >1,000-fold its activity toward the zymogen protein C (3). Activated protein C generated from the thrombin-thrombomodulin complex down-regulates both the amplification and progression of the coagulation cascade (3) and acts as a potent cytoprotective agent upon engagement of EPCR and PAR1 (4).The dual nature of thrombin has long motivated interest in dissociating its procoagulant and anticoagulant activities (5–12). Thrombin mutants with anticoagulant activity help rationalize the bleeding phenotypes of several naturally occurring mutations and could eventually provide new tools for pharmacological intervention (13) by exploiting the natural protein C pathway (3, 14, 15). Previous mutagenesis studies have led to the identification of the E217A and E217K mutations that significantly shift thrombin specificity from fibrinogen toward protein C relative to the wild type (10–12). Both constructs were found to display anticoagulant activity in vivo (10, 12). The subsequent discovery of the role of Trp-215 in controlling the balance between pro- and anti-coagulant activities of thrombin (16) made it possible to construct the double mutant W215A/E217A (WE) featuring >19,000-fold reduced activity toward fibrinogen but only 7-fold loss of activity toward protein C (7). These properties make WE the most potent anticoagulant thrombin mutant engineered to date and a prototype for a new class of anticoagulants (13). In vivo studies have revealed an extraordinary potency, efficacy, and safety profile of WE when compared with direct administration of activated protein C or heparin (17–19). Importantly, WE elicits cytoprotective effects (20) and acts as an antithrombotic by antagonizing the platelet receptor GpIb in its interaction with von Willebrand factor (21).What is the molecular mechanism underscoring the remarkable functional properties of WE? The mutant features very low activity toward synthetic and physiological substrates, including protein C. However, in the presence of thrombomodulin, protein C is activated efficiently (7). A possible explanation is that WE assumes an inactive conformation when free but is converted into an active form in the presence of thrombomodulin. The ability of WE to switch from inactive to active forms is consistent with recent kinetic (22) and structural (23, 24) evidence of the significant plasticity of the trypsin fold. The active form of the protease, E, coexists with an inactive form, E*, that is distinct from the zymogen conformation (25). Biological activity of the protease depends on the equilibrium distribution of E* and E, which is obviously different for different proteases depending on their physiological role and environmental conditions (25). The E* form features a collapse of the 215–217 β-strand into the active site and a flip of the peptide bond between residues Glu-192 and Gly-193, which disrupts the oxyanion hole. These changes have been documented crystallographically in thrombin and other trypsin-like proteases such as αI-tryptase (26), the high temperature requirement-like protease (27), complement factor D (28), granzyme K (29), hepatocyte growth factor activator (30), prostate kallikrein (31), prostasin (32, 33), complement factor B (34), and the arterivirus protease nsp4 (35). Hence, the questions that arise about the molecular mechanism of WE function are whether the mutant is indeed stabilized in the inactive E* form and whether it can be converted to the active E form upon thrombomodulin binding.Structural studies of the anticoagulant mutants E217K (36) and WE (37) show a partial collapse of the 215–217 β-strand into the active site that abrogates substrate binding. The collapse is similar to, but less pronounced than, that observed in the structure of the inactive E* form of thrombin where Trp-215 relinquishes its hydrophobic interaction with Phe-227 to engage the catalytic His-57 and residues of the 60-loop after a 10 Å shift in its position (24). These more substantial changes have been observed recently in the structure of the anticoagulant mutant Δ146–149e (38), which has proved that stabilization of E* is indeed a molecular mechanism capable of switching thrombin into an anticoagulant. It would be simple to assume that both E217K and WE, like Δ146–149e, are stabilized in the E* form. However, unlike Δ146–149e, both E217K and WE carry substitutions in the critical 215–217 β-strand that could result into additional functional effects overlapping with or mimicking a perturbation of the E*-E equilibrium. A significant concern is that both structures suffer from crystal packing interactions that may have biased the conformation of side chains and loops near the active site (24). The collapsed structures of E217K and WE may be artifactual unless validated by additional structural studies where crystal packing is substantially different.To address the second question, kinetic measurements of chromogenic substrate hydrolysis by WE in the presence of saturating amounts of thrombomodulin have been carried out (37), but these show only a modest improvement of the k_cat/K_m as opposed to >57,000-fold increase observed when protein C is used as a substrate (7, 37). The modest effect of thrombomodulin on the hydrolysis of chromogenic substrates is practically identical to that seen upon binding of hirugen to exosite I (37) and echoes the results obtained with the wild type (39) and other anticoagulant thrombin mutants (7, 9, 10, 12, 38). That argues against the ability of thrombomodulin alone to significantly shift the E*-E equilibrium in favor of the E form. Binding of a fragment of the platelet receptor PAR1 to exosite I in the D102N mutant stabilized in the E* form (24) does trigger the transition to the E form (23), but evidence that a similar long-range effect exists for the E217K or WE mutants has not been presented.In this study we have addressed the two unresolved questions about the mechanism of action of the anticoagulant thrombin mutant WE. Here we present new structures of the mutant in its human and murine versions, free and bound to a fragment of the thrombin receptor PAR1 at exosite I. The structures are complemented by direct energetic assessment of the binding of ligands to exosite I and its effect on the E*-E equilibrium.