Interaction of Designed Sulfated Flavanoids with Antithrombin: Lessons on the Design of Organic Activators

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Abstract
Recently, we designed (−)-epicatechin sulfate (ECS), the first small nonsaccharide molecule, as an activator of antithrombin for the accelerated inhibition of factor Xa, a key proteinase of the coagulation cascade (Gunnarsson, G. T.; Desai, U. R. J. Med. Chem.2002, 45, 1233−1243). Although sulfated flavanoid ECS was found to bind antithrombin with an affinity (∼10.7 μM) comparable to the reference trisaccharide DEF (∼4.5 μM), it accelerated the inhibition of factor Xa only 10-fold as compared to the ∼300-fold observed with DEF. To determine whether this conformational activation of the inhibitor is dependent on the structure of the organic activator and to probe the basis for the deficiency in activation, we studied the interaction of similar sulfated flavanoids with antithrombin. (+)-Catechin sulfate (CS), a chiral stereoisomer of ECS, bound plasma antithrombin with a 3-fold higher affinity (KD = 3.5 μM) and a 2-fold higher second-order rate constant for factor Xa inhibition (kACT = 6750 M-1 s-1). On the contrary, the KD and kACT were found to be lower ∼7.4- and ∼2.4-fold, respectively, for its racemic counterpart, (±)-catechin sulfate. Dependence of the equilibrium dissociation constant on the ionic strength of the medium at pH 6.0 and 7.4 suggests that nonionic interactions contribute a major proportion (∼55−73%) of the total binding energy, and only 1−2 ion pairs, in comparison to the expected ∼4 ion pairs for the reference trisaccharide, are formed in the interaction. Competitive binding experiments indicate that activator CS does not compete with a saccharide ligand that binds antithrombin in the pentasaccharide binding site, while it competes with full-length low-affinity heparin. A molecular docking study suggests plausible binding of CS in the extended heparin binding site, which is adjacent to the binding domain for the reference trisaccharide DEF. In combination, the results demonstrate that although conformational activation of antithrombin with small sulfated flavanoids is dependent on the structure of the activator, the designed activators do not bind in the pentasaccharide binding site in antithrombin resulting in weak activation. The mechanistic investigation highlights plausible directions to take in the rational design of specific high-affinity organic antithrombin activators.