Elucidation of a common structure of selective fibrinogen receptor antagonists

The in-vitro effect of tirofiban, glycoprotein IIb/IIIa antagonist, on various responses of porcine blood platelets

The present study systematically evaluates the in-vitro effect of tirofiban, glycoprotein IIb/IIIa (integrins alphaIIbbetaIII) antagonist, on porcine blood platelets. It was found that tirofiban at concentrations up to 5,000 ng/ml did not affect the calcium signal produced by thrombin. Tirofiban, in a concentration-dependent manner reduced platelet aggregation evoked by ADP (IC50 approximately 70 ng/ml), collagen (IC50 approximately 200 ng/ml), and thrombin (IC50 approximately 5,000 ng/ml). Substantial thrombin-evoked platelet aggregation still occurred at high (5,000 ng/ml) tirofiban concentrations. The concentrations of tirofiban completely blocking the optical aggregation evoked by ADP or collagen failed to eliminate microaggregate formation totally. Tirofiban strongly inhibited the dense-granule and lysosome secretion induced by ADP (IC50 approximately 70-170 ng/ml), moderately inhibited that induced by collagen (IC50 approximately 420-500 ng/ml) and very poorly inhibited that elicited by thrombin (IC50 approximately 1,500-5,000 ng/ml). The extent of the inhibition of aggregation and secretion rose as concentrations of the stimulus lowered. Tirofiban was a moderate inhibitor (IC50 approximately 200 ng/ml) of adhesion and a poor inhibitor of platelet procoagulant response induced by collagen. Thromboelastography measurements indicate that, in whole blood, tirofiban, up to concentrations of 2,000 ng/ml, did not affect the kinetics of tissue factor induced clot formation. The obtained results reveal that in porcine platelets, the maximal concentrations of tirofiban used in human medicine (250 ng/ml), effectively block platelet responses triggered by ADP, partly block those induced by collagen and very poorly block those evoked by thrombin. The reason for this phenomenon seems to be the inability of tirofiban to reduce platelet secretion completely.

Combining pharmacophore search, automated docking, and molecular dynamics simulations as a novel strategy for flexible docking. Proof of concept: docking of arginine-glycine-aspartic acid-like compounds into the alphavbeta3 binding site

A novel and highly efficient flexible docking approach is presented where the conformations (internal degrees of freedom) and orientations (external degrees of freedom) of the ligands are successively considered. This hybrid method takes advantage of the synergistic effects of structure-based and ligand-based drug design techniques. Preliminary antagonist-derived pharmacophore determination provides the postulated bioactive conformation. Subsequent docking of this pharmacophore to the receptor crystal structure results in a postulated pharmacophore/receptor binding mode. Pharmacophore-oriented docking of antagonists is subsequently achieved by matching ligand interacting groups with pharmacophore points. Molecular dynamics in water refines the proposed complexes. To validate the method, arginine-glycine-aspartic acid (RGD) containing peptides, pseudopeptides, and RGD-like antagonists were docked to the crystal structure of alphavbeta3 holoprotein and apoprotein. The proposed directed docking was found to be more accurate, faster, and less biased with respect to the protein structure (holo and apoprotein) than DOCK, Autodock, and FlexX docking methods. The successful docking of an antagonist recently cocrystallized with the receptor to both apo and holoprotein is particularly appealing. The results summarized in this report illustrated the efficiency of our light CoMFA/rigid body docking hybrid method.

A comparative docking study and the design of potentially selective MMP inhibitors

As part of a program aimed at the design and synthesis of constrained MMP inhibitors, a survey of the reported X-ray and NMR structures of MMP/inhibitor complexes was performed, revealing mutations of key amino acids at different subsites between MMPs. A comparative study of fully automated docking programs AutoDock and DOCK in closely approximating the X-ray crystal structures of ten selected MMP inhibitors was performed. AutoDock proved to be highly reliable, efficient and predictive for a set of inhibitors with less than six atom types.

Binding of a fibrinogen mimetic stabilizes integrin alphaIIbbeta3's open conformation

The platelet integrin alphaIIbbeta3 is representative of a class of heterodimeric receptors that upon activation bind extracellular macromolecular ligands and form signaling clusters. This study examined how occupancy of alphaIIbbeta3's fibrinogen binding site affected the receptor's solution structure and stability. Eptifibatide, an integrin antagonist developed to treat cardiovascular disease, served as a high-affinity, monovalent model ligand with fibrinogen-like selectivity for alphaIIbbeta3. Eptifibatide binding promptly and reversibly perturbed the conformation of the alphaIIbbeta3 complex. Ligand-specific decreases in its diffusion and sedimentation coefficient were observed at near-stoichiometric eptifibatide concentrations, in contrast to the receptor-perturbing effects of RGD ligands that we previously observed only at a 70-fold molar excess. Eptifibatide promoted alphaIIbbeta3 dimerization 10-fold more effectively than less selective RGD ligands, as determined by sedimentation equilibrium. Eptifibatide-bound integrin receptors displayed an ectodomain separation and enhanced assembly of dimers and larger oligomers linked through their stalk regions, as seen by transmission electron microscopy. Ligation with eptifibatide protected alphaIIbbeta3 from SDS-induced subunit dissociation, an effect on electrophoretic mobility not seen with RGD ligands. Despite its distinct cleft, the open conformer resisted guanidine unfolding as effectively as the ligand-free integrin. Thus, we provide the first demonstration that binding a monovalent ligand to alphaIIbbeta3's extracellular fibrinogen-recognition site stabilizes the receptor's open conformation and enhances self-association through its distant transmembrane and/or cytoplasmic domains. By showing how eptifibatide and RGD peptides, ligands with distinct binding sites, each affects alphaIIbbeta3's conformation, our findings provide new mechanistic insights into ligand-linked integrin activation, clustering and signaling.

Design, synthesis and preliminary biological evaluation of a focused combinatorial library of stereodiverse carbohydrate-scaffold-based peptidomimetics

A focused combinatorial library of 126 mimetics of the RGD sequence based on sugar scaffolds have been rationally constructed using molecular modeling, with a particular emphasis on the stereodiversity of the library. A liquid phase, mix and divide synthesis was used, active compounds being identified by using orthogonal libraries and recursive deconvolution strategies.

Structural analysis of the KGD sequence loop of barbourin, an alphaIIbbeta3-specific disintegrin

Disintegrins constitute a class of small proteins that inhibit platelet aggregation by binding to the fibrinogen receptor, also referred to as integrin alphaIIbbeta3. Contrarily to other disintegrins that bind to a series of integrins via their Arg-Gly-Asp domain, the recognition site of barbourin contains a Lys-Gly-Asp sequence that ensures its specificity towards alphaIIbbeta3. In this article, a three-dimensional model of barbourin is proposed using homology modeling and large-scale molecular dynamics simulations. The conformations of the Lys-Gly-Asp sequence of barbourin are analyzed and compared to those of peptidomimetics that exhibit similar specificity towards alphaIIbbeta3. The tryptophan residue following the Lys-Gly-Asp sequence of the binding domain is shown to play a crucial role in the biological activity and the specificity of barbourin. Our results suggest that this disintegrin anchors to the binding pocket of the gamma-chain of fibrinogen rather than to those of the Arg-Gly-Asp sequence.