title: Potent anticoagulant aptamer directed against factor IXa blocks macromolecular substrate interaction.
abstract: An aptamer targeting factor IXa has been evaluated in animal models and several clinical studies as a potential antithombotic therapy. We elucidate the molecular mechanism by which this aptamer acts as an anticoagulant. The aptamer binds tightly to factor IXa and prolongs the clotting time of human plasma. The aptamer completely blocks factor IXa activation of factor X regardless of the presence of factor VIIIa. However, the aptamer does not completely block small synthetic substrate cleavage, although it does slow the rate of cleavage. These data are consistent with the aptamer binding to the catalytic domain of factor IXa in such a way as to block an extended substrate-binding site. Therefore, unlike small molecule inhibitors, aptamers appear to be able to bind surfaces surrounding an active site and thereby sterically interfere with enzyme activity. Thus, aptamers may be useful agents to probe and block substrate-binding sites outside of the active site of an enzyme.
authors.affiliation: Duke Translational Research Institute, Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA.
authors.forename: Bruce
authors.initials: B
authors.lastname: Sullenger
authors.forename: Rebecca
authors.initials: R
authors.lastname: Woodruff
authors.forename: Dougald M
authors.initials: DM
authors.lastname: Monroe
mesh_terms: D000925:Anticoagulants / Q000378:metabolism* / Q000494:pharmacology; D052158:Aptamers, Peptide / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D001777:Blood Coagulation / Q000187:drug effects* / Q000502:physiology; D020134:Catalytic Domain; D015195:Drug Design; D005164:Factor IX / Q000737:chemistry / Q000378:metabolism; D015949:Factor IXa / Q000737:chemistry / Q000378:metabolism*; D015944:Factor VIIIa / Q000378:metabolism; D015942:Factor VIIa / Q000378:metabolism; D005170:Factor X / Q000378:metabolism; D006801:Humans; D008024:Ligands; D010447:Peptide Hydrolases / Q000737:chemistry / Q000378:metabolism; D054730:Protein Interaction Domains and Motifs / Q000187:drug effects / Q000502:physiology; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity / Q000502:physiology; D013927:Thrombosis / Q000188:drug therapy* / Q000378:metabolism*
chemical_list: D000925:Anticoagulants; D052158:Aptamers, Peptide; D008024:Ligands; D015944:Factor VIIIa; D005164:Factor IX; D005170:Factor X; D010447:Peptide Hydrolases; D015942:Factor VIIa; D015949:Factor IXa