Crystal Structure of Factor IXa with an Anticoagulant Aptamer Bound to an Allosteric Site

Vladimir N. Kolyadko, Ph.D.
The Children’s Hospital of Philadelphia
Philadelphia, Pennsylvania, U.S.

The intrinsic factor Xase complex consists of an enzyme, factor IXa, and a cofactor, factor VIIIa, assembled on a phospholipid surface in the presence of calcium ions. The enzyme complex proteolytically cleaves a short activation peptide from the NH2 terminus of the heavy chain of factor X, thus expressing the active site function of factor Xa. DTRI-177, an RNA aptamer, was selected as a subnanomolar binder of the zymogen, factor IX, and the proteinase, factor IXa. This aptamer serves as a potent anticoagulant by inhibiting factor X activation but with a minor effect on active site function of IXa. Evidence suggests that DTRI-177 may allosterically modulate IXa function and also possibly interfere with the IXa/VIIIa interaction within intrinsic Xase, but this is still unknown. This was the focal point of the presentation delivered by Vladimir Kolyadko of The Children’s Hospital of Philadelphia on Sunday, July 18, 2021. Vladimir looked to resolve the X-ray structure of the IXa aptamer inhibitory complex and obtain additional insights into the mechanism of inhibition of IXa. Commentary provided on the findings from the study suggested that the surface on IXa occupied by the aptamer reveals an important site for regulation of the intrinsic Xase function. The aptamer binds to the proteinase domain of IXa without occluding the active site, with predominant interactions involving IXa residues shown to be important for the binding of heparin or VIIIa. The extensive and complementary interaction surface with a buried area of 790 A₂ explains the high affinity and specificity of the interaction between DTRI-177 and IXa.