Summary information

PDB id
8tqs
Class
blood clotting
Method
X-ray (2.207 Å)
Summary
Complex of human thrombin (s195a) bound to a bivalent inhibitor comprised of DNA aptamer hd22 conjugated to dabigatran with a linker.
Reference
Yu H, Kumar S, Frederiksen JW, Kolyadko VN, Pitoc G, Layzer J, Yan A, Rempel R, Francis S, Krishnaswamy S, Sullenger BA (2024): "Aptameric hirudins as selective and reversible EXosite-ACTive site (EXACT) inhibitors." Nat Commun, 15, 3977. doi: 10.1038/s41467-024-48211-6.
Abstract
Potent and selective inhibition of the structurally homologous proteases of coagulation poses challenges for drug development. Hematophagous organisms frequently accomplish this by fashioning peptide inhibitors combining exosite and active site binding motifs. Inspired by this biological strategy, we create several EXACT inhibitors targeting thrombin and factor Xa de novo by linking EXosite-binding aptamers with small molecule ACTive site inhibitors. The aptamer component within the EXACT inhibitor (1) synergizes with and enhances the potency of small-molecule active site inhibitors by many hundred-fold (2) can redirect an active site inhibitor's selectivity towards a different protease, and (3) enable efficient reversal of inhibition by an antidote that disrupts bivalent binding. One EXACT inhibitor, HD22-7A-DAB, demonstrates extraordinary anticoagulation activity, exhibiting great potential as a potent, rapid onset anticoagulant to support cardiovascular surgeries. Using this generalizable molecular engineering strategy, selective, potent, and rapidly reversible EXACT inhibitors can be created against many enzymes through simple oligonucleotide conjugation for numerous research and therapeutic applications.
G4 notes
1 G-tetrad

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 1 G-tetrad

 1 glyco-bond=-s-s sugar=-3-- groove=wnwn planarity=0.874 type=bowl   nts=4 GGGG D.DG16,D.DG28,D.DG25,D.DG19

List of 3 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#-1 nts=4 GTAG D.DG16,D.DT17,D.DA18,D.DG19
 2 type=lateral   helix=#-1 nts=7 GGGCAGG D.DG19,D.DG20,D.DG21,D.DC22,D.DA23,D.DG24,D.DG25
 3 type=lateral   helix=#-1 nts=4 GTTG D.DG25,D.DT26,D.DT27,D.DG28