Jj. Slonusakiewicz et al., NONPOLAR INTERACTIONS OF THROMBIN S' SUBSITES WITH ITS BIVALENT INHIBITOR - METHYL SCAN OF THE INHIBITOR LINKER, Biochemistry, 36(44), 1997, pp. 13494-13502
We have designed bivalent thrombin inhibitors, consisting of a nonsubs
trate type active site blocking segment, a hirudin-based fibrinogen re
cognition exosite blocking segment, and a linker connecting these segm
ents. The inhibition provided by the bivalent inhibitors with various
linker lengths revealed that a minimum of 15 atoms was required for si
multaneous binding of the two blocking segments of the inhibitor to th
rombin without significant distortion. The crystal structure of the in
hibitors with a 16-atom linker showed some conformational flexibility
in the linker portion which still lies deep in the groove joining the
active site and the fibrinogen recognition exosite. Since the thrombin
S' subsites are not well characterized, we designed a new strategy to
search for possible nonpolar interactions between the linker and the
thrombin S' subsites. This strategy, the ''methyl scan'', is based on
the incorporation of a methyl side chain at each atom position of the
linker by using sarcosine, D,L-alanine, D,L-3-aminoisobutyric acid, or
N-methyl-beta-alanine. The methyl groups on the second and the eighth
atom positions of the linker, which correspond to the side chains of
the P1' and the P3' residues, respectively, improved the affinity of t
he inhibitors significantly. Further study of the stereospecificity sh
owed that L-Ala at the P1' residue and D-Ala at the P3' residue prefer
ably improved the affinity of the inhibitors 20- and 25-fold, respecti
vely. Molecular modeling calculations using a methyl probe were also c
arried out to identify favorable nonpolar interacting sites on the thr
ombin surface. Two sites were identified in the vicinity of the P1' an
d the P3' residues, supporting the validity of the methyl scan method.
Thus, this study has improved our understanding of the interactions t
aking place in this groove. In particular, we have been able to show t
hat some specific structural features, such as hydrophobic complementa
rity between the linker and the thrombin S' subsites, could be exploit
ed and make these inhibitors trivalent.