Defense Date


Document Type


Degree Name

Doctor of Philosophy


Pharmaceutical Sciences

First Advisor

Umesh Desai


Sulfated low molecular weight lignins (LMWLs), CDSO3 and FDSO3, designed recently as macromolecular mimetics of heparin, were found to exhibit potent anticoagulant activity. Small molecules based on the same scaffold, SBD and SBT, showed promising thrombin inhibition. We were able to address the mechanism of the inhibition using Michaelis-Menten kinetics. All the molecules were found to be allosterically impairing thrombin activity using either noncompetitive or uncompetitive mechanism. Absence of competition with hirugen, an exosite 1 ligand, and competition with polymeric heparin points to exosite 2 as the site of interaction for these inhibitors. Yet mixed competition results with other exosite 2 ligands indicated that the molecules utilize different sub-sites within exosite 2 for interaction. Site-directed mutagenesis was used to pin point the key residues important for inhibition. All of all positively charged exosite 2 residues were mutated one at a time to alanine to abolish its charge. The data showed that Arg93 and Arg175 are the major residues involved in CDSO3 binding. FDSO3 showed a progressively greater defect in inhibition with double point mutations, the triple mutant Arg93,97,101Ala displayed a 50 fold drop in inhibition. A single mutant, Arg173Ala, displayed 22-fold reduction in IC50 of SBD, while Arg233Ala was the only mutation that impaired SBT inhibition. This proves the fact that inspite of the structural similarity between the two polymers and the two small molecules, thtey do not share the same binding space in exosite 2. To understand the types of interactions involved in thrombin interaction with the polymers, we resorted to salt-dependence studies. This showed that CDSO3 had fewer ionic contacts with thrombin, with most of its binding energy derived from non-ionic interactions. FDSO3 on the other hand had a balanced contribution of ionic and non-ionic forces. Thermodynamic studies showed that both polymers have a positive ΔCp of binding, which proves the involvement of electrostatic forces and signals the burial of the polar residues on thrombin exosite 2. These molecules offer a rare chance to study thrombin allostery. Little is known about the interplay between exosite 2, active site and sodium binding site. The allosteric nature of inhibition indicated that, for the first time, a link is proven to exist between exosite 2 and the active site that could be used to inhibit the enzyme. The presence of sodium was found to enhance the binding of FDSO3 at exosite 2, which establish the energetic coupling between exosite 2 and sodium binding site. The results identify novel binding sub-sites within exosite 2 that are energetically coupled to thrombin’s catalytic function and linked to the sodium binding site. The design of high affinity small molecules based on LMWLs scaffold presents major opportunities for developing clinically relevant, allosteric modulators of thrombin.


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VCU Theses and Dissertations

Date of Submission

March 2013