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Discovery of a Reversible Sub-Picomolar Thrombin Inhibitor Using DCC.

Millicent Dockerill1, Richard J Payne2,3, Nicolas Winssinger1

  • 1Department of Organic Chemistry, Faculty of Sciences, University of Geneva, Geneva, Switzerland.

Angewandte Chemie (International Ed. in English)
|July 15, 2026
PubMed
Summary

This study introduces a peptide nucleic acid (PNA)-templated dynamic combinatorial chemistry (DCC) platform for rapid discovery of ultrahigh-affinity, reversible thrombin inhibitors. The method enables programmable multivalent therapeutics with on-demand reversibility.

Keywords:
active sitechemistrycombinatorial chemistryligandmass spectrometrymass spectrometry imagingnucleic acidpeptide nucleic acidthrombin

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Area of Science:

  • Molecular Biology
  • Medicinal Chemistry
  • Biochemistry

Background:

  • Dynamic combinatorial chemistry (DCC) is a powerful strategy for ligand discovery.
  • Current DCC methods face limitations due to kinetic constraints and analytical challenges.

Purpose of the Study:

  • To develop a peptide nucleic acid (PNA)-templated trivalent DCC platform for rapid identification of ultrahigh-affinity and reversible thrombin inhibitors.

Main Methods:

  • Utilized a PNA-templated trivalent DCC platform for exploring 125,000 assemblies.
  • Employed short hybridization handles for unbiased fragment library equilibration.
  • Integrated size-exclusion filtration and MALDI-MS for rapid selection and readout.

Main Results:

  • Identified ultrahigh-affinity and reversible thrombin inhibitors with apparent sub-picomolar affinity (KD ≈ 84 fM).
  • Achieved near-stoichiometric inhibition due to synergistic fragment combinations engaging multiple thrombin sites.
  • Demonstrated on-demand reversibility of inhibition via a toehold antidote.

Conclusions:

  • Established hybridization-guided DCC as a fast, scalable method for programmable multivalent therapeutics.
  • Highlighted the potential for designing reversible inhibitors with precise control over activity.