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Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage

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High-Throughput Binding Kinetic Measurements of DNA-Encoded Library-Derived Hits By Focal Molography.

Nicholas Favalli¹, Carola Velti¹, Lorenzo Campari¹

¹Philochem AG, Libernstrasse 3, Otelfingen CH-8112, Switzerland.

Journal of Medicinal Chemistry

|June 16, 2026

Summary

Focal molography offers high-throughput, label-free kinetic measurements for DNA-encoded libraries (DELs). This method enables quantitative validation of DEL-derived ligands, improving hit characterization.

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Area of Science:

Biochemistry
Chemical Biology
Drug Discovery

Background:

DNA-encoded libraries (DELs) facilitate the discovery of small organic ligands for target proteins.
Current methods for validating DEL hits struggle with high-throughput kinetic characterization, leaving many potential binders unassessed.

Purpose of the Study:

To introduce focal molography as a novel, high-throughput, label-free optical technique for parallel kinetic measurements.
To validate focal molography for characterizing binding kinetics and dissociation constants of DEL-derived ligands.

Main Methods:

Application of focal molography to measure kinetic parameters (kon, koff) and dissociation constants (Kd).
Testing the methodology on DEL-derived ligands against carbonic anhydrase IX and known ligands for fibroblast activation protein.

Main Results:

Focal molography successfully measured binding kinetics and Kd values for DEL-derived ligands.
Obtained binding parameters demonstrated consistency with established techniques like fluorescence polarization, surface plasmon resonance, and inhibition assays.

Conclusions:

Focal molography is a robust, DEL-compatible technology for quantitative, high-throughput hit validation.
This method enhances the characterization of ligands identified through DEL screening, addressing limitations in current validation approaches.