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Sidebars : Mar 15, 2009 (Vol. 29, No. 6)

Determining Small Molecule Binding Kinetic Constants

Determining and evaluating the affinity of small molecule binding to a therapeutic target is a major component of drug discovery and lead optimization.

In a technical note entitled “Label-free determination of kinetic constants for small molecule binding to proteins using FortéBio’s Octet Red Multi-Channel Platform,” Charles Wartchow, et al., report on a method for determining kinetic constants for the binding of small molecule inhibitors (<500 Daltons) to carbonic anhydrase, including rate constants and affinity constants. These parameters are derived from data obtained using the Octet RED System, a label-free, eight-channel system that is compatible with 96-well microplates, according to the research team.

In a typical experiment, biotinylated protein targets are immobilized onto a high-binding capacity streptavidin surface, and the association and dissociation of small molecules with molecular weights ranging from ~150–350 Daltons is monitored in parallel. Kinetic constants for the binding of compounds to carbonic anhydrase with micromolar and nanomolar affinities agree closely with published values, say the scientists, who add that evaluations conducted on proteins obtained from major pharmaceutical partners show agreement of the results between Octet RED and other SPR-based methods.