Small Molecule Detection


The determination and evaluation of the affinity of small molecule binding to a therapeutic target is a significant component of drug discovery and lead optimization. The Octet RED and Octet HTX systems are designed with rapid data acquisition and sensitivity to enable the detection of small molecules and peptides in a simple, user-friendly workflow in conjunction with Super Streptavidin Biosensors.

Label-free analysis of the association and dissociation of a small molecule with the target protein of interest results in the determination of kinetic constants including the association rate constant (ka), dissociation rate constant (kd), and equilibrium dissociation constant (KD). A well-established model system1, 2, the binding of carbonic anhydrase inhibitors, was examined to assess the Octet RED System's ability to determine kinetic constants for small molecules.

To demonstrate the accuracy of results obtained from the Octet RED System, the three inhibitors binding to carbonic anhydrase were assayed and compared to reported values. The inhibitors were selected for low (˜200 mM), medium (˜1 mM), and high affinity (˜40 nM): sulpiride (341 Daltons), furosemide (330 Daltons), and azetazolamide (222 Daltons), respectively. The biotinylated protein targets were immobilized onto Super Streptavidin Biosensors, and the association and dissociation of the molecules was monitored in parallel to minimize time to results.

Medium Affinity: Carbonic Anhydrase:Furosemide (330 Daltons)

furosemide:carbonic anhydrase binding data
furosemide:carbonic anhydrase binding data

Figure 1a & 1b: Analysis of furosemide:carbonic anhydrase binding data at 30-0.12 µM furosemide (3X dilution series, N=5) in PBS with 0.5% DMSO.

Low Affinity: Carbonic Anhydrase: Sulpiride (341 Daltons)

sulpiride: carbonic anhydrase binding data

Figure 2: Analysis of a weak binding interaction (KD 239 µM). Sulpiride:carbonic anhydrase binding data at 500-63 µM sulpiride (2X dilution series) in PBS with 1% DMSO.

High Affinity: Carbonic Anhydrase: Azetazolamide (222 Daltons)

acetazolamide : carbonic anhydrase binding data

Figure 3: Analysis of a high affinity interaction (KD= 39 nM). Acetazolamide:carbonic anhydrase binding data at 1-0.012 µM acetazolamide (3X dilution series) in PBS with 0.5% DMSO.

1. Papalia et al, Analytical Biochem 359 (2006), 94-105.
2. Myszka, Analytical Biochem 329 (2004), 316-323.