Surface plasmon resonance biosensor technology was used to directly measure the binding interactions of small molecules to the ligand-binding domain of human estrogen receptor. In a screening mode, specific ligands of the receptor were easily discerned from nonligands. In a high-resolution mode, the association and dissociation phase binding responses were shown to be reproducible and could be fit globally to a simple interaction model to extract reaction rate constants. On average, antagonist ligands (such as tamoxifen and nafoxidine) were observed to bind to the receptor with association rates that were 500-fold slower than agonists (such as estriol and -estradiol). This finding is consistent with these antagonists binding to an altered conformation of the receptor. The biosensor assay also could identify subtle differences in how the same ligand interacted with two different isoforms of the receptor (␣ and ). The biosensor's ability to determine kinetic rate constants for small molecule͞protein interactions provides unique opportunities to understand the mechanisms associated with complex formation as well as new information to drive the optimization of drug candidates.S urface plasmon resonance (SPR) biosensor technology has advanced to the point where it is possible to measure directly small molecules interacting with immobilized macromolecular targets (1, 2). This development suggests that biosensor analysis will become an important secondary screening tool in drug discovery, confirming hits from primary screens and providing detailed kinetics for lead optimization (3, 4). To illustrate the utility of current SPR technology, the binding properties of small compounds (200-500 Da) interacting with human estrogen receptor (ER) were analyzed.Ligand binding to ER is responsible for controlling the basic biology of estrogen-sensitive tissues. Using selective agonists or antagonists to modulate this biology is the focus of significant activity in the pharmaceutical industry (5-9). To date, a ligand's binding properties for ER have mainly been determined by equilibrium binding assays that often employ radiolabeled compounds and require overnight incubations. Here, we demonstrate how optical biosensors may be used to determine both kinetic and equilibrium binding constants for compounds interacting with ER in real time without labeling either binding partner.SPR biosensor experiments require immobilizing one reactant on a surface and monitoring its binding to a second reactant in solution. An antibody-capturing method was used to study the dynamics of ER͞ligand interactions. This assay format created a chemically homogenous receptor surface and allowed us to determine rapidly the binding properties of a variety of compounds. We examined the binding of 12 compounds (shown in Fig. 1) having differing receptor activities: both estrogen and non-estrogen agonists, SERMs (selective ER modulators, which for this discussion are referred to as antagonists), and nonbinding control compounds that possess core structures sim...