Detecting S-adenosyl-l-methionine-induced conformational change of a histone methyltransferase using a homogeneous time-resolved fluorescence-based binding assay

A homogeneous time-resolved fluorescence (HTRF)-based binding assay has been established to measure the binding of the histone methyltransferase (HMT) G9a to its inhibitor CJP702 (a biotin analog of the known peptide–pocket inhibitor, BIX-01294). This assay was used to characterize G9a inhibitors. As expected, the peptide–pocket inhibitors decreased the G9a–CJP702 binding signal in a concentration-dependent manner. In contrast, the S-adenosyl-l-methionine (SAM)–pocket compounds, SAM and sinefungin, significantly increased the G9a–CJP702 binding signal, whereas S-adenosyl-l-homocysteine (SAH) showed minimal effect. Enzyme kinetic studies showed that CJP702 is an uncompetitive inhibitor (vs. SAM) that has a strong preference for the E:SAM form of the enzyme. Other data presented suggest that the SAM/sinefungin-induced increase in the HTRF signal is secondary to an increased E:SAM or E:sinefungin concentration. Thus, the G9a–CJP702 binding assay not only can be used to characterize the peptide–pocket inhibitors but also can detect the subtle conformational differences induced by the binding of different SAM–pocket compounds. To our knowledge, this is the first demonstration of using an uncompetitive inhibitor as a probe to monitor the conformational change induced by compound binding with an HTRF assay.