The antiproliferative agent didemnin B uncompetitively inhibits palmitoyl protein thioesterase

Dynamic protein palmitoylation has been proposed to regulate GTP-binding proteins by controlling their membrane association and thus their access to key signaling proteins. While the palmitoyl protein thioesterase(s) responsible for depalmitoylation of plasma membrane-associated signaling proteins has (have) not been identified, the lysosomal palmitoyl protein thioesterase 1 (PPT1) has proven useful in in vitro studies of membrane localization requirements of GTP-binding proteins. We have previously reported the binding of the antiproliferative cyclic depsipeptide didemnin B to PPT1. To investigate the nature of this binding and its possible effects on PPT1 enzymatic activity, human PPT1 was expressed in an insect cell baculoviral system, and inhibition assays were performed using both [3H]palmitoyl Ha-Ras and myristoyl-CoA as PPT1 substrates. Didemnin B was shown to inhibit recombinant human PPT1 with a Ki of 92 nM. Kinetic analysis of this inhibition revealed that didemnin B inhibits PPT1 uncompetitively. Providing biochemical support for an uncompetitive mode of inhibition, in vitro binding studies of PPT1 and didemnin indicate that the natural product binds preferentially to the enzyme-substrate complex PPT1-palmitoyl-CoA. As the first described inhibitor of PPT1, didemnin B may prove to be a useful tool in the investigation of protein palmitoylation regulation.