An allosteric mechanism for potent inhibition of human ATP-citrate lyase

ATP-citrate lyase (ACLY) is a central metabolic enzyme and catalyses the ATP-dependent conversion of citrate and coenzyme A (CoA) to oxaloacetate and acetyl-CoA(1-5). The acetyl-CoA product is crucial for the metabolism of fatty acids(6,7), the biosynthesis of cholesterol(8), and the acetylation and prenylation of proteins(9,10). There has been considerable interest in ACLY as a target for anticancer drugs, because many cancer cells depend on its activity for proliferation(2,5,11). ACLY is also a target against dyslipidaemia and hepatic steatosis, with a compound currently in phase 3 clinical trials(4,5). Many inhibitors of ACLY have been reported, but most of them have weak activity(5). Here we report the development of a series of low nanomolar, small-molecule inhibitors of human ACLY. We have also determined the structure of the full-length human ACLY homo-tetramer in complex with one of these inhibitors (NDI-091143) by cryo-electron microscopy, which reveals an unexpected mechanism of inhibition. The compound is located in an allosteric, mostly hydrophobic cavity next to the citrate-binding site, and requires extensive conformational changes in the enzyme that indirectly disrupt citrate binding. The observed binding mode is supported by and explains the structure-activity relationships of these compounds. This allosteric site greatly enhances the 'druggability' of ACLY and represents an attractive target for the development of new ACLY inhibitors.