Activity-based probes and chemical proteomics uncover the biological impact of targeting HMG-CoA Synthase 1 in the mevalonate pathway

Mevalonate is a precursor for essential metabolites, such as isoprenoids and sterols. Its synthesis starts with 3-hydroxy-3-methylglutaryl-coenzyme A synthase 1 (HMGCS1) producing HMG-CoA, which is then converted to mevalonate by HMG-CoA reductase (HMGCR), a target of statins. Cancer cells often upregulate enzymes in the mevalonate pathway to meet their metabolic demands, leading to the development of inhibitors targeting several enzymes in this pathway. However, current inhibitors have not yet shown significant anticancer activity. While HMGCS1 has unique biochemical properties that distinguish it from other mevalonate pathway enzymes, the effects of inhibiting HMGCS1 have not been thoroughly investigated. Here, we present a set of chemical probes that enable us to systematically assess the proteome-wide selectivity and potency of Hymeglusin, the primary inhibitor of HMGCS1 used in the field, confirming it as a useful tool for short-term HMGCS1 inhibition. Inhibiting HMGCS1 with Hymeglusin causes proteome changes that are nearly identical to those caused by inhibiting HMGCR or degrading HMGCS1. Accordingly, simultaneously targeting HMGCS1 and HMGCR effectively suppresses the growth of statin-resistant cells and xenograft models, without increasing the risk of side effects. Finally, we find that while Hymeglusin is a valuable tool for short-term mechanistic studies, its usefulness is limited for long-term efficacy studies due to its poor stability in serum. Together, this study highlights the biological implications of targeting HMGCS1 as monotherapy or in combination with statins, and caution is required when using Hymeglusin as a tool.