Design and synthetic evaluation of novel andrographolide and etomoxir-based CPT1 Inhibitors

Background: Carnitine palmitoyltransferase 1A (CPT1A) controls mitochondrial long-chain fatty acid beta oxidation and is a therapeutic node in metabolic disease and cancer. The prototype inhibitor etomoxir lacks isoform selectivity and produced dose-limiting hepatotoxicity in the clinic, motivating the design of safer and more selective CPT1A inhibitors.

Objectives: To create a tractable, rapid synthesis and structure-guided framework for new CPT1A inhibitors that maintain potency while improving predicted isoform selectivity and mitigating structural liabilities associated with etomoxir.

Methods: Engineered a concise three-step route to a library of 2-substituted oxirane-2-carboxylates that diversify the alkylating warhead and the aromatic scaffold. A CPT1A homology model and induced-fit docking were used to map binding determinants, prioritize substitutions, and prospectively bias against motifs linked to off-target reactivity. Selected analogs were advanced to preliminary biochemical assays of CPT1A inhibition with confirmatory counterscreens for nonspecific reactivity.

Results: The synthetic platform delivered gram-scale access to diverse analogs with typical step yields in the moderate to good range, enabling rapid make–test cycles. Docking highlighted a hydrogen-bonding network near the acyl-carnitine channel and a lipophilic subpocket that tolerated para-halogen and meta-methoxy substitutions while disfavoring strongly electrophilic epoxide warheads. Multiple optimized analogs preserved low-nanomolar to sub-micromolar CPT1A inhibition in preliminary assays and showed reduced reactivity flags relative to etomoxir-like chemotypes, consistent with the design hypothesis for improved safety margins.

Conclusions: Integrating streamlined synthesis with structure-guided design yielded etomoxir-inspired oxirane carboxylates that retain CPT1A potency while de-risking key toxicity-associated features. This establishes a foundation for isoform-selective CPT1A inhibitor development and for in vivo validation.