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The coordinated processes of lipid synthesis, degradation and transport are mediated by enzymes, cofactors, and transport proteins. Accordingly, lipid-metabolizing enzymes represent logical targets for the treatment of dyslipidemia, a major risk factor for type 2 diabetes, atherosclerosis, and other disorders. Small molecule tool compounds, modulating the function of such proteins, can substantially facilitate the characterization of target proteins. Such molecules complement genetic studies allowing a time- and dose-dependent control of protein activity in biological systems. This can improve our understanding of physiological processes, give insights into the druggability of target proteins, and may finally result in the development of therapeutic compounds. In this review, we summarize the current state of available inhibitors targeting key proteins in neutral lipid metabolism with a focus on metabolic lipases, acyltransferases, and fatty acid binding proteins.