Chemical proteomics combined with metabonomics reveals berberine targets NDUFV1 of complex I in the respiratory chain to regulate energy metabolism

Berberine (BBR) is the primary alkaloid compound of the heat-clearing traditional Chinese medicine Huanglian (Coptis chinensis) and exerts regulatory effects on energy metabolism. However, the specific targets and molecular mechanisms are not clear. In this paper, the BBR-affected energy metabolism pathway was screened by nontargeted metabolomics, and a BBR-derived photoaffinity labeled (PAL) probe was designed to identify potential targets via a chemical proteomics approach. NDUFV1, a subunit of complex I on mitochondria, was identified as a potential target of BBR. In the respiratory chain, BBR suppressed the activity of complex I, reduced the electrochemical potential in the mitochondrial intermembrane and inhibited the generation of ATP and heat via competitive binding with NDUFV1. The results illustrated the underlying mechanism of BBR in the downregulation of energy metabolism.