Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors

Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS). Idebenone and menadione are redox-active molecules capable of rescuing OXPHOS activity by engaging complex I-independent pathways of entry, often referred to as “complex I bypass.” In the present study, we created a cellular model of complex I deficiency by using CRISPR genome editing to knock out Ndufa9 in mouse myoblasts, and utilized this cell line to develop a high-throughput screening platform for novel complex I bypass factors. We screened a library of ~40,000 natural product extracts and performed bioassay-guided fractionation on a subset of the top scoring hits. We isolated four plant-derived 1,4-naphthoquinone complex I bypass factors with structural similarity to menadione: chimaphilin and 3-chloro-chimaphilin from Chimaphila umbellata and dehydro-α-lapachone and dehydroiso-α-lapachone from Stereospermum euphoroides. We also tested a small number of structurally related naphthoquinones from commercial sources and identified two additional compounds with complex I bypass activity: 2-methoxy-1,4-naphthoquinone and 2-methoxy-3-methyl-1,4,-naphthoquinone. The six novel complex I bypass factors reported here expand this class of molecules and will be useful as tool compounds for investigating complex I disease biology

Natural Product Screen and Follow-up.

<p>(A) Scatter plot of the normalized luminescence scores for the two original replicates of the natural product screening data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162686#pone.0162686.s005" target="_blank">S1 Table</a> (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162686#pone.0162686.s006" target="_blank">S2 Table</a> for data from the plates retested with and without antimycin). The data are plotted on a Log2 scale. The extract plates included DMSO wells and empty wells, which are plotted as the “negative controls.” The positive control plates contained wells with 2.4 mM idebenone, which was diluted upon transfer to the cell plate. These points are labeled “idebenone.” (B) Seahorse data for the three compounds isolated from <i>Chimaphila umbellata</i>. (C) Seahorse data for the four compounds isolated from <i>Sterospermum euphoroides</i>. For (B) and (C), each experiment was performed three times and data from a single representative experiment is shown.</p

Validation of Complex I Deficient Cell Line and Bypass Screening Assay.

<p>(A) Western blot of wild-type and <i>Ndufa9</i> knockout C2C12 cells. (B) Complex I and complex IV dipstick assays for wild-type and <i>Ndufa9</i> knockout C2C12 cells, with technical triplicates shown for each. (C) Seahorse comparing wild-type and <i>Ndufa9</i> knockout C2C12 cells. (D) Seahorse of <i>Ndufa9</i> knockout cells (left) and rotenone pre-treated wild-type C2C12s (right), each treated with a dose-response of idebenone. Doses are indicated in the legend below each plot. (E) Luminescence-based complex I bypass assay utilizing <i>Ndufa9</i> knockout cells. Cells treated with a dose-response of idebenone in the presence or absence of 125 nM antimycin. For (A-D), each experiment was performed three times, and a single representative experiment is shown. For (E) the data shown represent the average +/- SEM of data from three independent experiments.</p