A particularly intriguing result was found when brequinar sodium (NSC 368390, DUP785) was used as a seed to produce the COMPARE listing shown in the Table. This 4-quinolinecarboxylic acid inhibits de novo pyrimidine biosynthesis at dihydroorotate dehydrogenase, the fourth enzyme in the biosynthetic sequence (15, 16, 17). Inhibition of this mitochondrial enzyme, which catalyzes the conversion of dihydroorotate to orotate, leads to a blockage in the formation of uridine monophosphate (17). The closest match to brequinar (PCC = 0.838) was the naphthoquinone, dichloroallyl lawsone, an analogue of the cofactor ubiquinone (18). Dichloroallyl lawsone is a potent inhibitor of dihydroorotate dehydrogenase (19, 20). Thus, the cytotoxicities of both brequinar and its closest match, dichloroallyl lawsone, have been attributed to a common mechanism of action.
The next closest match was pyrazofurin, that is, pyrazole-5-carboxamide C-nucleoside (PCC = 0.785). This nucleoside inhibits de novo pyrimidine biosynthesis at orotidine-5'-monophosphate decarboxylase, a point two steps after the enzymatic target of brequinar (21), and this compound inhibits 5-aminoimidazole-4-carboxamide ribotide transformylase of the purine pathway (22). The remaining list shows antimetabolites to various targets, but the sixth closest match was phosphonoacetyl L-aspartic acid (PALA) (PCC = 0.750). This phosphonoacetyl aspartic acid salt inhibits L-aspartate transcarbamylase, an enzyme acting just two steps before the target enzyme of brequinar in the pyrimidine synthetic pathway (23).
The relationships among the reported enzyme targets for brequinar, dichloroallyl lawsone, pyrazofurin, and PALA support the hypothesis that COMPARE rankings are based on the biochemical mechanism of action. The in vitro cytotoxicity of each of these antimetabolites is caused by inhibition of nucleotide biosynthesis. The lack of similarity among the structures demonstrates that obtaining high PCC values with the COMPARE algorithm does not require structural similarity to the seed.
| Compound | NSC Number | 2D Structure | 3D Structure | Cell Inhibition Data |
|---|---|---|---|---|
| brequinar sodium | 368390 | 2D | 3D | get data |
| dichloroallyl lawsone | 126771 | 2D | 3D | get data |
| pyrazofurin | 143095 | 2D | 3D | get data |
| PALA | 224131 | 2D | 3D | get data |