Fluorescent substrates enable specific detection and structure-function insights into human aldehyde dehydrogenase isoforms.

Aldehyde dehydrogenase (ALDH) isoforms are widely used as biomarkers and potential drug targets in cancer research. Quantitation of ALDH enzymatic activity in biological samples often relies on the use of commercially available assays that are quite unspecific and do not discriminate between the various ALDH isoforms. The availability of highly purified recombinant ALDH isoforms allowed us to perform a full kinetic characterization of ALDH isoforms with fluorogenic substrates, BODIPY™-aminoacetaldehyde (BAAA), the ALDEFLUOR™ assay reagent, and two naphthaldedyde derivatives, 6-methoxy-2-naphthaldehyde (MONAL-62) and 7-methoxy-1-naphthaldehyde (MONAL-71). All ALDH1A isoforms were active to different extend with BAAA, while ALDH3A1 did not show any activity. Remarkable kinetic differences between ALDH1A1, ALDH1A2, ALDH1A3, ALDH2 and ALDH3A1 were observed with naphthaldehyde derivatives. Exquisite sensitivity was attained with MONAL-62 with a lower detection limit of 2 amol or 10 molecules of enzyme per microliter for ALDH1A1. The high substrate specificity of ALDH1A1 for MONAL-71 provides an alternative assay for the unambiguous identification of this isoform. Enzymatic properties of isoforms were accounted for by in silico simulations of substrate docking to the active site of ALDH structures. In addition to substrate specificity, inhibitor selectivity of each isoform, as assessed by incubation with DIMATE and ABD0171 inhibitors, provided additional information about isoform composition in low-activity samples isolated from cell extracts. The method was successfully applied to the detection of ALDH isoform activity in triple-negative breast cancer cells.