A covalent irreversible inhibitor binds in two mutually exclusive conformations to the active-site cysteine residue of human aldehyde dehydrogenase 1A3

Covaleda, D.; Vizarraga, D.; Upadhyay, T.; Zhu, J.; Abegg, D.; Pequerul, R.; Hugo, M.; Adibekian, A.; Fita, I.; Pares, X.; Aviles, F. X.; Boggyo, M.; Farres, J.

doi:10.64898/2026.07.14.738401

bioRxiv · 10.64898/2026.07.14.738401

A covalent irreversible inhibitor binds in two mutually exclusive conformations to the active-site cysteine residue of human aldehyde dehydrogenase 1A3

Covaleda, D.·Vizarraga, D.·Upadhyay, T.·Zhu, J.·Abegg, D.·Pequerul, R.·Hugo, M.·Adibekian, A.·Fita, I.·Pares, X.·Aviles, F. X.·Boggyo, M.·Farres, J.

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Abstract

Aldehyde dehydrogenases (ALDH) are enzymes that catalyze the NAD(P)+-dependent oxidation of aldehydes into carboxylic acids, playing roles in detoxification, biosynthesis, and regulatory functions. Dysfunction of ALDH is associated with serious conditions such as alcohol intolerance, cancer, cardiovascular problems, and neurological disorders. In humans, ALDH1A1 and ALDH1A3 isoforms act as retinaldehyde dehydrogenases and are overexpressed in various cancers, where high levels are associated with increased tumor malignancy, cancer stem cell traits, and therapeutic resistance. ALDH1A3 is recognized as a promising target for anticancer therapies, with several inhibitors, mainly reversible, developed to specifically target it or the enzyme family. Since ALDH enzymes can also display esterase activity, we used this property to develop an in vitro assay specifically targeting the esterase function of ALDH1A3. A highly conserved active-site cysteine in ALDH1A3 is located at the bottom of two converging channels, which define the substrate- and cofactor-binding pockets. To target this catalytic cysteine, we screened a library of 3,200 cysteine-focused covalent fragments. This led to the identification of Z3405279217 (Z34), an acrylamide-based covalent compound that inhibits both ALDH1A1 and ALDH1A3 at sub-micromolar levels. Biochemical and biophysical tests confirmed that Z34 acts as a time-dependent, covalent, and irreversible binder to the active-site cysteine. In this work, we determined the Cryo-EM structure of the ALDH1A3-Z34 complex at 2.26 [A] resolution, confirming the covalent attachment to the catalytic cysteine of Z34. Notably, two mutually exclusive covalent binding modes were observed: one occupying the substrate-binding pocket and the other the cofactor-binding region. Z34 displayed unexpected binding modes within the active site and holds promise as a lead compound for future drug development. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/738401v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1d9ebd2org.highwire.dtl.DTLVardef@96470org.highwire.dtl.DTLVardef@a110c7org.highwire.dtl.DTLVardef@548a93_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Covaleda, D., Vizarraga, D., Upadhyay, T., Zhu, J., Abegg, D., Pequerul, R., Hugo, M., Adibekian, A., Fita, I., Pares, X., Aviles, F. X., Boggyo, M., Farres, J.. 2026-07-15. A covalent irreversible inhibitor binds in two mutually exclusive conformations to the active-site cysteine residue of human aldehyde dehydrogenase 1A3. https://doi.org/10.64898/2026.07.14.738401

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