Four substrate analogs, 4-(2-naphthyloxy)-2-butyn-1-amine (1), 1,4-diamino-2-chloro-2-butene (2), 1,6-diamino-2,4-hexadiyne (3), and 2-chloro-5-phthalimidopentylamine (4) have been tested as inhibitors against mammalian, plant, bacterial, and fungal copper-containing amine oxidases: bovine plasma amine oxidase (BPAO), equine plasma amine oxidase (EPAO), pea seedling amine oxidase (PSAO), Arthrobacter globiformis amine oxidase (AGAO), Escherichia coli amine oxidase (ECAO), and Pichia pastoris lysyl oxidase (PPLO). Reactions of 1,4-diamino-2-butyne with selected amine oxidases were also examined. Each substrate analog contains a functional group that chemical precedent suggests could produce mechanism-based inactivation. Striking differences in selectivity and rates of inactivation were observed. For example, between two closely related plasma enzymes, BPAO is more sensitive than EPAO to 1 and 3, while the reverse is true for 2 and 4. In general, inactivation appears to arise in some cases from TPQ cofactor modification and in other cases from alkylation of protein residues in a manner that blocks access of substrate to the active site. Notably, 1 completely inhibits AGAO at stoichiometric concentrations and is not a substrate, but is an excellent substrate of PSAO and inhibition is observed only at very high concentrations. Structural models of 1 in Schiff base linkage to the TPQ cofactor in AGAO and PSAO (for which crystal structures are available) reveal substantial differences in the degree of interaction of bound 1 with sidechain residues, consistent with the widely divergent activities. Collectively, these results suggest that the development of highly selective amine oxidase inhibitors is feasible.Keywords: copper; amine oxidase; enzyme inhibition; mechanism-based inhibition.The copper-containing amine oxidases play a crucial role in metabolic oxidative deamination of primary amines to the corresponding aldehydes, with the concomitant production of hydrogen peroxide and ammonia [1]. The reaction proceeds through a transamination mechanism mediated by an active site 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor. The TPQ cofactor is formed from the posttranslational self-processing of a tyrosine residue within the highly conserved sequence Ser/Thr-X aa -X aa -Asn-Tyr(TPQ)-Asp/Glu-Tyr [1] that requires both copper and molecular oxygen [2][3][4][5][6][7]. The key step in catalysis (Scheme 1) is the conversion of the initial quinoneimine Ôsubstrate Schiff baseÕ (step 2) to a quinolaldimine Ôproduct Schiff baseÕ (step 3), facilitated by Ca proton abstraction by an absolutely conserved active-site aspartate acting as general base [8][9][10][11][12]. Hydrolytic release of aldehyde product gives a Cu(II)-aminoresorcinol (step 4), in equilibrium with Cu(I)-semiquinone (step 5), that is reoxidized to TPQ in the presence of O 2 , with release of H 2 O 2 and NH 4 + [13].Scheme 1. Proposed catalytic mechanism of turnover for amine oxidases.