Acyl-CoA dehydrogenases (ACDs) are FAD-dependent enzymes that catalyze the conversion of an appropriate fatty acyl-CoA thioester substrate to the corresponding trans-alpha,beta-enoyl-CoA product. Early studies have shown that the dehydrogenation is stereospecific and is initiated by the abstraction of the pro-R alpha-H, followed by the transfer of the pro-R beta-H, as a hydride equivalent, to the bound FAD. However, recent studies of the inactivation of ACDs by a metabolite of hypoglycin A, (methylenecyclopropyl)acetyl-CoA (MCPA-CoA), led to an alternative mechanism in which the reducing equivalent is delivered from the initially formed alpha-anion to the bound FAD via a single electron transfer process. To further explore the observed mechanistic discrepancy, we have reexamined the inhibitory properties of a closely related MCPA-CoA analogue, spiropentylacetyl-CoA (SPA-CoA), which was previously reported as a tight-binding inhibitor for ACDs. In contrast to early results, our data showed that SPA-CoA is a mechanism-based inhibitor for pig kidney medium-chain acyl-CoA dehydrogenase (MCAD) and Megasphaera elsdenii short-chain acyl-CoA dehydrogenase (SCAD) and that the inactivation is time-dependent, active-site-directed, and irreversible. More importantly, both (R)- and (S)-SPA-CoA could effectively inactivate MCAD, and the resulting inhibitor-FAD adducts appear to have one of the three-membered rings of The spiropentyl moiety cleaved. Since the inactivation is nonstereospecific with respect to C-beta-C bond scission, the ring opening of SPA-CoA leading to enzyme inactivation is likely initiated by a spiropentylcarbinyl radical. Such a radical-induced ring fragmentation is expected to be extremely facile and may bypass the chiral discrimination normally imposed by the enzyme. Thus, these results are consistent with our early notion that MCAD is capable of mediating one-electron redox chemistry. Interestingly, it was also found that (R)-SPA-CoA is an irreversible inhibitor for SCAD, while the S-epimer is only a competitive inhibitor for the same enzyme. The selective inhibition exhibited by these compounds against two closely related dehydrogenases is likely a consequence of the distinct steric and electronic demands imposed by the active sites of MCAD and SCAD. Such information is important for the design of novel class-selective inhibitors to control and/or regulate fatty acid metabolism.