Hydroxysafflor yellow A (HSYA) is a potent natural antioxidant that displays important neuroprotective activity. Inhibition of acetaldehyde dehydrogenase 1 (ALDH1) has attracted the attention of researchers due to its overexpression in several types of cancers. We studied the effects of HSYA on ALDH1 by evaluating the inhibitory kinetics based on its antioxidant properties and performing computational simulation integrating methods. HSYA reversibly inhibited human recombinant ALDH1 via non-competitive inhibition (K-i = 0.267 +/- 0.024 mM). We also investigated the tertiary structural changes via measuring intrinsic and ANS-binding fluorescence. The results indicated that the inactivation induced by HSYA was associated with structural changes. To obtain further information, we simulated the 3D structure of ALDH1 and conducted computational docking simulations as well as molecular dynamics simulations. The results indicated that 4 rings of HSYA interact with several residues near the ALDH1 active site. Our study provides insight into the inhibition of ALDH1 accompanied by structural changes. Based on its ALDH1-inhibiting effect and its potential as a natural antioxidant, HSYA is a potential agent for treating ALDH1-associated cancers. (C) 2014 Elsevier Ltd. All rights reserved.