The binding of inositol 1,4,5-trisphosphate (IP3) to the IP3 receptor (IP3R) is modulated by various compounds. Until now, limited progress has been made concerning the isoform-specific effects of these modulators. In this study, we examined how [3H]IP3 binding to the three IP3R isoforms is modulated by cyclic ADP-ribose (cADPR) and by the SH-reagent thimerosal. We used rabbit cerebellum, RBL-2H3 rat mucosal mast cells and 16HBE14o- human bronchial epithelial cells as model systems for IP3R-1, -2 and -3 respectively. [3H]IP3 binding was first characterized at various pH values. We showed that [3H]IP3 binding to RBL-2H3 microsomes was more enhanced by increasing the pH from 7.4 to 8.3 than that to rabbit cerebellar microsomes. In contrast, [3H]IP3 binding to 16HBE14o- microsomes was not stimulated at alkaline pH. At pH 7.4, cADPR (50 microM) increased [3H]IP3 binding to rabbit cerebellar microsomes, RBL-2H3 and 16HBE14o- microsomes 1.5-fold, 1.3-fold and 1.8-fold respectively. The effect of cADPR on IP3 binding was abolished at pH 8.3. Scatchard analysis indicated that cADPR induced in cerebellum a decrease in IP3 affinity (KD increases from 150 nM to 252 nM) of the IP3R and a parallel increase in Bmax (from 4.8 pmol/mg to 11.1 pmol/mg). Thimerosal dose-dependently increased [3H]IP3 binding to rabbit cerebellar microsomes. The stimulatory effects of cADPR and thimerosal were not additive. Binding to cerebellar microsomes returned to control level in the presence of 500 microM thimerosal. In contrast, thimerosal (up to 500 microM) had no stimulatory effect and only a very slight, if any, inhibitory effect on [3H]IP3 binding to RBL-2H3 and 16HBE14o- microsomes respectively. These results indicate that IP3 binding to the IP3R isoforms can be differentially modulated by cADPR and thimerosal.