We have previously found that the pi-isozyme of glutathione-S-transferase (GST-pi) is a strong and selective inhibitor of the phosphorylation of the transcriptional activating protein jun by its activating kinase, jun-N-terminal kinase (JNK). We further performed molecular dynamics calculations on the 3-dimensional structure of GST-pi free and bound to an inhibitor that blocks its ability to inhibit the JNK-jun activation. We thus identified 4 putative domains that may be involved in the interaction between GST-pi and the JNK-jun complex: residues 34-50, 99-121, 165-182 (with 2 overlapping sub-domains 165-175 and 169-182), and 194-201. We have synthesized each of these domains and tested them for their abilities to affect the GST-JNK-jun system, first in a cell-free system. We find that peptides corresponding to residues 99-121 and 194-201 strongly inhibit the binding of GST to the JNK-jun complex but do not inhibit JNK-induced phosphorylation of jun, while peptides corresponding to residues 34-50 and 165-182 do not inhibit GST binding but, except for the 165-175 subdomain peptide, strongly inhibit jun phosphorylation. A control peptide, X13, had no effect on either process. Peptide effects on jun phosphorylation appear to be selective for the JNK-jun system since the 34-50 peptide has no effect on other kinase systems (eg, casein kinase, MAP kinase). Three of the domain peptides, 34-50, 165-175, and 194-201 have been attached on their carboxyl-terminal ends to a penetratin sequence, enabling transmembrane transport into cells, and have been introduced into human astrocytes in which JNK was activated with anisomycin. We find that the 34-50-penetratin peptide strongly inhibits intracellular jun phosphorylation while the 194-201-penetratin peptide has no effect; the 165-175-penetratin peptide has a weak effect on this process. Thus, the effects in cells parallel those in the cell-free system. We conclude that all putative domains, identified in our prior structural studies, appear to interact with the JNK-jun complex. The 34-50 peptide may be useful in selectively blocking uncontrolled mitogenic signaling involving the JNK-jun pathway and may be a potential agent for blocking oncogenic ras-p21-induced cell transformation.