To dissect the enzyme inhibitory properties of the immunosuppressive cyclic undecapeptide cyclosporin A (CsA) and gain access to monospecific, non-calcineurin inhibiting CsA derivatives, [D-Ser]8 CsA was subjected to modifications at the D-Ser side chain. Thus, we modified a CsA residue flanking the calcineurin (CaN) and cyclophilin 18 (Cyp18) binding domains of CsA, instead of the residues of CaN binding domain, in order to develop a new specificity determining site within the cyclic peptide. The [O-(NH2(CH2)5NHC(O)CH2-) D-Ser]8 CsA (9), with an amino group on a tether, exhibits CsA-like inhibition of the peptidyl prolyl cis/trans isomerase (PPIase) activity of Cyp18, with an IC50 value of 3.2 nM, whereas the CaN inhibition by Cyp18/9 complex is completely abolished. Consequently, this compound is not able to inhibit the proliferation and cytokine production of activated T cells. Structure-activity relationship studies with a series of [D-Ser]8 CsA derivatives indicate that the positively charged side chain is an essential requirement for Cyp18/9 to be ineffective on CaN. Upon protecting the amino group in 9 with the photo-labile moiety NVOC (2-nitroveratryloxycarbonyl), the Cyp18/[O-(NVOC-NH(CH2)5NHC(O)CH2-) D-Ser]8 CsA (11) complex exhibits strong CaN inhibition, and shows potent immunosuppressive activity. In stimulated T cells pretreated with 11, a remarkable recovery of transcriptional activation of NFAT (nuclear factor of activated T cells) has been achieved through light irradiation, as assessed with a NFAT reporter gene assay.