Simultaneously isolating more than one receptor of natural product remains a challenge to chemical genetics. Using cyclosporine A as an affinity probe and an optimized phage display cloning procedure, not only cyclophilin A, but also cyclophilin B was isolated as the full-length gene clone from a human brain cDNA library. This optimized protocol can be used to select protein targets of chemicals dependent on the binding affinity rather than on the relative abundance in cells.