Structural Mimicry of Retroviral Tat Proteins by Constrained β-Hairpin Peptidomimetics:  Ligands with High Affinity and Selectivity for Viral TAR RNA Regulatory Elements

An approach is described to the design of β-hairpin peptidomimetic ligands for bovine immunodeficiency virus (BIV) Tat protein, which inhibit binding to its transactivator response element (TAR) RNA. A library of peptidomimetics was derived by grafting onto a hairpin-inducing d-Pro-l-Pro template sequences related to the RNA recognition element in Tat. One hairpin mimetic was identified that binds tightly (K d ≈ 150 nM) to BIV TAR, and another that binds also to HIV-1 TAR RNA (K d ≈ 1−2 μM). (In the same assay, the wild-type BIV Tat(65−81) peptide binds to BIV TAR with K d ≈ 50 nM.) The high-affinity BIV-Tat mimetic was shown to adopt a stable β-hairpin conformation in free solution by NMR methods. Amino acid substitutions in this mimetic were shown to impact on the hairpin structure and to disrupt binding to the RNA. This family of conformationally constrained peptidomimetics affords insights into the structural requirements for binding to TAR RNA and provides a basis for the design of new ligands with increased inhibitory activity and specificity to both BIV and HIV TAR RNAs.