Open AccessAn ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb
Author(s) -
Shortridge,
Paul T. Wille,
Alisha N Jones,
Amy Davidson,
Jasmina Bogdanović,
Eric J. Arts,
Jonathan Karn,
John A. Robinson,
Gabriele Varani
Publication year - 2018
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gky1197
Subject(s) - p tefb , biology , rna , hiv long terminal repeat , transcription (linguistics) , transcription preinitiation complex , ligand (biochemistry) , tar (computing) , biochemistry , microbiology and biotechnology , biophysics , gene , genome , promoter , gene expression , receptor , long terminal repeat , linguistics , philosophy , computer science , programming language
The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat-TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181-TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.