Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries.

Target TAR by NMR: Tripeptides containing arginines as terminal residues and non-natural amino acids as central residues are good leads for drug design to target the HIV trans-activation response element (TAR). The structural characterization of the RNA-ligand complex by NMR spectroscopy reveals two specific binding sites that are located at bulge residue U23 and around the pyrimidine-stretch U40-C41-U42 directly adjacent to the bulge.

A practical synthesis of the 16C/15N-labelled tripeptide N-formyl-Met-Leu-Phe, useful as a reference in solid-state NMR spectroscopy.

A mild synthetic method for N-formyl-Met-Leu-Phe-OH (1) is described. After Fmoc solid phase peptide synthesis, on-bead formylation and HPLC purification, more than 30 mg of the fully (13)C/(15)N-labelled tripeptide 1 could be isolated in a typical batch. This peptide can be easily crystallised and is therefore well suited as a standard sample for setting up solid-state NMR experiments.

Binding sites of the viral RNA element TAR and of TAR mutants for various peptide ligands, probed with LILBID: a new laser mass spectrometry.

A new laser-based mass spectrometry method, called laser induced liquid bead ion desorption (LILBID), was applied to investigate RNA:ligand interactions. As model system the HIV Tat:TAR transactivation complex and its binding behavior were analyzed. TARwt of HIV Type 1 and Type 2 and different artificial mutants were compared regarding their binding to Tat and different peptide ligands. Specific and nonspecific association to TAR was deduced, with the bulge being the well known specific binding site of TAR. In the case of triple arginine (RRR) as a nonspecific ligand, multiple electrostatic binding to TAR was found at higher concentration of RRR. This contrasted with the formation of only ternary complexes in competitive binding studies with TAR, Tat, and potential inhibitors. The fact that the stoichiometries of the complexes can be determined is a major advantage of MS methods over the widely applied fluorimetric methods. A quantitative evaluation of the spectra by a numeric model for ternary complex formation allows conclusions about the role and strength of the binding sites of the RNAs, the specificity and affinity of different ligands, the determination of apparent IC50 and KD values, and a comparison of the binding efficiencies of potential inhibitors.

The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA.

Principles of fragment-based molecular design are presented and discussed in the context of de novo drug design. The underlying idea is to dissect known drug molecules in fragments by straightforward pseudo-retro-synthesis. The resulting building blocks are then used for automated assembly of new molecules. A particular question has been whether this approach is actually able to perform scaffold-hopping. A prospective case study illustrates the usefulness of fragment-based de novo design for finding new scaffolds. We were able to identify a novel ligand disrupting the interaction between the Tat peptide and TAR RNA, which is part of the human immunodeficiency virus (HIV-1) mRNA. Using a single template structure (acetylpromazine) as reference molecule and a topological pharmacophore descriptor (CATS), new chemotypes were automatically generated by our de novo design software Flux. Flux features an evolutionary algorithm for fragment-based compound assembly and optimization. Pharmacophore superimposition and docking into the target RNA suggest perfect matching between the template molecule and the designed compound. Chemical synthesis was straightforward, and bioactivity of the designed molecule was confirmed in a FRET assay. This study demonstrates the practicability of de novo design to generating RNA ligands containing novel molecular scaffolds.