Interaction of new PNA-based molecules with TAR RNA of HIV-1: molecular modelling and biological evaluation.

During the HIV-1 replication process, interactions between the RNA sequence, named TAR RNA, and the viral protein, Tat, permit a fast and efficient transcription of viral DNA into RNA. Based on the NMR structure of TAR RNA from the PDB, two Peptidic Nucleic Analog- (PNA) based molecules were designed by molecular modelling, the first one targeting G32 U31 and the second targeting U31 C30 free loop bases. Before designing the molecules, the flexibility of the TAR RNA was evaluated by molecular dynamics (MD). The molecules studied are composed of three domains: an arginine, a linker, and two PNA bases. First, molecules were designed and the linker length was optimized to fit the TAR RNA; second, a MD simulation on the TAR RNA molecule complex was performed to validate the molecular structure. Optimal molecules were synthesized and tested on infected cells. The experimental results support the choices made in the design of the molecules.

Synthesis and biological activities of new carbaacyclonucleosides and 1'-oxaacyclonucleosides related to clitocine.

We describe the synthesis of two series of acyclonucleosides:carbaacyclonucleosides and 1'-oxaacyclonucleosides which possess the same aglycone as clitocine 3 which is a natural nucleoside exhibiting interesting biological properties. These compounds have been obtained by condensation of 4-aminobutanol or 3-silyloxypropoxyamine with 4,6-dichloro-5-nitropyrimidine. Structural modifications have been made on the heterocyclic base and the side chain to enhance their potential activity. All these compounds have been tested against different viruses: HIV-1, HSV-1, HSV-2, CMV, VZV, EBV. The carbaacyclonucleoside 10 was associated with an anti-EBV activity (EC50 = 0.86 microg/mL).

Synthesis and antiviral activity of ethidium-arginine conjugates directed against the TAR RNA of HIV-1.

The regulatory protein Tat is essential for viral gene expression and replication of the human immunodeficiency virus type 1 (HIV-1). Tat transactivates the HIV-1 long terminal repeat (LTR) via its binding to the transactivation responsive element (TAR) and increases the viral transcription. Studies have shown that the binding of arginine and arginine derivatives induces a conformational change of the TAR RNA at the Tat-binding site. The unpaired A17 residue delimits a small cavity which constitutes a receptor site for small molecules, especially for ethidium bromide. These binding characteristics have prompted us to design a series of ethidium-arginine conjugates capable of interacting with the TAR RNA. Here we report the synthesis of six ethidium derivatives equipped with arginine side chains. These molecules were biologically evaluated, and two compounds (17 and 20) exhibited in vitro anti-HIV-1 activity at micromolar concentration, without toxicity (up to 100 microM concentration). Melting temperature studies indicated that the most active molecule (20) bound strongly to TAR in vitro. RNase protection experiments agreed with the molecular modeling studies which suggested that the ethidium moiety of 20 was inserted next to the A17 residue while the arginine side chain occupied the pyrimidine bulge.

Modeling of the interaction between new ethidium derivatives and TAR RNA of HIV-1.

During the HIV-1 replication process, interactions between the first sequence of RNA synthesized named TAR RNA and a viral protein named Tat permit a fast and efficient transcription of viral DNA in RNA. Based on the NMR structure of TAR RNA found on the PDB, new derivatives of ethidium were designed by molecular modeling to inhibit this interaction. The studied molecules are composed of three domains: an arginine, a linker, and an ethidium. Three linkers of different lengths were considered in the first step, with the TAR RNA-arginine interaction and the intercalation of the ethidium simulated by docking methods. In a second step, the structure of the TAR RNA was completed to obtain a whole ethidium interaction site and docking of the whole studied molecules was investigated. Molecules were synthesized and tested on infected cells. The predicted models and activity are in good agreement with the reported experimental results.

Synthesis of a new class of HIV-1 inhibitors.

A new family of molecules potentially inhibitors of the HIV-1 Tat-TAR complex was prepared. These compounds are constituted by dinucleotide analogs (PNA dimer) bound, through a linker, to an arginine residue. In this series, several molecules inhibit viral development in cell culture with a micromolar IC50 and without cellular toxicity until 200 microM concentration.

Measurement of the anti-HIV agent 2',3'-didehydro-2',3'-dideoxythymidine (D4T) by competitive ELISA.

2',3'-didehydro-2',3'-dideoxythymidine (D4T) is a thymidine analogue with potent anti-HIV activity in vitro and is currently being investigated therapeutically in patients with advanced HIV infection. We describe a first one-step competitive ELISA method developed for D4T measurement. Anti-D4T rabbit antibodies were raised against a D4T hemisuccinate-bovine serum albumin immunogen. A D4T-hemisuccinate-horseradish peroxidase conjugate and a monoclonal anti-rabbit IgG antibody insolubilized onto a microtiter plate were used as a tracer and capture system, respectively. The method was capable of detecting 2 ng/ml of D4T in cell cultures and 20 ng/ml of D4T in plasma samples previously separated in microconcentrator devices. Cross-reactivity analysis showed that thymidine, D4T monophosphate, or azidothymidine, were weakly recognized by the ELISA and that thymine or other nucleosides were unreactive. The test was successfully used for the quantification of D4T in cell extracts from CEM or Molt 4 cell lines cultured with D4T and in the plasma of patients with advanced HIV infection, receiving D4T therapy. Moreover this ELISA could be used for the indirect quantification of D4T phosphorylated intracellular metabolites previously separated by reverse phase HPLC and hydrolyzed with alkaline phosphatase.

Simultaneous radioimmunoassay of 5alpha-androstane-3alpha, 17beta-diol and 5alpha-androstane-3beta, 17beta-diol unconjugated and conjugated in human serum.

The simultaneous determinations of both 3alpha and 3beta epimers of 5alpha-androstane-3,17beta-diol as their glucuronides, sulfates and in their unconjugated forms are described. The diol estimation is carried out by radioimmunoassay with two specific immune sera after purification of the serum by use of chromatography on Sephadex LH-20. The values obtained (mean +/- S.D.) in pg/ml for the unconjugated 3alpha and 3beta epimers were, respectively, 267 +/- 67 and 816 +/- 76 for men; 114 +/- 33 and 515 +/- 177 for women; 142+/- 77 and 779 +/- 200 for hirsute women. Among the conjugates, the most important were the sulfoconjugates, their rates being, respectively (men +/- S.D. in ng/ml 41.6 +/- 9.5 and 103+/- 40 for men; 12.4 +/- 3.1 and 51.2 +/- 14.9 for women and 36 +/- 22 and 72 +/- 36 for hirsute women. Differences in the conjugation of both epimers were also noticed.