Nadia Patino

Cyclic PNA hexamer-based compound: modelling, synthesis and inhibition of the HIV-1 RNA dimerization process

Abstract A cyclic molecule constituted by (i) a hexameric PNA moiety complementary to six among the nine residues of the dimerization initiation site loop of HIV-1 and (ii) a spacer tethering the N- to the C-extremities of the PNA, has been elaborated to inhibit the dimerization process of HIV-1 genome. This compound has been synthesized following a liquid-phase procedure (fully protected backbone approach). Preliminary agarose gel electrophoresis analyses have shown that the cyclic PNA conjugate is able to inhibit the HIV-1 dimerization.

Liquid phase synthesis of a peptidic nucleic acid dimer

Abstract The first liquid phase synthesis of a peptidic nucleic acid (PNA_) dimer containing guinine and adenine has been achieved in good yields. A new strategy was elaborated in order to circumvent difficult coupling of the protected PNA.

LIQUID-PHASE SYNTHESIS OF POLYAMIDE NUCLEIC ACIDS (PNA)

Abstract Three liquid-phase processes for the elaboration of short orthogonally protected PNA have been devised. Two of these methods are similar to the convergent and divergent approaches in peptide synthesis. The third process consists in building a fully protected polyamide backbone, by using as many different and orthogonal protecting groups as there are different types of nucleic bases in the targeted polyPNA. Simultaneous and selective cleavage of one kind of protecting group allows the simultaneous attachment of several identical nucleobase units.

Liquid-phase synthesis of a cyclic hexameric peptide nucleic acid

Abstract A cyclic fully N-protected hexameric (aminoethylglycinamide) can be readily obtained by using a divergent approach in liquid phase and consists of coupling orthogonal fragments of suitable oligomers. This cyclic N-protected backbone is then converted into a peptide nucleic acid by a series of selective deprotection–coupling steps affording the desired structure in good overall yields. Such a procedure could provide a general approach for targeting any short cyclic peptide nucleic acids (containing every kind of nucleobase).

Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones

RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous ‘polyamide amino acids’ (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy–entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets.

Fluorinated peptides incorporating a 4-fluoroproline residue as potential inhibitors of HIV protease

Abstract N-Fmoc-4-fluoro-L-proline methyl ester was prepared as an attractive synthon for both solid and solution phase peptide synthesis. Its use for the synthesis of Fmoc-Phe-Pro(F)-OMe and Fmoc-Pro(F)-Val-Val-OMe is presented. Direct fluorination with DASTof a 4-hydroxy proline residue incorporated into a peptide and elongation from the terminal amino group allowed preparation of the hexapeptide Boc-AlaAla-Phe-Pro (F) -Val-Val-OMe, analogous to the p 17-p24 gag junction of structural HIV proteins. None of the fluoropeptides in the paper displayed anti-protease or anti-HIV activity.

An Efficient Biodelivery System for Antisense Polyamide Nucleic Acid (PNA)

With the aim of developing a general and straightforward procedure for the intracellular delivery of naked peptide nucleic acids (PNAs), we designed an intracellularly biodegradable triphenylphosphonium (TPP) cation based transporter system. In this system, TPP is linked, via a biolabile disulfide bridge, to an activated mercaptoethoxycarbonyl moiety, allowing its direct coupling to the N-terminal extremity of a free PNA through a carbamate bond. We found that such TPP-PNA-carbamate conjugates were highly stable in a cell culture medium containing fetal calf serum. In a glutathione-containing medium mimicking the cytosol, the conjugates were rapidly degraded into an unstable intermediate, which spontaneously decomposed, releasing the free PNA. Using a fluorescence-labeled PNA-TPP conjugate, we demonstrated that conjugates were taken up by cells. Efficient cellular uptake and release of the PNA into the cytosol was further confirmed by the anti-HIV activity measured for the TPP-conjugate of a 16-mer PNA targeting the TAR region of the HIV-1 genome. This conjugate exhibited an IC(50) value of 1 microM, while the free 16-mer PNA did not inhibit replication of HIV in the same cellular test.

LIQUID PHASE SYNTHESIS OF PEPTIDE NUCLEIC ACID (OR POLYAMIDE NUCLEIC ACID)DIMERS

Abstract The liquid phase synthesis of “polyamide nucleic acid” (PNA) dimers containing the purine nucleic acid bases adenine and guanine has been achieved in good yields. This strategy was elaborated in order to circumvent difficult direct coupling of protected PNA monomers. This method can be applied to the liquid phase synthesis of short protected polyPNAs fragments, which can then selectively be deprotected.

Modelling, synthesis and biological evaluation of an ethidium-arginine conjugate linked to a ribonuclease mimic directed against TAR RNA of HIV-1.

Using molecular modelling studies, an active anti-HIV ethidium-arginine conjugate targeted against the viral TAR RNA sequence has been linked to an artificial ribonuclease, with the aim to obtain an irreversible inhibitor. The ribonuclease moiety consists of an N-[N-(3-aminopropyl)-3-aminopropyl] glycine and has been constructed via two successive N-alkylations following the Fukuyama procedure.

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.