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Definitions

• Cationic siRNAs for small interfering ribonucleic acid
• automated synthesis and biological applications based on their intracellular penetration properties and involving the RNA interference mechanism are disclosed.
• RNA interference is an intracellular mechanism that allows sequence-specific control of the expression of an endogenous or exogenous gene.
• the mediators of this mechanism are small double-stranded ribonucleic acid helices of about 2 turns, the siRNAs, of identical sequence to a fragment of the target gene.
• RNA interference can result in permanent modification of the target gene in the chromatin of a cell, the most immediate effect of introducing siRNA into a cell is inactivation of messenger RNA -target.
• SiRNAs generally consist of two 19-mer oligoribonucleotides of complementary sequences with 3'-dTdT extensions, but some imperfect matches or up to 27-mer sequences may also be effective.
• Transfection of siRNA into the cytoplasm of cells - without rupture of the cell membrane - can be obtained after mixing with an excess of cationic carrier.
• Polycationic macromolecules such as polyethylenimine or aggregates of cationic lipids are able to play this role of vector (1).
• the polyanionic siRNA molecules indeed aggregate with an excess of carrier, forming a fine cationic precipitate. These particles allow efficient transfection of siRNA into a large number of cells in culture via anionic heparan sulphates present on the cell surface (2).
• a first article published in 2006 reports the conjugation of polyethylene glycol to a siRNA through a disulfide bridge, but the cell internalization still requires non-covalent association by mixing with a cationic polymer (5).
• two articles describe the use of siRNAs (40 anionic charges) conjugated to various cationic peptides with 7 or 8 cationic charges. These siRNAs remain highly anionic and, according to the authors themselves, intracellular penetration and efficacy are not increased (6) and (7).
• the invention therefore aims to provide intrinsically cationic siRNAs.
• It also relates to a method for synthesizing these cationic siRNAs that can be extended on an industrial scale for GMP production.
• the invention also relates to the applications of the new siRNAs in the pharmaceutical and biotechnological fields.
• the cationic siRNAs of the invention are characterized in that they are double-stranded RNA fragments, at the ends of which are grafted oligocations, the total number of grafted cationic charges being comparable to or greater than that of the anionic charges carried. by the internucleoside phosphates of the RNA strands.
• cationic siRNAs are capable of inducing RNA interference in the absence of any transfection agent.
• the demonstration is carried out in a controlled environment, on cells in culture, where cationic siRNA-oligopeptide conjugates remaining globally anionic have not shown any effect (vacuum above).
• double-stranded RNA is meant a family A nucleic acid double helix induced by the presence of an atom other than H at the 2 'position of ribose (as opposed to DNA which is helix B). .
• the overall charge ⁇ of the cationic siRNA that is to say the total sum of the chemically grafted cationic charges reduced by the total sum of the anionic charges of the internucleoside phosphate groups, is from -30 to +50.
• the complementarity of the bases of the RNA double helix may be perfect or partial.
• each oligoribonucleotide has a single-stranded extension 3 'of the double helix.
• the oligocations are grafted 3 'or / and 5' of the sense strand or / and 3 'of the antisense strand, the antisense strand being the one that guides the complex protein responsible for the degradation of messenger RNA.
• the 5 'grafting of the antisense strand abolishes the RNA interference effect.
• the cationic siRNAs which are the subject of the invention consist of long double-stranded RNA fragments of 15 to 30 ribonucleotides, in particular 19 to 30 ribonucleotides, at the ends of which are grafted, by covalent bond, 1 to 3 oligocations of which the number of cumulative cationic charges is comparable to or greater than the number of anionic charges carried by the RNA.
• the invention relates more particularly to cationic siRNAs in which at least one strand corresponds to formula (I)
• R 4 , R 5 and R 6 identical or different, representing a lower alkylene radical and X 1 being chosen from putrescine, spermidine or spermine, or
• R 7 and R 8 being identical or different, representing a lower alkylene radical
• lower alkylene radical is meant, in the description and claims, a linear, branched or substituted C1-C5 alkylene radical.
• the oligocations are oligoamines. These oligoamines are advantageously chosen from the group comprising spermine, spermidine or putrescine.
• Corresponding cationic siRNAs are advantageously oligonucleotide oligospermines of structure (V)
• N, i and j are as defined above.
• RNA interference The fields of application of RNA interference are growing.
• SiRNAs are used by the pharmaceutical and biotechnology industry to link potentially active genes, diseases and molecules against these diseases; these are essentially high-throughput screening techniques on animal cells.
• the cationic siRNAs of the invention make it possible to simplify the screening, and especially to extend the technique to animals where physiology, biodistribution, excretion, would be taken into account in the validation of a compound in the preclinical phase, thus increasing the chances of success and reducing costly failures in the clinical phase.
• siRNAs lie in their direct use as drugs to inhibit the biosynthesis of an RNA or protein in the cells of a patient. Very different pathologies such as cancer, viral infections, asthma or autoimmune diseases become curable.
• the invention therefore covers the use of cationic siRNAs for these applications.
• the invention thus aims at the cationic siRNAs defined above for use as medicaments.
• compositions characterized in that they contain an effective amount of at least one siRNA as defined above, in association with a pharmaceutically inert vehicle.
• the invention also relates to a method for automated synthesis of a cationic siRNA strand, characterized in that it comprises: the 3 'to 5' sequential coupling of ribonucleotides on a solid support, preceded and / or followed by the sequential coupling of synthons cationic, the strand corresponding to the formula
• the invention is more particularly directed to a process for the synthesis of cationic siRNAs in which the cationic synthons are oligoamines phosphoramidites and
• X 1 is a putrescine, spermidine or spermine with appropriate protective groups
• R 9 and R 10 are as defined above;
• Figure 1 HPLC analysis showing the degradation of the oligonucleotide ⁇ GL3ss> S 5 in water.
• Figure 4 Extinction of the gene of luciferase according to the number of spermines.
• Figure 5 Extinction of the luciferase gene according to the concentration of siRNA.
• ⁇ GL3ss> is a 21-mer oligonucleotide
• S is a phosphospermine residue
• n 0, 1, 3, 5, 20, 30
• the CE phosphoramidites, Ultramild supports and general reagents used for automated synthesis come from Glen Research (Eurogentec).
• the phosphoramidite spermine is from Novalyst.
• Ultramild reagents allow the deprotection of the nucleobase protecting groups and the simultaneous cleavage of the solid support oligo under milder alkaline conditions.
• the monomers used namely A protected by the phenoxyacetyl (Pac-A-CE) group, G protected by the 4-isopropyl-phenoxyacetyl ((iPr-Pac) -G-CE) group and C protected by an acetyl group (Ac -C-CE) have avoided the degradation of the compounds during the work-up.
• the 2'-OH position of the nucleotides was protected by the tertiobutyldimethylsilyl protecting group TBDMS.
• a negative control sequence comprising 20 spermines SEQ ID No. 4, the sequence of which is derived from the corresponding luciferase region of plasmid GL2 (Proméga) 3 ' dTdT-AG CUU CA UAAG GCG CAU GC 5' .
• the ⁇ GL2ss> S20 oligonucleotide has 3 mismatches relative to the homogamous sequence of GL3 and therefore the corresponding siRNA does not have the ability to interfere with the GL3 luciferase messenger RNA produced by the cells.
• an antisense sequence SEQ ID No. 5 3 ' dTdT-G AAUGCGACUCAUGAAGC U 5 comprising a 5' spermine.
• it is the other strand ⁇ GL3as> Si of the double helix of siRNA which carries the cationic part.
• Post-synthetic treatment After the automated synthesis, the oligomers were released from the solid support and deprotected simultaneously under the conditions Ultramild standard, by treatment with ammonia 28% at room temperature, overnight.
• the second step consisted in the deprotection of the TBDMS group at the 2'-OH position, using a 1.0 M solution of tetrabutylammonium fluoride TBAF in THF (Aldrich).
• TBAF tetrabutylammonium fluoride
• the oligonucleotides were purified using Poly-Pak II TM columns (Glen Research / Eurogentec) according to the instructions given by the supplier. The final elution was carried out using an acetonitrile / water (50/50) mixture in all cases, except for oligonucleotides comprising 20 and 30 spermines which required the use of aqueous acetonitrile / aqueous ammonia 28%. diluted to 1 / 20e (20/80). Fractions containing the oligonucleotide were revealed by placing a drop on a thin-layer fluorescent silica plate and were immediately pooled and lyophilized to remove the solvents and avoid degradation. A white powder has thus been obtained.
• oligoribonucleotides have also necessitated the careful exclusion of the sources of ribonucleases. It has therefore been essential to wear gloves to avoid contamination with RNAses present on the hands. Sterile equipment (pipettes, Eppendorf tubes) was used, all under a laminar flow hood. Initially, the RNA samples were solubilized in water and kept in the freezer. If the unmodified strands remained stable, even after several months under these conditions, HPLC analysis showed that oligoribonucleotide-oligospermines degraded very rapidly (FIG. 1, see HPLC conditions below).
• the oligonucleotides were thus solubilized in a phosphate buffer pH 5.6 (50 mM) and stored at -20 ° C., which made it possible to avoid the degradation of the compounds by hydrolysis catalyzed by spermines, even after 3 months (monitoring HPLC).
• oligonucleotides of globally negative charge comprising respectively 0, 1, 3, and 5 spermines were analyzed by anion exchange HPLC (Macherey Nagel SAX 1000-8) with a linear gradient of B ranging from 0 to 100% in 15 minutes ( A: KH 2 PO 4 20mM, 20% AcCn, B: A, 1M NaCl). HPLC profiles are shown in Figure 2.
• the oligonucleotides were solubilized in 500 ⁇ l of distilled water.
• the sample and the betahydroxypyruvic acid matrix were mixed together on the plate. Once crystallized, the sample was analyzed on a BRUKER Ultrafex device. The mass spectra are given in Figure 3.
• Example 2 RNA interference; extinction of the luciferase gene by cationic siRNAs. Effect of the number of cationic charges.
• the A549Luc cell line originates from human bronchial epithelial cells (CCL-185, ATCC) by stable transfection of plasmid pGL3 (Proméga).
• the A549Luc cells were cultured in RPMI 1640 complete medium (Eurobio) supplemented with 10% fetal calf serum (FCS, Perbio), 2 mM glutamax (Eurobio), 100 U / ml penicillin (Eurobio) and 100 ⁇ g / ml streptomycin (Eurobio) and incubated at 37 ° C., 5% CO 2 in a saturated humidity atmosphere.
• FCS fetal calf serum
• Eurobio 2 mM glutamax
• Eurobio 100 U / ml penicillin
• Eurobio 100 ⁇ g / ml streptomycin
• 24-well plates were prepared with 25,000 cells per well in 1 ml of complete medium.
• siRNA duplexes Formation of the siRNA duplexes and incubation with the cells: Initially siRNA duplexes were prepared by equimolar mixing of their two complementary strands, hybridization by heating at 70 ° C. and cooling. Concentrations were adjusted to final concentrations on cells of 1, 10, or 100 nM. The duplexes formed were then diluted in 100 ⁇ l of RPMI medium.
• the positive siRNA penetration control in the cells was performed using the INTERFERin lipid transfection agent (Polyplus-transfection) used according to the manufacturer's recommendations.
• INTERFERin (2 ⁇ l) was added to siRNA. The mixture was immediately homogenized and allowed to stand for 10 minutes at room temperature to promote the formation of the complexes.
• the cell culture medium was aspirated and the adherent cells were washed with phosphate buffer (PBS). Then 500 ⁇ l of RPMI were added to each well.
• PBS phosphate buffer
• siRNA duplexes or siRNA / INTERFERin were added to the cells (100 ⁇ l / well).
• the plate was homogenized by manual rotation. Each condition has been realized in triplica.
• the plate was incubated at 37 ° C., 5% CO2 for 4 hours. At the end of this time, the cells were observed under a microscope to verify the absence of toxicity and 500 ⁇ l of RMPI medium supplemented with 20% FCS were added to each well.
• the plate was incubated in an oven at 37 ° C. and 5% CO 2 for 48 hours. Measurement of the Expression of the Luciferase Gene: After 48h, the cells were washed with PBS and then lysed using a 5x diluted commercial stock solution (Proméga). The plate was then incubated for 30 minutes at room temperature. The solutions were recovered in microtubes and centrifuged for 5 min at 1400 rpm at 4 ° C.
• a BSA (bovine serum albumin) range was previously prepared to serve as a calibration. 15 ⁇ l of lysis buffer were added per tube. 15 .mu.l of each sample to be analyzed were introduced into tubes. 3 blanks consisting of 15 ⁇ l of lysis buffer each were made. 1 ml of BCA solution (bicinchoninic acid) mix was added to each tube. The mixtures obtained were then placed in a water bath at 60 ° C. for 30 minutes. Absorbance was read at 562 nm.
• luciferase gene silencing The results were first expressed in RLU (Relative Light Unit) integrated over 10 seconds, normalized per milligram of proteins of the cell lysate. Gene suppression efficiency for each condition was then expressed as a percentage of luciferase expression in non-incubated cells in the presence of siRNA. Each bar represents the average value of the luciferase gene expression percentage as well as its standard deviation.
• siRNA ⁇ GL3ss> ⁇ GL3as> formed from the sense (ss) and antisense (as) strands of the luciferase GL3 sequence is not active;
• siRNA quenches the expression of luciferase when it is vectorized by the cationic lipid INTERFERin; the introduction of 1 -3 spermines into the molecule has little effect on the expression of luciferase;
• Example 3 RNA interference; extinction of the luciferase gene by cationic siRNAs. Effect of concentration.
• Figure 5 shows from top to bottom
• luciferase GL3 is not diminished when the cells are incubated with siRNA without grafted spermine and without INTERFERin, whatever the concentration;
• siRNAs comprising 20 and 30 spermines.
• Example 4 RNA interference; extinction of the luciferase gene by cationic siRNAs. Validation experiments.
• Figure 6 validates the claims and specificity of the RNA interference.
• the siRNA ⁇ GL3ss> ⁇ GL3as> Si comprising this time a spermine grafted at the 5 'position of the antisense strand was tested.
• Bars 3 to 6 show that the grafting of spermine at the 5 'position of the antisense strand removes the extinction effect of luciferase. It is indeed known that this siRNA position must be previously phosphorylated by the cell in order to observe the RNA interference phenomenon.
• Bars 7 and 8 show that, even at a concentration 10 times higher, the siRNA GL2 with 20 spermines, having 3 mismatch relative to the target GL3, does not decrease the expression of luciferase GL3.
• RNAi-mediated gene silencing in non-human primates Nature 441, 111-114

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