Molecular Basis for Nucleotide Conservation at the Ends of the Dengue Virus Genome

International audienceThe dengue virus (DV) is an important human pathogen from the Flavivirus genus, whose genome- and antigenome RNAs start with the strictly conserved sequence pppAG. The RNA-dependent RNA polymerase (RdRp), a product of the NS5 gene, initiates RNA synthesis de novo, i.e., without the use of a pre-existing primer. Very little is known about the mechanism of this de novo initiation and how conservation of the starting adenosine is achieved. The polymerase domain NS5PolDV of NS5, upon initiation on viral RNA templates, synthesizes mainly dinucleotide primers that are then elongated in a processive manner. We show here that NS5PolDV contains a specific priming site for adenosine 59-triphosphate as the first transcribed nucleotide. Remarkably, in the absence of any RNA template the enzyme is able to selectively synthesize the dinucleotide pppAG when Mn 2+ is present as catalytic ion. The T794 to A799 priming loop is essential for initiation and provides at least part of the ATP-specific priming site. The H798 loop residue is of central importance for the ATP-specific initiation step. In addition to ATP selection, NS5PolDV ensures the conservation of the 59-adenosine by strongly discriminating against viral templates containing an erroneous 39-end nucleotide in the presence of Mg 2+. In the presence of Mn2+, NS5Pol DV is remarkably able to generate and elongate the correct pppAG primer on these erroneous templates. This can be regarded as a genomic/antigenomic RNA end repair mechanism. These conservational mechanisms, mediated by the polymerase alone, may extend to other RNA virus families having RdRps initiating RNA synthesis de novo

Solid-phase synthesis of 5’-triphosphates RNAs en and 5’-capped RNAs

Les ARN 5'-triphosphates (TP) et 5'-coiffés sont des molécules très convoitées des biologistes pour des études structurales par cristallographie ou comme outils thérapeutiques. Actuellement, ces oligonucléotides sont produits dans de faibles quantités via des procédés enzymatiques dépendants de la nature du nucléoside situé à l'extrémité 5'. Ces travaux se sont donc inscrits dans l'enjeu majeur de mettre au point une méthode chimique sur support solide qui permette l'accès à ces ARN 5'-fonctionnalisés en quantités importantes et sans restriction de séquences. Ce manuscrit rapporte une nouvelle méthode efficace de synthèse sur support solide d'ARN 5'-TP à grande échelle indépendante du nucléotide situé à l'extrémité 5' ou de la longueur de la séquence ARN. De plus, cette stratégie a été étendue avec quelques modifications à la synthèse d'analogues enzymatiquement plus stables de type: ARN 5'-β,γ-méthylène-TP, -(α-P-thio)-TP et -(α-P-thio)-(β,γ-méthylène)-TP. Une deuxième partie présente la synthèse supportée et l'évaluation antivirale de courts adénylates 2-5A 5'-TP portant des groupements enzymolabiles de type acétalesters en position 3' du ribose. Une dernière partie est consacrée à l'élaboration de nouvelles stratégies pour la synthèse d'ARN 5-coiffés. La première approche est un procédé en deux étapes où la structure coiffe (Gppp) est ajoutée sur support solide suivie d'une N7- méthylation enzymatique en solution, alors que la seconde est une méthode plus directe entièrement chimique. Par ailleurs, le couplage chimique de la coiffe sur les ARN supportés nécessite l'emploi d'un acide de Lewis. Ainsi l'utilisation de chlorures métalliques « verts » produits à partir de métaux de transition extraits de la biomasse a été évaluée dans la réaction du couplage de la coiffe sur les ARN.5'-triphosphates RNAand 5'-capped RNA are high valuable molecules which serve as important substrates for structural and mechanistic studies or drugs. To date, these oligonucléotides are produced by enzymatic process in low yields with a weak variability of the 5'-end. To overcome this bottleneck we aimed to develop a chemical access on solid-support of these 5'-functionalized RNA in great amount without any limitations in the RNA sequence.Here, a robust, reproducible, and scalable method for the solid-phase synthesis of 5′-triphosphate RNA is presented. Furthermore, this strategy was extended to produce enzymatic resistant analogs of the triphosphate counterpart like: 5'-β,γ-methylene-TP, -(α-P-thio)-TP et -(α-P-thio)-(β,γ-methylene)-TP RNA.In a second part, the solid-phase synthesis of short adenylates 2-5A 5'-TP bearing biolabile acetalester groups on nucleosides 3'-hydroxyls and their antiviral activities are described.Finally, we focused on developing two approaches for the production of 5'-capped RNA. One is a two-steps process which consists in the coupling of the cap structure on solid-support followed by an enzymatic N7-methylation in solution while the other one is a straightforward chemical strategy. Beside, the chemical coupling of the cap moiety on solid-supported RNA requires the use of Lewis acids. Then, the ability of « green » metal chlorides prepared from phytoextracted heavy metals to promote this reaction was studied

Solid-phase synthesis of 5’-triphosphates RNAs en and 5’-capped RNAs

Les ARN 5'-triphosphates (TP) et 5'-coiffés sont des molécules très convoitées des biologistes pour des études structurales par cristallographie ou comme outils thérapeutiques. Actuellement, ces oligonucléotides sont produits dans de faibles quantités via des procédés enzymatiques dépendants de la nature du nucléoside situé à l'extrémité 5'. Ces travaux se sont donc inscrits dans l'enjeu majeur de mettre au point une méthode chimique sur support solide qui permette l'accès à ces ARN 5'-fonctionnalisés en quantités importantes et sans restriction de séquences.Ce manuscrit rapporte une nouvelle méthode efficace de synthèse sur support solide d'ARN 5'-TP à grande échelle indépendante du nucléotide situé à l'extrémité 5' ou de la longueur de la séquence ARN. De plus, cette stratégie a été étendue avec quelques modifications à la synthèse d'analogues enzymatiquement plus stables de type: ARN 5'-β,γ-méthylène-TP, -(α-P-thio)-TP et -(α-P-thio)-(β,γ-méthylène)-TP.Une deuxième partie présente la synthèse supportée et l'évaluation antivirale de courts adénylates 2-5A 5'-TP portant des groupements enzymolabiles de type acétalesters en position 3' du ribose. Une dernière partie est consacrée à l'élaboration de nouvelles stratégies pour la synthèse d'ARN 5-coiffés. La première approche est un procédé en deux étapes où la structure coiffe (Gppp) est ajoutée sur support solide suivie d'une N7- méthylation enzymatique en solution, alors que la seconde est une méthode plus directe entièrement chimique. Par ailleurs, le couplage chimique de la coiffe sur les ARN supportés nécessite l'emploi d'un acide de Lewis. Ainsi l'utilisation de chlorures métalliques « verts » produits à partir de métaux de transition extraits de la biomasse a été évaluée dans la réaction du couplage de la coiffe sur les ARN.5'-triphosphates RNAand 5'-capped RNA are high valuable molecules which serve as important substrates for structural and mechanistic studies or drugs. To date, these oligonucléotides are produced by enzymatic process in low yields with a weak variability of the 5'-end. To overcome this bottleneck we aimed to develop a chemical access on solid-support of these 5'-functionalized RNA in great amount without any limitations in the RNA sequence.Here, a robust, reproducible, and scalable method for the solid-phase synthesis of 5′-triphosphate RNA is presented. Furthermore, this strategy was extended to produce enzymatic resistant analogs of the triphosphate counterpart like: 5'-β,γ-methylene-TP, -(α-P-thio)-TP et -(α-P-thio)-(β,γ-methylene)-TP RNA.In a second part, the solid-phase synthesis of short adenylates 2-5A 5'-TP bearing biolabile acetalester groups on nucleosides 3'-hydroxyls and their antiviral activities are described.Finally, we focused on developing two approaches for the production of 5'-capped RNA. One is a two-steps process which consists in the coupling of the cap structure on solid-support followed by an enzymatic N7-methylation in solution while the other one is a straightforward chemical strategy. Beside, the chemical coupling of the cap moiety on solid-supported RNA requires the use of Lewis acids. Then, the ability of « green » metal chlorides prepared from phytoextracted heavy metals to promote this reaction was studied

Synthèse chimique sur support solide d'ARN 5'-triphosphates et 5'-coiffés

Les ARN 5'-triphosphates (TP) et 5'-coiffés sont des molécules très convoitées des biologistes pour des études structurales par cristallographie ou comme outils thérapeutiques. Actuellement, ces oligonucléotides sont produits dans de faibles quantités via des procédés enzymatiques dépendants de la nature du nucléoside situé à l'extrémité 5'. Ces travaux se sont donc inscrits dans l'enjeu majeur de mettre au point une méthode chimique sur support solide qui permette l'accès à ces ARN 5'-fonctionnalisés en quantités importantes et sans restriction de séquences.Ce manuscrit rapporte une nouvelle méthode efficace de synthèse sur support solide d'ARN 5'-TP à grande échelle indépendante du nucléotide situé à l'extrémité 5' ou de la longueur de la séquence ARN. De plus, cette stratégie a été étendue avec quelques modifications à la synthèse d'analogues enzymatiquement plus stables de type: ARN 5'-b,g-méthylène-TP, -(a-P-thio)-TP et -(a-P-thio)-(b,g-méthylène)-TP.Une deuxième partie présente la synthèse supportée et l'évaluation antivirale de courts adénylates 2-5A 5'-TP portant des groupements enzymolabiles de type acétalesters en position 3' du ribose. Une dernière partie est consacrée à l'élaboration de nouvelles stratégies pour la synthèse d'ARN 5-coiffés. La première approche est un procédé en deux étapes où la structure coiffe (Gppp) est ajoutée sur support solide suivie d'une N7- méthylation enzymatique en solution, alors que la seconde est une méthode plus directe entièrement chimique. Par ailleurs, le couplage chimique de la coiffe sur les ARN supportés nécessite l'emploi d'un acide de Lewis. Ainsi l'utilisation de chlorures métalliques verts produits à partir de métaux de transition extraits de la biomasse a été évaluée dans la réaction du couplage de la coiffe sur les ARN.5'-triphosphates RNAand 5'-capped RNA are high valuable molecules which serve as important substrates for structural and mechanistic studies or drugs. To date, these oligonucléotides are produced by enzymatic process in low yields with a weak variability of the 5'-end. To overcome this bottleneck we aimed to develop a chemical access on solid-support of these 5'-functionalized RNA in great amount without any limitations in the RNA sequence.Here, a robust, reproducible, and scalable method for the solid-phase synthesis of 5 -triphosphate RNA is presented. Furthermore, this strategy was extended to produce enzymatic resistant analogs of the triphosphate counterpart like: 5'-b,g-methylene-TP, -(a-P-thio)-TP et -(a-P-thio)-(b,g-methylene)-TP RNA.In a second part, the solid-phase synthesis of short adenylates 2-5A 5'-TP bearing biolabile acetalester groups on nucleosides 3'-hydroxyls and their antiviral activities are described.Finally, we focused on developing two approaches for the production of 5'-capped RNA. One is a two-steps process which consists in the coupling of the cap structure on solid-support followed by an enzymatic N7-methylation in solution while the other one is a straightforward chemical strategy. Beside, the chemical coupling of the cap moiety on solid-supported RNA requires the use of Lewis acids. Then, the ability of green metal chlorides prepared from phytoextracted heavy metals to promote this reaction was studied.MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

Synthesis of 5' cap-0 and cap-1 RNAs using solid-phase chemistry coupled with enzymatic methylation by human (guanine-N 7)-methyl transferase

International audienceThe 5' end of eukaryotic mRNA carries a N 7-methylguanosine residue linked by a 5'-5' triphosphate bond. This cap moiety ( 7mGpppN) is an essential RNA structural modification allowing its efficient translation, limiting its degradation by cellular 5' exonucleases and avoiding its recognition as ''nonself'' by the innate immunity machinery. In vitro synthesis of capped RNA is an important bottleneck for many biological studies. Moreover, the lack of methods allowing the synthesis of large amounts of RNA starting with a specific 5'-end sequence have hampered biological and structural studies of proteins recognizing the cap structure or involved in the capping pathway. Due to the chemical nature of N 7-methylguanosine, the synthesis of RNAs possessing a cap structure at the 59 end is still a significant challenge. In the present work, we combined a chemical synthesis method and an enzymatic methylation assay in order to produce large amounts of RNA oligonucleotides carrying a cap-0 or cap-1. Short RNAs were synthesized on solid support by the phosphoramidite 29-O-pivaloyloxymethyl chemistry. The cap structure was then coupled by the addition of GDP after phosphorylation of the terminal 59-OH and activation by imidazole. After deprotection and release from the support, GpppN-RNAs or GpppN2'-Om-RNAs were purified before the N 7-methyl group was added by enzymatic means using the human (guanine-N 7)-methyl transferase to yield 7mGpppN-RNAs (cap-0) or 7mGpppN 2'-Om-RNAs (cap-1). The RNAs carrying different cap structures (cap, cap-0 or, cap-1) act as bona fide substrates mimicking cellular capped RNAs and can be used for biochemical and structural studies

Metallophyte wastes and polymetallic catalysis: a promising combination in green chemistry. The illustrative synthesis of 59-capped RNA3

International audienceThe compatibility of metallic catalysts derived from plants was studied for the chemical solid-phase synthesis of a high added-value biomolecule: 59-capped RNA (GpppRNA or 7m GpppRNA) involved in many essential biological processes. These molecules are of great interest for biologists for structural and mechanistic studies of their complexes with RNA capping enzymes. Several polymetallic catalysts were prepared from various metallophytes species growing in mine sites in a context of phytoremediation programs. Their catalytic efficacy was evaluated for the coupling reaction of guanosine diphosphate (GDP) with a preactivated 59-monophosphate hexathymidylate (pT 6) or a pRNA to form 59-GpppT 6 or 59-GpppRNA respectively. The direct coupling of 7m GDP with pRNA was also investigated. With Znenriched catalysts obtained from Zn metallophytes, the capping yields were better than those obtained with conventional catalyst ZnCl 2. Interestingly with Ni-enriched plant extracts the yield was higher than with NiCl 2 , a polymetallic catalysis was certainly involved. With this plant-inspired catalysis, metallophytes wastes become efficient and greener polymetallic catalysts. Finally, environmental benefits and effectiveness can be combined

Solid-phase synthesis of 5′-triphosphate 2′-5′-oligoadenylates analogs with 3′-O-biolabile groups and their evaluation as RNase L activators and antiviral drugs.

International audience5′-Triphosphate 2′-5′-oligoadenylate (2-5A) is the central player in the 2-5A system that is an innate immunity pathway in response to the presence of infectious agents. Intracellular endoribonuclease RNase L activated by 2-5A cleaves viral and cellular RNA resulting in apoptosis. The major limitations of 2-5A for therapeutic applications is the short biological half-life and poor cellular uptake. Modification of 2-5A with biolabile and lipophilic groups that facilitate its uptake, increase its in vivo stability and release the parent 2-5A drug in an intact form offer an alternative approach to therapeutic use of 2-5A. Here we have synthesized the trimeric and tetrameric 2-5A species bearing hydrophobic and enzymolabile pivaloyloxymethyl groups at 3′-positions and a triphosphate at the 5′-end. Both analogs were able to activate RNase L and the production of the trimer 2-5A (the most active) was scaled up to the milligram scale for antiviral evaluation in cells infected by influenza virus or respiratory syncytial virus. The trimer analog demonstrated some significant antiviral activity

Ecological catalysis and phytoextraction: symbiosis for future

International audienceMetallophyte plants derived from phytoextraction are used as starting materials to prepare novel polymetallic catalysts. Polymetallic catalyst activity is used in many Lewis acid catalyzed reactions according to the polymetallic catalyst preparation. The synergetic catalysis of these systems leads to efficient syntheses of complex biomolecules such as dihydropyrimidinone, 5'-capped DNA and RNA, and glycosyl aminoacid. These new polymetallic catalysts also bring new possibilities in Green Catalysis, that we named "Ecological Catalysis"