Synthesis of Adenine Dinucleosides 2′,5′-Bridged by Sulfur-Containing Linkers as Bisubstrate SAM Analogues for Viral RNA 2′-O -Methyltransferases (original) (raw)
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European Journal of Organic Chemistry, 2019
Viral RNA 2'-O-methyltransferases play a crucial role for luring the host cell innate antiviral response during a viral infection by catalyzing either the methylation of the 5'-end RNA cap-structure at 2'-OH of nucleoside N1 or by inducing internal 2'-O-methylation of adenosines within RNA sequence using S-adenosyl-L-methionine (SAM) as the methyl donor. Our goal is to synthetized bisubstrate SAM analogues mimicking the transition state of the 2'-O-methylation of the RNA in order to block viral 2'-O-methyltransferases and struggle against emerging viruses. Here we designed and synthesized five dinucleosides by connecting a 5'-thioadenosine representing the SAM to the 2'-OH of another adenosine unit mimicking the RNA substrate, via various sized sulfur-containing linkers such as alkylthioether linkers, sulfoxide or sulfone derivatives, or a disulfide bond.
European Journal of Medicinal Chemistry, 2020
The spreading of new viruses is known to provoke global human health threat. The current COVID-19 pandemic caused by the recently emerged coronavirus SARS-CoV-2 is one significant and unfortunate example of what the world will have to face in the future with emerging viruses in absence of appropriate treatment. The discovery of potent and specific antiviral inhibitors and/or vaccines to fight these massive outbreaks is an urgent research priority. Enzymes involved in the capping pathway of viruses and more specifically RNA N7-or 2 0 O-methyltransferases (MTases) are now admitted as potential targets for antiviral chemotherapy. We designed bisubstrate inhibitors by mimicking the transition state of the 2 0-O-methylation of the cap RNA in order to block viral 2 0-O MTases. This work resulted in the synthesis of 16 adenine dinucleosides with both adenosines connected by various nitrogen-containing linkers. Unexpectedly, all the bisubstrate compounds were barely active against 2 0-O MTases of several flaviviruses or SARS-CoV but surprisingly, seven of them showed efficient and specific inhibition against SARS-CoV N7-MTase (nsp14) in the micromolar to submicromolar range. The most active nsp14 inhibitor identified is as potent as but particularly more specific than the broad-spectrum MTase inhibitor, sinefungin. Molecular docking suggests that the inhibitor binds to a pocket formed by the S-adenosyl methionine (SAM) and cap RNA binding sites, conserved among SARS-CoV nsp14. These dinucleoside SAM analogs will serve as starting points for the development of next inhibitors for SARS-CoV-2 nsp14 N7-MTase.
Journal of Medicinal Chemistry, 2010
Bioisosteric deaza analogues of 6-methyl-9-β-D-ribofuranosylpurine, a hydrophobic analogue of adenosine, were synthesized and evaluated for antiviral activity. Whereas the 1-deaza and 3-deaza analogues were essentially inactive in plaque assays of infectivity, a novel 7-deaza-6-methyl-9-β-Dribofuranosylpurine analogue, structurally related to the natural product tubercidin, potently inhibited replication of poliovirus (PV) in HeLa cells (IC 50 = 11 nM) and dengue virus (DENV) in Vero cells (IC 50 = 62 nM). Selectivity against PV over cytotoxic effects to HeLa cells was >100-fold after incubation for 7 h. Mechanistic studies of the 5 0 -triphosphate of 7-deaza-6-methyl-9-β-D-ribofuranosylpurine revealed that this compound is an efficient substrate of PV RNA-dependent RNA polymerase (RdRP) and is incorporated into RNA mimicking both ATP and GTP.
Pharmacological Reports
Background SARS-CoV-2 is a newly emerged human coronavirus that severely affected human health and the economy. The viral RNA-dependent RNA polymerase (RdRp) is a crucial protein target to stop virus replication. The adenosine derivative, remdesivir, was authorized for emergency use 10 months ago by the United States FDA against COVID-19 despite its doubtful efficacy against SARS-CoV-2. Methods A dozen modifications based on remdesivir are tested against SARS-CoV-2 RdRp using combined molecular docking and dynamics simulation in this work. Results The results reveal a better binding affinity of 11 modifications compared to remdesivir. Compounds 8, 9, 10, and 11 show the best binding affinities against SARS-CoV-2 RdRp conformations gathered during 100 ns of the Molecular Dynamics Simulation (MDS) run (− 8.13 ± 0.45 kcal/mol, − 8.09 ± 0.67 kcal/mol, − 8.09 ± 0.64 kcal/mol, and − 8.07 ± 0.73 kcal/ mol, respectively). Conclusions The present study suggests these four compounds as potential SARS-CoV-2 RdRp inhibitors, which need to be validated experimentally.
Making the Mark: The Role of Adenosine Modifications in the Life Cycle of RNA Viruses
Cell Host & Microbe, 2017
Viral epitranscriptomics is a newly emerging field that has identified unique roles for RNA modifications in modulating life cycles of RNA viruses. Despite the observation of a handful of modified viral RNAs five decades ago, very little was known about how these modifications regulate viral life cycles, until recently. Here we review the pro-and anti-viral effects of methyl-6-adenosine in distinct viral life cycles, the role of 2 0 O-methyl modifications in RNA stability and innate immune sensing, and functions of adenosine to inosine modifications in retroviral life cycles. With roles for over 100 modifications in RNA still unknown, this is a rapidly emerging field that is destined to suggest novel antiviral therapies.
Journal of Medicinal Chemistry, 2022
Enzymes involved in RNA capping of SARS-CoV-2 are essential for the stability of viral RNA, translation of mRNAs, and virus evasion from innate immunity, making them attractive targets for antiviral agents. In this work, we focused on the design and synthesis of nucleoside-derived inhibitors against the SARS-CoV-2 nsp14 (N7-guanine)-methyltransferase (N7-MTase) that catalyzes the transfer of the methyl group from the S-adenosyl-L-methionine (SAM) cofactor to the N7-guanosine cap. Seven compounds out of 39 SAM analogues showed remarkable double-digit nanomolar inhibitory activity against the N7-MTase nsp14. Molecular docking supported the structure−activity relationships of these inhibitors and a bisubstrate-based mechanism of action. The three most potent inhibitors significantly stabilized nsp14 (ΔT m ≈ 11°C), and the best inhibitor demonstrated high selectivity for nsp14 over human RNA N7-MTase.
Chemistry & Biology, 1994
The stability of hybrids of 2'-O-methylribonucleotides with complementary RNA is considerably higher than that of the corresponding DNA*RNA duplexes. The 2'-O-modified ribonucleotides are thus an attractive class of compounds for antisense applications. Understanding how these substituents stabilize the structure of the hybrid duplex may be important in the design of ribonucleotides with novel properties. Results: The crystal structure of a dimer of the selfcomplementary DNA strand d(GCGT)02'm"r(A)d(TACGC), which has a 2'-0-methylated ribonucleotide incorporated at position 5, was determined at 2.1 A resolution. This strand forms a duplex with an overall A-type conformation; the methyl groups of the two modified adenosines point into the relatively wide minor groove. Both 2'-methoxy groups are hydrogen-bonded to solvent molecules. These results allowed us to build a model of a fully 2'-0-methylated RNA double helix. Conclusions: Insertion of 2'-O-modified RNA residues into a stretch of DNA can nucleate a local A-type conformation, in part because modification with a bulky residue at this position stabilizes a C3'4nda type sugar pucker. The increased stability of fully 2'-0-methylated RNA may result from hydrophobic interactions between substituents in the minor groove. As the 2'-O-methyl groups are directed into the minor groove, it may be worthwhile to introduce tailor-made 2'-0-substituents into RNA; it might be possible to design groups that both stabilize the hybrid duplexes and carry a nuclease function, further improving the efficacy of these modified RNAs in antisense applications.
Journal of Medicinal Chemistry, 1989
The neplanocin A analogue 3-deazaneplanocin A (2b) has been synthesized. A direct SN2 displacement on the cyclopentenyl mesylate 3 by the sodium salt of 6-chloro-3-deazapurine afforded the desired regioisomer 4 as the major product. After deprotection, this material was converted to 3-deazaneplanocin A in two steps. X-ray crystallographic analysis confirmed the assigned structure. Consistent with its potent inhibition of S-adenosylhomocysteine hydrolase, 3-deazaneplanocin A displayed excellent antiviral activity in cell culture against vesicular stomatitis, parainfluenza type 3, yellow fever, and vaccinia viruses. Antiviral activity was also displayed in vivo against vaccinia virus by using a mouse tailpox assay. The significantly lower cytotoxicity of 3-deazaneplanocin A, relative to its parent compound neplanocin A, may be due to its lack of conversion to 5'-triphosphate and S-adenosylmethionine metabolites. S-Adenosylhomocysteine hydrolase (AdoHcy-ase) is a pivotal enzyme in the regulation of S-adenosylmethionine (AdoMet) dependent methylation reactions because its substrate, S-adenosylhomocysteine (AdoHcy), is a competitive inhibitor of all methyltransferases.' Physiologically, the reaction proceeds in the catabolic direction due to the efficient removal of adenosine (Ado) and homocysteine (Hcy) by further metabolism (i.e., deamination or phosphorylation of Ado and remethylation of Hcy back to methionine).2 Despite the anticipated multiplicity of effects that could result from the inhibition of AdoHcy-ase by different Ado or AdoHcy analogues, the pharmacological effects of the various inhibitors studied to date appear to be rather specific.2 Since most of the AdoHcy congeners do not enter cells efficiently, most of the interest in the area of AdoHcy-ase inhibitors has focused on the development of Ado analogue^.^ Recently, an excellent correlation between the antiviral potency against vesicular stomatitis virus (VSV) and the inhibitory effect (KJK,) on AdoHcy-ase, for a series of Ado analogues, was e~tablished.~ The antiviral activity observed for these compounds is believed to result from the inhibition of the AdoMet-dependent methylation of the 5'-cap of viral mRNA, caused by the increased accumulation of AdoHcy inside the cell. Inhibition of this critical methylation reaction hinders translation of viral mRNA into viral proteins.6 One very important discovery in the search for selective AdoHcy-ase inhibitors was that the replacement of the adenine aglycon moiety in Ado by 3-deazaadenine abolished the substrate properties of the resulting compound toward both adenosine deaminase and adenosine kinase." Thus, 3-deazaadenosine interacted preferentially with AdoHcy-ase and, as expected, demonstrated significant antiviral activity.6 Later, another important discovery indicated that replacement of the sugar moiety of Ado by a carbocyclic ring increased the affinity of the compound toward AdoHcy-ase by 2-3 orders of m a g n i t~d e .~ However, the resulting carbocyclic adenosine analogue (aristeromycin) still functioned as a substrate for both aden
2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase
PLoS Pathogens, 2012
RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 29-O methyltransferase activities that are required for the formation of 59 type I cap (m 7 GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 29-Omethyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N 6methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 29-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 29-Omethyladenosine. Importantly, genomic RNA purified from DENV virion contains 29-O-methyladenosine. The 29-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 29-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 29-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNAs in vitro.