- MeSH
- antivirové látky farmakologie terapeutické užití MeSH
- hepatitida D * diagnóza farmakoterapie patologie MeSH
- imunizace metody MeSH
- interferon alfa terapeutické užití MeSH
- lidé MeSH
- lipopeptidy farmakologie terapeutické užití MeSH
- screeningové diagnostické programy MeSH
- virus hepatitidy delta metabolismus patogenita MeSH
- Check Tag
- lidé MeSH
Defective viral genomes (DVGs) are truncated and/or rearranged viral genomes produced during virus replication. Described in many RNA virus families, some of them have interfering activity on their parental virus and/or strong immunostimulatory potential, and are being considered in antiviral approaches. Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes spp. that infected millions of humans in the last 15 years. Here, we describe the DVGs arising during CHIKV infection in vitro in mammalian and mosquito cells, and in vivo in experimentally infected Aedes aegypti mosquitoes. We combined experimental and computational approaches to select DVG candidates most likely to have inhibitory activity and showed that, indeed, they strongly interfere with CHIKV replication both in mammalian and mosquito cells. We further demonstrated that some DVGs present broad-spectrum activity, inhibiting several CHIKV strains and other alphaviruses. Finally, we showed that pre-treating Aedes aegypti with DVGs prevented viral dissemination in vivo.
- MeSH
- Aedes virologie MeSH
- antivirové látky farmakologie MeSH
- defektní viry genetika MeSH
- genom virový * MeSH
- horečka chikungunya imunologie přenos virologie MeSH
- komáří přenašeči virologie MeSH
- lidé MeSH
- replikace viru * MeSH
- virus chikungunya genetika růst a vývoj izolace a purifikace MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Using high-throughput sequencing, a novel waikavirus was identified in a mixed virus infection of red clover (Trifolium pratense L.). Its complete genomic sequence was determined and characterized. The virus, tentatively named red clover associated virus 1 (RCaV1), is phylogenetically related to members of the genus Waikavirus (family Secoviridae, order Picornavirales).
- MeSH
- fylogeneze MeSH
- genom virový * MeSH
- molekulární sekvence - údaje MeSH
- nemoci rostlin virologie MeSH
- otevřené čtecí rámce MeSH
- satelitní viry klasifikace genetika izolace a purifikace MeSH
- sekvence nukleotidů MeSH
- sekvenční analýza DNA MeSH
- Trifolium virologie MeSH
- Waikavirus klasifikace genetika izolace a purifikace MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- antivirové látky terapeutické užití MeSH
- fosforothioátové oligonukleotidy terapeutické užití MeSH
- hepatitida D * imunologie patofyziologie terapie MeSH
- lidé MeSH
- randomizované kontrolované studie jako téma MeSH
- RNA virová MeSH
- virus hepatitidy B * genetika MeSH
- virus hepatitidy delta * genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape.
- MeSH
- katalytická doména MeSH
- katalýza MeSH
- kinetika MeSH
- konformace nukleové kyseliny MeSH
- krystalografie rentgenová MeSH
- molekulární modely MeSH
- rezonanční přenos fluorescenční energie metody MeSH
- RNA katalytická chemie MeSH
- RNA malá jaderná chemie metabolismus MeSH
- RNA virová chemie MeSH
- simulace molekulární dynamiky MeSH
- štěpení RNA MeSH
- virus hepatitidy delta enzymologie genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- MeSH
- hepatitida D diagnóza epidemiologie farmakoterapie komplikace MeSH
- lidé MeSH
- virus hepatitidy delta fyziologie genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- souhrny MeSH
An efficient method for the synthesis of N(9)-[3-fluoro-2-(phosphonomethoxy)propyl] (FPMP) derivatives of purine bases has been developed. Both (R)- and (S)-enantiomers of the N(6)-substituted FPMP derivatives of adenine and 2,6-diaminopurine were prepared and their anti-human immunodeficiency virus (HIV) and anti-Moloney murine sarcoma virus (MSV) activity was evaluated. Whereas none of the 6-substituted FPMPA derivatives showed any antiviral activity, several FPMPDAP derivatives had a moderate antiretroviral activity. Moreover, the data obtained from the study of the substrate activity of the active derivatives towards N(6)-methyl-AMP aminohydrolase support the notion that the studied N(6)-substituted FPMPDAP derivatives act as prodrugs of the antiretroviral FPMPG analogues.
- MeSH
- 2-aminopurin analogy a deriváty chemická syntéza chemie farmakologie MeSH
- adenin analogy a deriváty chemická syntéza chemie farmakologie MeSH
- antivirové látky chemická syntéza chemie farmakologie MeSH
- buňky 3T3 MeSH
- HIV-1 účinky léků MeSH
- HIV-2 účinky léků MeSH
- krystalografie rentgenová MeSH
- kultivované buňky MeSH
- kyseliny fosforité chemická syntéza chemie farmakologie MeSH
- lidé MeSH
- Moloneyho virus myšího sarkomu účinky léků MeSH
- myši inbrední C3H MeSH
- myši MeSH
- puriny chemická syntéza chemie farmakologie MeSH
- vztah mezi dávkou a účinkem léčiva MeSH
- vztahy mezi strukturou a aktivitou MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The hepatitis delta virus (HDV) ribozyme is an RNA motif embedded in human pathogenic HDV RNA. Previous experimental studies have established that the active-site nucleotide C75 is essential for self-cleavage of the ribozyme, although its exact catalytic role in the process remains debated. Structural data from X-ray crystallography generally indicate that C75 acts as the general base that initiates catalysis by deprotonating the 2'-OH nucleophile at the cleavage site, while a hydrated magnesium ion likely protonates the 5'-oxygen leaving group. In contrast, some mechanistic studies support the role of C75 acting as general acid and thus being protonated before the reaction. We report combined quantum chemical/molecular mechanical calculations for the C75 general base pathway, utilizing the available structural data for the wild type HDV genomic ribozyme as a starting point. Several starting configurations differing in magnesium ion placement were considered and both one-dimensional and two-dimensional potential energy surface scans were used to explore plausible reaction paths. Our calculations show that C75 is readily capable of acting as the general base, in concert with the hydrated magnesium ion as the general acid. We identify a most likely position for the magnesium ion, which also suggests it acts as a Lewis acid. The calculated energy barrier of the proposed mechanism, approximately 20 kcal/mol, would lower the reaction barrier by approximately 15 kcal/mol compared with the uncatalyzed reaction and is in good agreement with experimental data.
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.
- MeSH
- financování organizované MeSH
- hořčík chemie MeSH
- kationty dvojmocné chemie MeSH
- kationty jednomocné chemie MeSH
- konformace nukleové kyseliny MeSH
- molekulární modely MeSH
- molekulární sekvence - údaje MeSH
- RNA katalytická chemie MeSH
- sekvence nukleotidů MeSH
- sodík chemie MeSH
- vazebná místa MeSH
- virus hepatitidy delta enzymologie MeSH
- voda chemie MeSH
- vodíková vazba MeSH
