Category: 69205-79-4

Seelam, Preethi P.; Mitra, Abhijit; Sharma, Purshotam published the artcile< Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies>, COA of Formula: C7H5N5O, the main research area is nucleobases ligands riboswitches crystal structure.

In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for anal. of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chem. constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. The anal. was further extended to study the biol. importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in the context of RNA:ligand recognition. This can, in turn, contribute toward current efforts to develop antimicrobials that target RNAs.

RNA published new progress about Amino acids Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, COA of Formula: C7H5N5O.

Referemce:
Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Luo, Min; Groaz, Elisabetta; De Jonghe, Steven; Schols, Dominique; Herdewijn, Piet published the artcile< Synthesis and anti-HIV activity of guanine modified fluorinated acyclic nucleoside phosphonate derivatives>, SDS of cas: 69205-79-4, the main research area is acyclic nucleoside phosphonate preparation anti HIV activity evaluation; HIV; Mitsunobu reaction, prodrugs; acyclic nucleoside phosphonates; antiviral activity; cytotoxicity.

The preparation of an unprecedented series of nucleobase-modified 3-fluoro-2-(phosphonomethoxy)propyl (FPMP) acyclic nucleosides in both their (R) and (S) enantiomerically pure forms is described. The synthesis focused on a Mitsunobu alkylation reaction to construct the C-N(9) bond between a chiral fluorinated side-chain residue and 6- or 7-modified guanine analogs. Prodrugs of FPMP-7-deazaguanine were also synthesized by derivatization of the corresponding phosphonic acid functionality with (bis)diamyl aspartate amidate groups, leading to moderate activity against human immunodeficiency virus type 1 (HIV-1).

Chemistry & Biodiversity published new progress about Anti-HIV agents. 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, SDS of cas: 69205-79-4.

Referemce:
Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Kot, Witold; Olsen, Nikoline S.; Nielsen, Tue K.; Hutinet, Geoffrey; de Crecy-Lagard, Valerie; Cui, Liang; Dedon, Peter C.; Carstens, Alexander B.; Moineau, Sylvain; Swairjo, Manal A.; Hansen, Lars H. published the artcile< Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs>, COA of Formula: C7H5N5O, the main research area is deazaguanine modification bacteriophage DNA nanopore sequencing.

In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two sep. DNA sequence contexts: GA and GGC. Homol. modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.

Nucleic Acids Research published new progress about Bacteriophage. 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, COA of Formula: C7H5N5O.

Referemce:
Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Wang, Zengmeng; Zhao, Jiulong; Wang, Long; Li, Chengcheng; Liu, Jianhui; Zhang, Lihua; Zhang, Yongyu published the artcile< A novel benthic phage infecting Shewanella with strong replication ability>, Product Details of C7H5N5O, the main research area is coastal sediment benthic phage shewanella phylogenetic analysis; Shewanella; benthic phage; coastal sediments; phage genome; phylogenetic analysis.

The coastal sediments were considered to contain diverse phages playing important roles in driving biogeochem. cycles based on genetic anal. However, till now, benthic phages in coastal sediments were very rarely isolated, which largely limits our understanding of their biol. characteristics. Here, we describe a novel lytic phage (named Shewanella phage S0112) isolated from the coastal sediments of the Yellow Sea infecting a sediment bacterium of the genus Shewanella. The phage has a very high replication capability, with the burst size of ca. 1170 phage particles per infected cell, which is 5-10 times higher than that of most phages isolated before. Meanwhile, the latent period of this phage is relatively longer, which might ensure adequate time for phage replication. The phage has a double-stranded DNA genome comprising 62,286 bp with 102 ORFs, ca. 60% of which are functionally unknown. The expression products of 16 ORF genes, mainly structural proteins, were identified by LC-MS/MS anal. Besides the general DNA metabolism and structure assembly genes in the phage genome, there is a cluster of auxiliary metabolic genes that may be involved in 7-cyano-7-deazaguanine (preQ0) biosynthesis. Meanwhile, a pyrophosphohydrolase (MazG) gene being considered as a regulator of programmed cell death or involving in host stringer responses is inserted in this gene cluster. Comparative genomic and phylogenetic anal. both revealed a great novelty of phage S0112. This study represents the first report of a benthic phage infecting Shewanella, which also sheds light on the phage-host interactions in coastal sediments.

Viruses published new progress about Coastal sediments. 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, Product Details of C7H5N5O.

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Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Ferreira, Everton Geraldo Capote; Gomes, Douglas Fabiano; Delai, Caroline Vanzzo; Barreiros, Marco Antonio Bacellar; Grange, Luciana; Rodrigues, Elisete Pains; Henning, Liliane Marcia Mertz; Barcellos, Fernando Gomes; Hungria, Mariangela published the artcile< Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15)>, Synthetic Route of 69205-79-4, the main research area is Bradyrhizobium genistein cobalamin amino acids symbiosis Squalene hopene cyclase; Biological nitrogen fixation; Functional inference; Gene expression; Symbiosis.

Bradyrhizobium japonicum strain SEMIA 5079 (= CPAC 15) is a nitrogen-fixing symbiont of soybean broadly used in com. inoculants in Brazil. Its genome has about 50% of hypothetical (HP) protein-coding genes, many in the symbiosis island, raising questions about their putative role on the biol. nitrogen fixation (BNF) process. This study aimed to infer functional roles to 15 HP genes localized in the symbiosis island of SEMIA 5079, and to analyze their expression in the presence of a nod-gene inducer. A workflow of bioinformatics tools/databases was established and allowed the functional annotation of the HP genes. Most were enzymes, including transferases in the biosynthetic pathways of cobalamin, amino acids and secondary metabolites that may help in saprophytic ability and stress tolerance, and hydrolases, that may be important for competitiveness, plant infection, and stress tolerance. Putative roles for other enzymes and transporters identified are discussed. Some HP proteins were specific to the genus Bradyrhizobium, others to specific host legumes, and the anal. of orthologues helped to predict roles in BNF. All 15 HP genes were induced by genistein and high induction was confirmed in five of them, suggesting major roles in the BNF process.

BMC Microbiology published new progress about Acacia auriculiformis. 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, Synthetic Route of 69205-79-4.

Referemce:
Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Kieft, Kristopher; Zhou, Zhichao; Anantharaman, Karthik published the artcile< VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences>, Safety of 2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile, the main research area is Crohn disease Enterobacteriale VIBRANT genomic microbiome environment dysbiosis ecosystem; Auxiliary metabolism; Bacteriophage; Machine learning; Metagenome; Software; Virome; Virus.

Viruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed microbial and viral sequences provides the opportunity to tease apart complex microbiome dynamics, but these analyses are currently limited by the tools available for analyses of viral genomes and assessing their metabolic impacts on microbiomes. Here we present VIBRANT, the first method to utilize a hybrid machine learning and protein similarity approach that is not reliant on sequence features for automated recovery and annotation of viruses, determination of genome quality and completeness, and characterization of viral community function from metagenomic assemblies. VIBRANT uses neural networks of protein signatures and a newly developed v-score metric that circumvents traditional boundaries to maximize identification of lytic viral genomes and integrated proviruses, including highly diverse viruses. VIBRANT highlights viral auxiliary metabolic genes and metabolic pathways, thereby serving as a user-friendly platform for evaluating viral community function. VIBRANT was trained and validated on reference virus datasets as well as microbiome and virome data. VIBRANT showed superior performance in recovering higher quality viruses and concurrently reduced the false identification of non-viral genome fragments in comparison to other virus identification programs, specifically VirSorter, VirFinder, and MARVEL. When applied to 120,834 metagenome-derived viral sequences representing several human and natural environments, VIBRANT recovered an average of 94% of the viruses, whereas VirFinder, VirSorter, and MARVEL achieved less powerful performance, averaging 48%, 87%, and 71%, resp. Similarly, VIBRANT identified more total viral sequence and proteins when applied to real metagenomes. When compared to PHASTER, Prophage Hunter, and VirSorter for the ability to extract integrated provirus regions from host scaffolds, VIBRANT performed comparably and even identified proviruses that the other programs did not. To demonstrate applications of VIBRANT, we studied viromes associated with Crohn’s disease to show that specific viral groups, namely Enterobacteriales-like viruses, as well as putative dysbiosis associated viral proteins are more abundant compared to healthy individuals, providing a possible viral link to maintenance of diseased states. The ability to accurately recover viruses and explore viral impacts on microbial community metabolism will greatly advance our understanding of microbiomes, host-microbe interactions, and ecosystem dynamics. [media not available: see fulltext].

Microbiome published new progress about Algorithm. 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, Safety of 2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile.

Referemce:
Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Fergus, Claire; Al-qasem, Mashael; Cotter, Michelle; McDonnell, Ciara M.; Sorrentino, Emiliano; Chevot, Franciane; Hokamp, Karsten; Senge, Mathias O.; Southern, John M.; Connon, Stephen J.; Kelly, Vincent P. published the artcile< The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity>, SDS of cas: 69205-79-4, the main research area is human tRNA guanine transglycosylase deazaguanine derivative queuosine protein translation.

Base-modification can occur throughout a tRNA mol.; however, elaboration is particularly prevalent at position 34 of the anticodon loop (the wobble position), where it functions to influence protein translation. Previously, we demonstrated that the queuosine modification at position 34 can be substituted with an artificial analog via the queuine tRNA ribosyltransferase enzyme to induce disease recovery in an animal model of multiple sclerosis. Here, we demonstrate that the human enzyme can recognize a very broad range of artificial 7-deazaguanine derivatives for tRNA incorporation. By contrast, the enzyme displays strict specificity for tRNA species decoding the dual synonymous NAU/C codons, determined using a novel enzyme-RNA capture-release method. Our data highlight the broad scope and therapeutic potential of exploiting the queuosine incorporation pathway to intentionally engineer chem. diversity into the tRNA anticodon.

Nucleic Acids Research published new progress about Anticodons Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, SDS of cas: 69205-79-4.

Referemce:
Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Flemmich, Laurin; Moreno, Sarah; Micura, Ronald published the artcile< Synthesis of O6-alkylated preQ1 derivatives>, Computed Properties of 69205-79-4, the main research area is alkoxy pyrrolopyrimidinyl aminotrifluoroacetate salt preparation; RNA cofactors; RNA methylation; deazapurines; heterocycles; pyrrolopyrimidines; queuosine.

A robust synthesis for the class of pyrrolo[2,3-d]pyrimidines starting from readily accessible N2-pivaloyl-protected 6-chloro-7-cyano-7-deazaguanine. Substitution of the 6-chloro atom with the alcoholate of interest proceeded straightforward. The transformation of the 7-cyano substituent into the required aminomethyl group turned out to be challenging and was solved by a hydration reaction sequence on a well-soluble dimethoxytritylated precursor via in situ oxime formation. The synthetic path provided a solid foundation to access O6-alkylated 7-aminomethyl-7-deazaguanines for the development of RNA labeling tools based on the preQ1 class-I riboswitch scaffold.

Beilstein Journal of Organic Chemistry published new progress about Aliphatic amines Role: RCT (Reactant), SPN (Synthetic Preparation), RACT (Reactant or Reagent), PREP (Preparation). 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, Computed Properties of 69205-79-4.

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Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Brooks, Allen F.; Garcia, George A.; Showalter, Hollis D. published the artcile< Synthesis of azide congeners of preQ1 as potential substrates for tRNA guanine transglycosylase>, Reference of 69205-79-4, the main research area is tRNA guanine transglycosylase preQ azide congener.

PreQ1 (2) is a precursor of queuine (1) that in eubacteria is incorporated into tRNA (tRNA) by tRNA guanine transglycosylase (TGT) before being further elaborated into queuine. The queuine modification is unusual and occurs across all eukaryotes and eubacteria with few exceptions, but its function remains unclear. As the modified nucleotide occurs through incorporation of a specially synthesized nucleotide instead of via modification of a genetically encoded base, a study of the sites of modification by prepared probes is possible. We report the synthesis of two novel azide congeners (3,4) of preQ1 for this purpose. The evaluation of their interaction with TGT shows that both probes act as weak competitive inhibitors of guanine exchange of guanine(34) tRNATyr with a Ki of ∼70 μM. However, we could not show that these are substrates for TGT-catalyzed incorporation into tRNA. We believe the reason for this is a marked loss of binding due to the azide functionality of 3 and 4 abrogating the possibility of two hydrogen bonds to the carbonyl group of Leu231 and Met260 of TGT, previously observed for the terminal methylene amine of preQ1 by x-ray crystallog.

Journal of Heterocyclic Chemistry published new progress about Enzyme functional sites, substrate-binding. 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, Reference of 69205-79-4.

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Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts

Williamson, Douglas S.; Smith, Garrick P.; Mikkelsen, Gitte K.; Jensen, Thomas; Acheson-Dossang, Pamela; Badolo, Lassina; Bedford, Simon T.; Chell, Victoria; Chen, I-Jen; Dokurno, Pawel; Hentzer, Morten; Newland, Samantha; Ray, Stuart C.; Shaw, Terry; Surgenor, Allan E.; Terry, Lindsey; Wang, Yikang; Christensen, Kenneth V. published the artcile< Design and Synthesis of Pyrrolo[2,3-d]pyrimidine-Derived Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Checkpoint Kinase 1 (CHK1)-Derived Crystallographic Surrogate>, Reference of 69205-79-4, the main research area is pyrrolopyrimidine preparation leucine rich repeat kinase Parkinson crystal structure.

Inhibitors of leucine-rich repeat kinase 2 (LRRK2) and mutants, such as G2019S, have potential utility in Parkinson’s disease treatment. Fragment hit-derived pyrrolo[2,3-d]pyrimidines underwent optimization using X-ray structures of LRRK2 kinase domain surrogates, based on checkpoint kinase 1 (CHK1) and a CHK1 10-point mutant. (2R)-2-Methylpyrrolidin-1-yl derivative I (LRRK2 G2019S cKi 0.7 nM, LE 0.66) was identified, with increased potency consistent with an X-ray structure of 18/CHK1 10-pt. mutant showing the 2-Me substituent proximal to Ala147 (Ala2016 in LRRK2). Further structure-guided elaboration of I gave the 2-[(1,3-dimethyl-1H-pyrazol-4-yl)amino] deriv II. Optimization of II afforded diastereomeric oxolan-3-yl derivatives III and IV, which demonstrated a favorable in vitro PK profile, although they displayed species disconnects in the in vivo PK profile, and a propensity for P-gp- and/or BCRP-mediated efflux in a mouse model. Compounds III and IV demonstrated high potency and exquisite selectivity for LRRK2 and utility as chem. probes for the study of LRRK2 inhibition.

Journal of Medicinal Chemistry published new progress about Crystal structure. 69205-79-4 belongs to class nitriles-buliding-blocks, and the molecular formula is C7H5N5O, Reference of 69205-79-4.

Referemce:
Nitrile – Wikipedia,
Nitriles – Chemistry LibreTexts