{"title":"Cover Picture: (Isr. J. Chem. 1-2/2024)","authors":"","doi":"10.1002/ijch.202480101","DOIUrl":"https://doi.org/10.1002/ijch.202480101","url":null,"abstract":"<p>The cover picture shows a cyclic voltammogram and catalytically active intermediates, highlighting the importance of a rationale for innovations in the rapidly evolving field of molecular electrosynthesis. Also, as a product structure, a C7 substituted indole, derived through electrocatalysis, is depicted.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure>\u0000 </p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 1-2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202480101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139976533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cellular Metabolic Labeling of Nucleic Acids and Its Applications","authors":"Dr. Zhiyong He, Prof. Xiang Zhou","doi":"10.1002/ijch.202300165","DOIUrl":"10.1002/ijch.202300165","url":null,"abstract":"<p>Nucleic acids are considered as fundamental molecules of living systems, which serve as universal genetic information messengers and repositories. To uncover the multifaceted aspects of nucleic acid function and metabolism within cells, labeling has become indispensable. This labeling technique enables the visualization, isolation, characterization, and even quantification of specific nucleic acid species. This review delves into cellular metabolic approaches for nucleic acid labeling, wherein enzymatic steps are employed to introduce nucleic acid modifications before conjugation with a label for detection or isolation. The discussion begins with metabolic labeling for DNA, RNA with various reactive groups and post-transcriptional RNA labeling for RNA methylation and acetylation sites, emphasizing recent advancements in the field and then, we spotlighted pertinent applications for cellular imaging and sequencing. of labeling.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139945608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Special Issue on Electrochemically-Driven Organic Synthesis","authors":"Prof. Dr. Lutz Ackermann","doi":"10.1002/ijch.202400022","DOIUrl":"10.1002/ijch.202400022","url":null,"abstract":"<p>Molecular synthesis has gained considerable momentum through the impetus provided by electrochemically-enabled redox manipulation.<span><sup>1</sup></span> Organic electrosynthesis and electrocatalysis bear a unique potential to substantially improve molecular chemistry and provide a wide range of innovative transformations. While a first electrochemically-driven organic synthesis dates back to Kolbe's decarboxylative homocoupling in 1848,<span><sup>2</sup></span> organic electrosynthesis has remained largely underexplored. Particularly, recent years have witnessed a remarkable renaissance of electrochemically-enabled organic reactions. Pioneering contributions have during the past several years illustrated the unique opportunities that electrochemistry offers for the assembly of novel molecular structures, while improving the efficiency and sustainability of molecular synthesis. In this Special Issue, the <i>Israelian Journal of Chemistry</i> highlights the latest progress in this field.</p><p>Articles enclosed in this Special Issue cover overviews of important recent achievements in electrochemically driven organic synthesis as well as important original research articles on molecular organic electrosynthesis. Thus, Xu reviewed strategies that exploit ferrocene as redox catalyst, emphasizing the power towards catalyzed radical formation.<span><sup>3</sup></span> Likewise, Onomura summarized the potential of halogen mediators for environmentally-benign and at the same time efficient alcohol oxidations.<span><sup>4</sup></span> Jiao and Mei showed the power of paired electrolysis for organic reactions with ideal resource-economy,<span><sup>5</sup></span> while Cheng outlined the challenges and benefits of water as a particularly benign reaction medium.<span><sup>6</sup></span> Besides electrooxidative strategies, electroreductive transformations have garnered major recent attention. In this context, Weix summarized electrochemical nickel-catalyzed C−C bond formations through cross-electrophile coupling,<span><sup>7</sup></span> while Gosmini provided an overview on powerful transition metal-catalyzed electroreductive approachess for C−C bond formation.<span><sup>8</sup></span> On a different note, de Sarkar focused on electroreductive transformations involving C−C and C−O multiple bonds.<span><sup>9</sup></span> Novel innovative concepts in the realm of organic electrosynthesis, are presented in selected research articles highlighting exciting recent advances. Here, Ruan established an electrochemical cascade cyclization for a convenient access to 3-selenylindoles,<span><sup>10</sup></span> while Ackermann established C7-indole alkenylations based on rhodaelectrocatalysis.<span><sup>11</sup></span> The elegant design of an off/on switching enabled Kakiuchi to establish a one-pot cross-coupling/C−H bromination for bromoarylpyridines.<span><sup>12</sup></span> Finally, Fuchigami systematically compared the impact of the anode materials on the pe","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 1-2","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139956863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Engineered RNA-Binding Proteins: Studying and Controlling RNA Regulation","authors":"Riley W. Sinnott, Yang Cao, Bryan C. Dickinson","doi":"10.1002/ijch.202300169","DOIUrl":"10.1002/ijch.202300169","url":null,"abstract":"<p>The complexity of eukaryotic organisms is intricately tied to transcriptome-level processes, notably alternative splicing and the precise modulation of gene expression through a sophisticated interplay involving RNA-binding protein (RBP) networks and their RNA targets. Recent advances in our understanding of the molecular pathways responsible for this control have paved the way for the development of tools capable of steering and managing RNA regulation and gene expression. The fusion between a rapidly developing understanding of endogenous RNA regulation and the burgeoning capabilities of CRISPR-Cas and other programmable RBP platforms has given rise to an exciting frontier in engineered RNA regulators. This review offers an overview of the existing toolkit for constructing synthetic RNA regulators using programmable RBPs and effector domains, capable of altering RNA sequence composition or fate, and explores their diverse applications in both basic research and therapeutic contexts.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300169","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139927994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chao Yan, Qian Zhang, Pan Xiao, Xinyun Xie, Ming Li, Yuanlai Qiu, Liufa Wen, Xiaomin Song, Ze Dong, Cai-Guang Yang
{"title":"Structure-Activity Relationships of 2-(Arylthio)benzoic Acid FTO Inhibitors","authors":"Chao Yan, Qian Zhang, Pan Xiao, Xinyun Xie, Ming Li, Yuanlai Qiu, Liufa Wen, Xiaomin Song, Ze Dong, Cai-Guang Yang","doi":"10.1002/ijch.202300166","DOIUrl":"10.1002/ijch.202300166","url":null,"abstract":"<p>The biological role of the fat mass and obesity-associated protein (FTO) in the initiation and progress of acute myeloid leukemia (AML) has been elucidated, and several representative FTO inhibitors can markedly suppress the proliferation of AML cells. We previously developed FTO inhibitors including FB23. In this study, we adopted bioisosteric replacement of the intramolecular hydrogen bond in FB23 with a sulfur-oxygen interaction to generate a series of 2-(arylthio)benzoic acid FTO inhibitors and established their structure-activity relationships. Compound <b>8c</b> was the most potent 2-(arylthio)benzoic acid FTO inhibitor with an IC<sub>50</sub> value of 0.3±0.1 μM, which was comparable with that of FB23 <i>in vitro</i>. To enhance the antiproliferative effects in AML cell lines, we applied a prodrug strategy and prepared some esters. <b>7l</b>, the methyl ester of <b>8l</b>, exerted a superior inhibitory effect on a panel of AML cancer cell lines. Additionally, <b>7l</b> treatment notably increased global m<sup>6</sup>A abundance in AML cells. Collectively, our data suggest that 2-(arylthio)benzoic acid may be a new lead compound for inhibition of FTO, and the prodrug analog exhibit potential in the treatment of AML.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139771114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xin Wang, Dr. Xiao-Yang Jin, Prof. Dr. Liang Cheng
{"title":"Recent Advance in the Study on 5-Formylcytosine (f5C) RNA Modification","authors":"Xin Wang, Dr. Xiao-Yang Jin, Prof. Dr. Liang Cheng","doi":"10.1002/ijch.202300178","DOIUrl":"10.1002/ijch.202300178","url":null,"abstract":"<p>The widespread involvement of 5-formylcytosine f<sup>5</sup>C RNA in gene function regulation and its impact on crucial life processes like cell differentiation, embryonic development, and disease development underscores the significance of detecting this specific base modification. This detection holds great importance for basic epigenetics research and the early diagnosis and pathogenesis research of various diseases. This review aims to summarize recent research progress in f<sup>5</sup>C detection methods using selective chemical labeling, with the hope of aiding future research endeavors.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139770938","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Protein Glycosylation Patterns Shaped By the IRE1-XBP1s Arm of the Unfolded Protein Response","authors":"Kenny Chen, Matthew D. Shoulders","doi":"10.1002/ijch.202300162","DOIUrl":"https://doi.org/10.1002/ijch.202300162","url":null,"abstract":"<h2> Protein Glycosylation</h2>\u0000<p>Protein post-translational modifications, including phosphorylation, acetylation, ubiquitylation, and more, confer key levels of regulation and can dramatically alter the structure and function of proteins, acting as molecular switches or rheostats for tuning activity.<span><sup>1</sup></span> Many post-translational modifications are specialized to specific subcellular compartments and clientele, such as the sophisticated pathways for protein <i>N-</i>glycosylation in the endoplasmic reticulum (ER) and Golgi mediated by a suite of glycosyltransferase and glycosidase enzymes. Protein glycosylation involves covalent modification of amino acid sidechains with sugars to yield linear or branched structures (glycans; Figure 1). The consequences of glycosylation shape protein function, cell–cell recognition, cell–matrix interactions, and more.<span><sup>2</sup></span>\u0000</p>\u0000<figure><picture>\u0000<source media=\"(min-width: 1650px)\" srcset=\"/cms/asset/42668d07-8a7d-4cdf-b366-41629a41fe4c/ijch202300162-fig-0001-m.jpg\"/><img alt=\"Details are in the caption following the image\" data-lg-src=\"/cms/asset/42668d07-8a7d-4cdf-b366-41629a41fe4c/ijch202300162-fig-0001-m.jpg\" loading=\"lazy\" src=\"/cms/asset/821703d3-642e-4abd-a95c-a22057767b00/ijch202300162-fig-0001-m.png\" title=\"Details are in the caption following the image\"/></picture><figcaption>\u0000<div><strong>Figure 1<span style=\"font-weight:normal\"></span></strong><div>Open in figure viewer<i aria-hidden=\"true\"></i><span>PowerPoint</span></div>\u0000</div>\u0000<div>\u0000<p>Protein <i>N</i>-linked glycosylation is a co- and post-translational modification that involves the installation of glycans on asparagine side chains in specific amino acid sequons in proteins traversing the secretory pathway. <i>A</i>: A 14-residue precursor oligosaccharide is first synthesized in a step-wise fashion while attached to a dolichol pyrophosphate molecule on the ER membrane. Monosaccharide substrates in the form of nucleotide sugars are each added to the growing sugar chain by their respective transferase enzymes. The dolichol-linked precursor then requires the action of flippase enzymes, prior to being added to a nascent ER client protein by the oligosaccharyltransferase (OST) complex as the polypeptide translocates from the ribosome to the ER. Note that <i>N</i>-glycans can also be installed post-translationally by OST. After installation of the precursor, folding and initial trimming occurs in the ER and the nascent glycoprotein is trafficked to the Golgi for further processing. <i>B</i>: Glycan-modifying enzymes in the ER and Golgi process the <i>N</i>-glycan via sequential removal and addition of monosaccharides by specific enzymes, ultimately yielding a vast array of potential glycan structures, including hybrid glycans, complex glycans, core fucosylated glycans, and sialylated glycans. The specific identity of the glycan has important and varied consequences for cellular communication and the function of ","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"94 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139771087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Prof. Aaron M. Fleming, Justin C. Dingman, Yizhou Wu, Spencer S. Hoon, Prof. Cynthia J. Burrows
{"title":"Nanopore Direct RNA Sequencing for Modified Uridine Nucleotides Yields Signals Dependent on the Physical Properties of the Modified Base","authors":"Prof. Aaron M. Fleming, Justin C. Dingman, Yizhou Wu, Spencer S. Hoon, Prof. Cynthia J. Burrows","doi":"10.1002/ijch.202300177","DOIUrl":"10.1002/ijch.202300177","url":null,"abstract":"<p>Sequencing for RNA modifications with the nanopore direct RNA sequencing platform provides ionic current levels, helicase dwell times, and base call data that differentiate the modifications from the canonical form. Herein, model RNAs were synthesized with site-specific uridine (U) base modifications that enable the study of increasing an alkyl group size, halogen identity, or a change in base acidity to impact the nanopore data. The analysis concluded that increases in alkyl size trend with greater current blockage but a similar change in base-call error was not found. The addition of a halogen series to C5 of U revealed that the current levels recorded a trend with the water-octanol partition coefficient of the base, as well as the base call error. Studies with U modifications that are deprotonated (i. e., anionic) under the sequencing conditions gave broad current levels that influenced the base call error. Some modifications led to helicase dwell time changes. These insights provide design parameters for modification-specific chemical reagents that can shift nanopore signatures to minimize false positive reads, a known issue with this sequencing approach.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300177","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139581993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Pathogenicity Prediction of GABAA Receptor Missense Variants","authors":"Ya-Juan Wang, Giang H. Vu, Ting-Wei Mu","doi":"10.1002/ijch.202300161","DOIUrl":"https://doi.org/10.1002/ijch.202300161","url":null,"abstract":"<h2> Introduction</h2>\u0000<p>Epilepsy is one of the most common neurological diseases in the world with a broad phenotypic spectrum.<span><sup>1</sup></span> Recent advances in genome sequencing identified an increasing number of genes that are associated with epilepsy.<span><sup>2</sup></span> According to protein functions, epilepsy-associated genes can be grouped to ion channels, enzymes and enzyme modulators, transports and receptors, and others.<span><sup>3</sup></span> Genetic epilepsy is often linked to developmental delay, movement disorder, and other comorbidities.<span><sup>4</sup></span> Due to the important role of neurotransmitter-gated ion channels in controlling the excitation-inhibition balance in the central nervous system, genes encoding these ion channels, including excitatory N-methyl-D-aspartate (NMDA) receptors and inhibitory γ-aminobutyric acid type A (GABA<sub>A</sub>) receptors, are recognized as prominent epilepsy-causing genes.<span><sup>5</sup></span> Here, we focus on GABA<sub>A</sub> receptors, the primary inhibitory neurotransmitter-gated ion channels in the human brain.<span><sup>6</sup></span> They mediate the fast inhibitory GABA-induced chloride currents and hyperpolarize the postsynaptic membranes to reduce neuronal firing.</p>\u0000<p>Proteostasis maintenance of GABA<sub>A</sub> receptors is essential for their function in the central nervous system.<span><sup>7</sup></span> GABA<sub>A</sub> receptors are assembled as pentamers from a specific combination of 19 subunits, including α1-α6 (GABRA1-A6), β1-β3 (GABRB1-B3), γ1-γ3 (GABRG1-G3), δ (GABRD), ϵ (GABRE), θ (GABRQ), π (GABRP), and ρ1-ρ3 (GABRR1-R3). The distribution of GABA<sub>A</sub> receptors is throughout the brain regions, and the most abundant subtype is composed of two α1 subunits, two β2 subunits, and one γ2 subunit.<span><sup>8</sup></span> To function, GABA<sub>A</sub> receptor subunits need to fold in the endoplasmic reticulum (ER) with the assistance of molecular chaperones and subsequently assemble with other subunits to form heteropentamers. The properly assembled receptors exit the ER and traffic to the plasma membrane to act as chloride channels. Unassembled and misfolded subunits are retained in the ER, which could be routed to the degradation pathway by the ER-associated degradation.<span><sup>9</sup></span> Recent quantitative proteomics analysis identified the proteostasis network that regulates the folding, assembly, trafficking, and degradation of GABA<sub>A</sub> receptors.<span><sup>10</sup></span></p>\u0000<p>Recent cryo-electron microscopy (cryo-EM) studies solved the high-resolution structures of pentameric GABA<sub>A</sub> receptors, including α1β2γ2 receptors<span><sup>11</sup></span> and α1β3γ2 receptors.<span><sup>12</sup></span> The pentameric receptors are arranged as β-α1-β-α1-γ2 counterclockwise when viewed from the synaptic cleft (Figure 1A). Each pentamer has two binding sites for the neurotransmitter, GABA, at the interfaces between","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"33 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139581952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}