Israel Journal of Chemistry最新文献

{"title":"Approximations of Symbolic Substitution Systems in One Dimension","authors":"Lior Tenenbaum","doi":"10.1002/ijch.202300121","DOIUrl":"10.1002/ijch.202300121","url":null,"abstract":"<p>Periodic approximations of quasicrystals are a powerful tool in analyzing spectra of Schrödinger operators arising from quasicrystals, given the known theory for periodic crystals. Namely, we seek periodic operators whose spectra approximate the spectrum of the limiting operator (of the quasicrystal). This naturally leads to study the convergence of the underlying dynamical systems.</p><p>We treat dynamical systems which are based on one-dimensional substitutions. We first find natural candidates of dynamical subsystems to approximate the substitution dynamical system. Subsequently, we offer a characterization of their convergence and provide estimates for the rate of convergence. We apply the proposed theory to some guiding examples.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 10-11","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202300121","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140203997","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":"Non-Canonical Amino Acids for Engineering Peptides and Proteins with new Functions","authors":"Kelly Zhi Qi Zhou,&nbsp;Richard Obexer","doi":"10.1002/ijch.202400006","DOIUrl":"10.1002/ijch.202400006","url":null,"abstract":"<p>The universal genetic code, which specifies the 20 standard amino acids (AAs), forms the basis for all natural proteins. Researchers have developed efficient and robust <i>in vivo</i> and <i>in vitro</i> strategies to overcome the constraints of the genetic code to expand the repertoire of AA building blocks that can be ribosomally incorporated into proteins. This review summarizes the development of these <i>in vivo</i> and <i>in vitro</i> systems and their subsequent use for engineering of peptides and proteins with new functions. <i>In vivo</i> genetic code expansion employing engineered othogonal tRNA/aaRS pairs has led to the development of proteins that selectively bind small molecules, cleave nucleic acids and catalyze non-natural chemical transformations. <i>In vitro</i> genetic code reprogramming using Flexizymes coupled with mRNA display has resulted in potent macrocyclic peptides that selectively bind to therapeutically important proteins. Through these examples, we hope to illustrate how genetic code expansion and reprogramming, especially when coupled with directed evolution or <i>in vitro</i> selection techniques, have emerged as powerful tools for expanding the functional capabilities of peptides and proteins.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140204339","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":"Recent Advances in Non-Standard Macrocyclic Peptide Ligand Discovery using mRNA Display","authors":"Yizhen Yin,&nbsp;Christopher John Hipolito","doi":"10.1002/ijch.202300167","DOIUrl":"10.1002/ijch.202300167","url":null,"abstract":"<p>Advancements in platform technologies have facilitated the production of libraries consisting of macrocyclic peptides composed of natural and non-canonical amino acids for more drug-like characteristics. Identification of macrocyclic peptide ligands against targets of interest can be accomplished using mRNA display. Despite numerous successful <i>in vitro</i> selections for macrocyclic peptide ligands against extracellular targets, identifying macrocyclic peptide hits that can reach intracellular targets continue to be a challenge. Breakthroughs in defining the features of a macrocyclic peptide that promote cell permeability have recently been disclosed. Here, we review the successful selections of non-standard macrocyclic peptide ligands using mRNA display in the last five years and chemical optimization of a drug-like macrocyclic peptide ligand for targeting intracellular KRAS.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127362","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":"Modulating the Acceptor Preference of His-C-Geranyltransferase LimF","authors":"Yuchen Zhang,&nbsp;Yuki Goto,&nbsp;Hiroaki Suga","doi":"10.1002/ijch.202300182","DOIUrl":"10.1002/ijch.202300182","url":null,"abstract":"<p>Lipidation stands as a pivotal strategy for enhancing the metabolic stability of target peptides. Prenyltransferases in cyanobactin biosynthesis have garnered significant attention as potential peptide lipidation biocatalysts because of their exceptional regio- and chemoselectivity. However, these enzymes often exhibit a biased preference for certain acceptor substrates, requiring specific amino acids adjacent to the modifying residue. In this study, we demonstrate the structure-guided engineering of LimF, a His-<i>C</i>-geranyltransferase, to broaden its peptide substrate tolerance. By altering key residues in the peptide-binding pocket, we created a LimF variant capable of modifying sequence motifs previously inaccessible to the wildtype enzyme. The variant successfully modified some previously unfavored sequence motifs in artificial peptide substrates and bioactive peptide agents, validating the engineered substrate scope. With the discovery of novel peptide prenyltransferases, this approach would lead to a more comprehensive toolbox of peptide prenylation biocatalysts.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140126971","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":"The Transthyretin Protein and Amyloidosis – an Extraordinary Chemical Biology Platform","authors":"Per Hammarström","doi":"10.1002/ijch.202300164","DOIUrl":"https://doi.org/10.1002/ijch.202300164","url":null,"abstract":"The amyloidoses are diseases caused by accumulation of amyloid fibrils from over 40 different human misfolded proteins in various organs of the body depending on precursor protein. Amyloidogenesis is a self‐perpetuating reaction with deleterious consequences causing degeneration in cells and organs where depositions occur. Transthyretin, TTR, is an amyloidogenic protein causing sporadic disease from the wild‐type protein during aging and from numerous different autosomal dominant familial mutations at earlier ages depending on the sequence of the hereditary variant. Until recently the disease process was poorly understood, and therapies were scarce. Over the past decades, spurred by clinical data, using chemical biology research, the mechanisms of TTR production and misfolding have been elucidated affording almost complete coverage of the TTR amyloidogenesis pathway to be targeted. This translational science success has provided a plethora of therapeutic options for the TTR amyloidoses providing an inspiring example for success in previously intractable diseases.","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"274 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140057323","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":"Deamination- or N-Nitrosation-Based Methods for m6A Profiling","authors":"Weiguo Shen,&nbsp;Jing Wang","doi":"10.1002/ijch.202300180","DOIUrl":"10.1002/ijch.202300180","url":null,"abstract":"<p>The addition of various chemical modifications to RNA introduces an additional layer of complexity to the regulation of gene expression. Among all RNA modifications, <i>N</i>⁶-methyladenosine (m⁶A) has earned its status as the most abundant and well-studied post-transcriptional modification in mammalian mRNA. Nevertheless, understanding the role of m⁶A in shaping the fate of RNA molecules and its influence on gene expression heavily depends on the development and application of detection technologies. Among all m⁶A detection methods, chemical-based sequencing methods show unique advantages. Our group recently developed an absolute quantification method named GLORI, which employs nitrite and glyoxal to convert adenosine to inosine efficiently. With its potential to emerge as the gold standard for m⁶A detection, GLORI showcases the promise of nitrite-based approaches. This review provides a comprehensive overview of m⁶A detection techniques based on deamination or nitrosation, evaluating their strengths and limitations. Furthermore, we offer insights into the future directions of innovative approaches in m⁶A profiling.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140033037","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":"RNA-Guided RNA Pseudouridylation and 2’-O-Methylation","authors":"Hironori Adachi,&nbsp;Jonathan L. Chen,&nbsp;W.-Matthias Leeder,&nbsp;Pedro Morais,&nbsp;Yi-Tao Yu","doi":"10.1002/ijch.202400005","DOIUrl":"10.1002/ijch.202400005","url":null,"abstract":"<p>RNA-guided RNA modifications, including pseudouridylation and 2′-O-methylation, are naturally occurring processes that introduce pseudouridines (Ψ) and 2’-O-methylated residues (2’-O−Me) into various types of RNA. This modification is orchestrated by two distinct families of ribonucleoprotein complexes: Box H/ACA RNP and Box C/D RNP. Each complex comprises a unique guide (g)RNA (Box H/ACA gRNA or Box C/D gRNA) and a set of core proteins responsible for pseudouridylation and 2’-O-methylation, respectively. The specificity of these modifications is conferred by base-pairing of Box H/ACA gRNA and Box C/D gRNA with their RNA substrates. Here, we discuss the mechanism and function of RNA-guided pseudouridylation and 2’-O-methylation.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139987577","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":"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,&nbsp;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":"&lt;p&gt;Molecular synthesis has gained considerable momentum through the impetus provided by electrochemically-enabled redox manipulation.&lt;span&gt;&lt;sup&gt;1&lt;/sup&gt;&lt;/span&gt; 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,&lt;span&gt;&lt;sup&gt;2&lt;/sup&gt;&lt;/span&gt; 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 &lt;i&gt;Israelian Journal of Chemistry&lt;/i&gt; highlights the latest progress in this field.&lt;/p&gt;&lt;p&gt;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.&lt;span&gt;&lt;sup&gt;3&lt;/sup&gt;&lt;/span&gt; Likewise, Onomura summarized the potential of halogen mediators for environmentally-benign and at the same time efficient alcohol oxidations.&lt;span&gt;&lt;sup&gt;4&lt;/sup&gt;&lt;/span&gt; Jiao and Mei showed the power of paired electrolysis for organic reactions with ideal resource-economy,&lt;span&gt;&lt;sup&gt;5&lt;/sup&gt;&lt;/span&gt; while Cheng outlined the challenges and benefits of water as a particularly benign reaction medium.&lt;span&gt;&lt;sup&gt;6&lt;/sup&gt;&lt;/span&gt; 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,&lt;span&gt;&lt;sup&gt;7&lt;/sup&gt;&lt;/span&gt; while Gosmini provided an overview on powerful transition metal-catalyzed electroreductive approachess for C−C bond formation.&lt;span&gt;&lt;sup&gt;8&lt;/sup&gt;&lt;/span&gt; On a different note, de Sarkar focused on electroreductive transformations involving C−C and C−O multiple bonds.&lt;span&gt;&lt;sup&gt;9&lt;/sup&gt;&lt;/span&gt; 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,&lt;span&gt;&lt;sup&gt;10&lt;/sup&gt;&lt;/span&gt; while Ackermann established C7-indole alkenylations based on rhodaelectrocatalysis.&lt;span&gt;&lt;sup&gt;11&lt;/sup&gt;&lt;/span&gt; The elegant design of an off/on switching enabled Kakiuchi to establish a one-pot cross-coupling/C−H bromination for bromoarylpyridines.&lt;span&gt;&lt;sup&gt;12&lt;/sup&gt;&lt;/span&gt; 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}