Cytokines play a central role in regulating cell communication and signal transduction, since they influence processes such as immunity, hematopoiesis, inflammatory disease, cancer, neurological disorders, and tissue healing. Notably, certain cytokines have been used clinically as protein therapeutics for conditions such as cancer, autoimmune diseases, and viral infections. Despite their therapeutic potential, cytokines often pose challenges, including side effects, stability constraints, and suboptimal pharmacokinetics. To address these limitations, there is growing interest in using diverse modalities to develop alternative cytokines with enhanced properties and therapeutic benefits. Of these modalities, effective high-throughput screening of macrocyclic peptides enabled by RNA-based catalysis has emerged as a promising candidate method for the development of alternative cytokines. Here, we focus on the development of cytokine alternatives using various approaches and explore prospects for their future use as therapeutic agents.
{"title":"Cytokine Mimetics with Various Modalities","authors":"Katsuya Sakai, Hiroki Sato, Kunio Matsumoto","doi":"10.1002/ijch.202300163","DOIUrl":"10.1002/ijch.202300163","url":null,"abstract":"<p>Cytokines play a central role in regulating cell communication and signal transduction, since they influence processes such as immunity, hematopoiesis, inflammatory disease, cancer, neurological disorders, and tissue healing. Notably, certain cytokines have been used clinically as protein therapeutics for conditions such as cancer, autoimmune diseases, and viral infections. Despite their therapeutic potential, cytokines often pose challenges, including side effects, stability constraints, and suboptimal pharmacokinetics. To address these limitations, there is growing interest in using diverse modalities to develop alternative cytokines with enhanced properties and therapeutic benefits. Of these modalities, effective high-throughput screening of macrocyclic peptides enabled by RNA-based catalysis has emerged as a promising candidate method for the development of alternative cytokines. Here, we focus on the development of cytokine alternatives using various approaches and explore prospects for their future use as therapeutic agents.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140980242","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}
Jing Xie, Meng-Wei Kan, Simon J. de Veer, Conan Wang, David J. Craik
Cyclotides are ultra-stable peptides originally discovered in plants based on their medicinal applications. Their natural function is as host defence agents. They are amenable to chemical synthesis for use as scaffolds for drug design applications. Cyclotides comprise ~30 amino acids and in addition to having a head-to-tail cyclic backbone, incorporate six conserved cystine residues connected in a cystine knot motif. The cyclic backbone and cystine knot contribute to their exceptional resistance to proteases or thermal denaturation, making them useful scaffolds for drug design applications. The backbone segments, or loops, between the conserved cysteine residues are amenable to combinatorial variation in native cyclotides and have also been used to incorporate selected bioactive peptide epitopes into a range of synthetic cyclotides and cyclotide-like scaffolds. In the past this was largely done via low throughput structure-based design approaches, but the discovery of novel cyclotide binders has been greatly enhanced by the use of combinatorial display approaches on cyclotide scaffolds using phage, bacterial, yeast and mRNA technologies, as reviewed herein.
{"title":"Display Technologies for Expanding the Pharmaceutical Applications of Cyclotides","authors":"Jing Xie, Meng-Wei Kan, Simon J. de Veer, Conan Wang, David J. Craik","doi":"10.1002/ijch.202400010","DOIUrl":"10.1002/ijch.202400010","url":null,"abstract":"<p>Cyclotides are ultra-stable peptides originally discovered in plants based on their medicinal applications. Their natural function is as host defence agents. They are amenable to chemical synthesis for use as scaffolds for drug design applications. Cyclotides comprise ~30 amino acids and in addition to having a head-to-tail cyclic backbone, incorporate six conserved cystine residues connected in a cystine knot motif. The cyclic backbone and cystine knot contribute to their exceptional resistance to proteases or thermal denaturation, making them useful scaffolds for drug design applications. The backbone segments, or loops, between the conserved cysteine residues are amenable to combinatorial variation in native cyclotides and have also been used to incorporate selected bioactive peptide epitopes into a range of synthetic cyclotides and cyclotide-like scaffolds. In the past this was largely done via low throughput structure-based design approaches, but the discovery of novel cyclotide binders has been greatly enhanced by the use of combinatorial display approaches on cyclotide scaffolds using phage, bacterial, yeast and mRNA technologies, as reviewed herein.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140883251","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}
Rylan R. Watkins, Arundhati Kavoor, Prof. Karin Musier-Forsyth
Aminoacyl-tRNA synthetases (aaRSs) maintain translational fidelity by ensuring the formation of correct aminoacyl-tRNA pairs. Numerous point mutations in human aaRSs have been linked to disease phenotypes. Structural studies of aaRSs from human pathogens encoding unique domains support these enzymes as potential candidates for therapeutics. Studies have shown that the identity of tRNA pools in cells changes between different cell types and under stress conditions. While traditional radioactive aminoacylation analyses can determine the effect of disease-causing mutations on aaRS function, these assays are not amenable to drug discovery campaigns and do not take into account the variability of the intracellular tRNA pools. Here, we review modern techniques to characterize aaRS activity in vitro and in cells. The cell-based approaches analyse the aminoacyl-tRNA pool to observe trends in aaRS activity and fidelity. Taken together, these approaches allow high-throughput drug screening of aaRS inhibitors and systems-level analyses of the dynamic tRNA population under a variety of conditions and disease states.
{"title":"Strategies for Detecting Aminoacylation and Aminoacyl-tRNA Editing in vitro and in Cells","authors":"Rylan R. Watkins, Arundhati Kavoor, Prof. Karin Musier-Forsyth","doi":"10.1002/ijch.202400009","DOIUrl":"10.1002/ijch.202400009","url":null,"abstract":"<p>Aminoacyl-tRNA synthetases (aaRSs) maintain translational fidelity by ensuring the formation of correct aminoacyl-tRNA pairs. Numerous point mutations in human aaRSs have been linked to disease phenotypes. Structural studies of aaRSs from human pathogens encoding unique domains support these enzymes as potential candidates for therapeutics. Studies have shown that the identity of tRNA pools in cells changes between different cell types and under stress conditions. While traditional radioactive aminoacylation analyses can determine the effect of disease-causing mutations on aaRS function, these assays are not amenable to drug discovery campaigns and do not take into account the variability of the intracellular tRNA pools. Here, we review modern techniques to characterize aaRS activity <i>in vitro</i> and in cells. The cell-based approaches analyse the aminoacyl-tRNA pool to observe trends in aaRS activity and fidelity. Taken together, these approaches allow high-throughput drug screening of aaRS inhibitors and systems-level analyses of the dynamic tRNA population under a variety of conditions and disease states.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 8-9","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140883430","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}
In this study, the occurrence of Diels–Alder reaction of cyclopentadiene yielding dicyclopentadiene within a confined closed space provided by octa acid (OA) in water at room temperature is established. The Diels–Alder reaction within the OA capsule occurs at least 2000 times faster than in water. Catalysis of Diels–Alder reaction by hosts such as cyclodextrin, cucurbituril, and Fujita's Pd nano–host occurs in water. Despite their similarity, these three hosts provide an open environment where the reactant molecules are exposed to aqueous environment. The only fully closed host known to catalyze the Diels–Alder reaction in water is OA. Although Rebek's host is established to catalyze Diels–Alder reaction it occurs in an organic solvent. The closed environment explored in this presentation provides an opportunity to better understand the origin of non–covalent catalysis in a restricted space and in water. Because the product binds stronger than the reactant, disappointingly, the capsule can't be recycled. We recognize that this aspect needs to be addressed for the OA capsule to become synthetically useful. We are in the process of understanding the origin of catalysis and finding ways to make reaction recyclable.
本研究证实,在室温下,环戊二烯在辛酸(OA)提供的密闭空间内发生 Diels-Alder 反应,生成二环戊二烯。在 OA 胶囊内发生的 Diels-Alder 反应比在水中至少快 2000 倍。环糊精、葫芦素和藤田钯纳米宿主等宿主在水中催化 Diels-Alder 反应。尽管它们很相似,但这三种宿主提供了一个开放的环境,使反应物分子暴露在水环境中。已知唯一能在水中催化 Diels-Alder 反应的全封闭宿主是 OA。虽然 Rebek 的宿主可以催化 Diels-Alder 反应,但它是在有机溶剂中发生的。本报告探讨的封闭环境为我们提供了一个机会,使我们能够更好地了解在受限空间和水中非共价催化作用的起源。令人失望的是,由于生成物比反应物的结合力更强,胶囊无法循环使用。我们认识到,要使 OA 胶囊在合成方面发挥作用,就必须解决这个问题。我们正在了解催化的起源,并寻找使反应可回收的方法。
{"title":"Confinement as a Tool in Chemistry: Accelerated Intracapsular Dimerization of Cyclopentadiene in Water","authors":"Amal Sam Sunny, Prof. Vaidhyanathan Ramamurthy","doi":"10.1002/ijch.202400017","DOIUrl":"10.1002/ijch.202400017","url":null,"abstract":"<p>In this study, the occurrence of Diels–Alder reaction of cyclopentadiene yielding dicyclopentadiene within a confined closed space provided by octa acid (OA) in water at room temperature is established. The Diels–Alder reaction within the OA capsule occurs at least 2000 times faster than in water. Catalysis of Diels–Alder reaction by hosts such as cyclodextrin, cucurbituril, and Fujita's Pd nano–host occurs in water. Despite their similarity, these three hosts provide an open environment where the reactant molecules are exposed to aqueous environment. The only <span>fully</span> closed host known to catalyze the Diels–Alder reaction in water is OA. Although Rebek's host is established to catalyze Diels–Alder reaction it occurs in an organic solvent. The closed environment explored in this presentation provides an opportunity to better understand the origin of non–covalent catalysis in a restricted space and in water. Because the product binds stronger than the reactant, disappointingly, the capsule can't be recycled. We recognize that this aspect needs to be addressed for the OA capsule to become synthetically useful. We are in the process of understanding the origin of catalysis and finding ways to make reaction recyclable.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 6-7","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140835296","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}
Shengyi Fei, Zheng William Fang, Prof. Boxuan Simen Zhao
This review navigates the evolving landscape of N6-methyladenosine (m6A) research approaches, emphasizing the importance of advanced technology in understanding RNA epigenetics. Beginning with the fundamentals of m6A and the need for high- throughput methods, the investigation progresses from low-throughput approaches to high-throughput technologies, encompassing antibody-dependent and antibody-free sequencing methods, as well as nanopore-based direct mRNA sequencing and computation methods for m6A detection. Spatial techniques and imaging tools for m6A are also introduced in addition. The discussion of their special applications emphasizes the biological significance of absolute quantification, single-nucleotide resolution, single-molecule detection, and single-cell profiling. The review concludes with a vision of ideal approaches that combine current technologies for comprehensive m6A sequencing, with the potential to further our understanding of gene regulation, cellular diversity, and their roles in health and disease.
{"title":"Unraveling the RNA Tapestry: A Symphony of Innovations in m6A Research Technology","authors":"Shengyi Fei, Zheng William Fang, Prof. Boxuan Simen Zhao","doi":"10.1002/ijch.202400014","DOIUrl":"https://doi.org/10.1002/ijch.202400014","url":null,"abstract":"<p>This review navigates the evolving landscape of N6-methyladenosine (m6A) research approaches, emphasizing the importance of advanced technology in understanding RNA epigenetics. Beginning with the fundamentals of m6A and the need for high- throughput methods, the investigation progresses from low-throughput approaches to high-throughput technologies, encompassing antibody-dependent and antibody-free sequencing methods, as well as nanopore-based direct mRNA sequencing and computation methods for m6A detection. Spatial techniques and imaging tools for m6A are also introduced in addition. The discussion of their special applications emphasizes the biological significance of absolute quantification, single-nucleotide resolution, single-molecule detection, and single-cell profiling. The review concludes with a vision of ideal approaches that combine current technologies for comprehensive m6A sequencing, with the potential to further our understanding of gene regulation, cellular diversity, and their roles in health and disease.</p>","PeriodicalId":14686,"journal":{"name":"Israel Journal of Chemistry","volume":"64 3-4","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/ijch.202400014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140648115","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}
Chemical Biology of Nucleic Acid Modifications Issue editor: Chun-Xiao Song, Guifang Jia, Seraphine Wegner, and Chengqi Yi. The cover picture highlights Chuan He's wide-ranging research contributions across chemical biology, nucleic acid chemistry, biology, and epigenetics. His work focused on understanding DNA and RNA modifications in gene regulation. His groundbreaking discovery of reversible RNA modification revealed a new mode of gene regulation by RNA alongside DNA — and protein-based epigenetic mechanisms, leading to the emergence of the epitranscriptomics field.