Accounts of Chemical Research最新文献

{"title":"Skeletal Editing Strategies Driven by Total Synthesis.","authors":"Sojung F Kim, Charis Amber, G Logan Bartholomew, Richmond Sarpong","doi":"10.1021/acs.accounts.5c00174","DOIUrl":"10.1021/acs.accounts.5c00174","url":null,"abstract":"<p><p>ConspectusSingle-atom skeletal editing strategies that precisely modify the core frameworks of molecules have the potential to streamline and accelerate organic synthesis by enabling conceptually simple, but otherwise synthetically challenging, retrosynthetic disconnections. In contrast to broader skeletal remodeling and rearrangement strategies, these methodologies more specifically target single-atom changes with high selectivity, even within complex molecules such as natural products or pharmaceuticals. For the past several years, our laboratory has developed several skeletal editing methodologies, including single-atom ring contractions, expansions, and transpositions of both saturated and unsaturated heterocycles, as well as other carbon scaffolds. This Account details the evolution of \"skeletal editing logic\" within the context of our extensive work on natural product total synthesis.Early work in the Sarpong group leveraged metal-mediated C-C bond cleavage of in situ-generated strained intermediates to accomplish total syntheses of natural products, such as the icetexane diterpenoids and cyathane diterpenes. Continuing our focus on leveraging C-C bond cleavage through \"break-it-to-make-it\" strategies, we then developed carvone remodeling strategies to access a variety of terpenoids (including longiborneol sesquiterpenoids, phomactins, and xishacorenes) from hydroxylated pinene derivatives. In applying this skeletal remodeling and C-C cleavage framework to alkaloid natural products, such as the preparaherquimides and lycodine-type alkaloids, we recognized that single-atom changes to the saturated nitrogen-containing rings within these natural products would enable the direct conversion between distinct but structurally related natural product families. Thus, we began developing methods that selectively modify the core frameworks of <i>N</i>-heterocycles; this focus led to our work on the deconstructive fluorination and diversification of piperidines and ultimately to our recent body of work on direct, single-atom core framework modifications (single-atom skeletal editing). In the context of saturated heterocycles, we developed photomediated enantioselective ring contractions of α-acylated motifs and reductive ring contractions of cyclic hydroxylamines. For unsaturated heterocycles, we have developed ring contractions of azines (e.g., pyrimidine to pyrazole), <sup>15</sup>N isotopic labeling of azines, and phototranspositions of indazoles to benzimidazoles. To direct our focus on reaction development, a cheminformatic analysis of heteroaromatic skeletal edits served to quantitatively inform which transformations would most significantly expand the accessible chemical space. Apart from heterocycles, we also reported single-nitrogen insertion through the reductive amination of carbonyl C-C bonds. Ultimately, the goal of this research is to develop mild and selective skeletal editing methodologies that can be applied to total synthesis an","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":" ","pages":"1786-1800"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144074832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":"58 11","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/arv058i011_1941466","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144427683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AI-Driven Antimicrobial Peptide Discovery: Mining and Generation","authors":"Paulina Szymczak, Wojciech Zarzecki, Jiejing Wang, Yiqian Duan, Jun Wang, Luis Pedro Coelho, Cesar de la Fuente-Nunez* and Ewa Szczurek*, ","doi":"10.1021/acs.accounts.0c0059410.1021/acs.accounts.0c00594","DOIUrl":"https://doi.org/10.1021/acs.accounts.0c00594https://doi.org/10.1021/acs.accounts.0c00594","url":null,"abstract":"<p >The escalating threat of antimicrobial resistance (AMR) poses a significant global health crisis, potentially surpassing cancer as a leading cause of death by 2050. Traditional antibiotic discovery methods have not kept pace with the rapidly evolving resistance mechanisms of pathogens, highlighting the urgent need for novel therapeutic strategies. In this context, antimicrobial peptides (AMPs) represent a promising class of therapeutics due to their selectivity toward bacteria and slower induction of resistance compared to classical, small molecule antibiotics. However, designing effective AMPs remains challenging because of the vast combinatorial sequence space and the need to balance efficacy with low toxicity. Addressing this issue is of paramount importance for chemists and researchers dedicated to developing next-generation antimicrobial agents.</p><p >Artificial intelligence (AI) presents a powerful tool to revolutionize AMP discovery. By leveraging AI, we can navigate the immense sequence space more efficiently, identifying peptides with optimal therapeutic properties. This Account explores the emerging application of AI in AMP discovery, focusing on two primary strategies: AMP mining, and AMP generation, as well as the use of discriminative methods as a valuable toolbox.</p><p >AMP mining involves scanning biological sequences to identify potential AMPs. Discriminative models are then used to predict the activity and toxicity of these peptides. This approach has successfully identified numerous promising candidates, which were subsequently validated experimentally, demonstrating the potential of AI in AMP design and discovery.</p><p >AMP generation, on the other hand, creates novel peptide sequences by learning from existing data through generative modeling. This class of models optimizes for desired properties, such as increased activity and reduced toxicity, potentially producing synthetic peptides that surpass naturally occurring ones. Despite the risk of generating unrealistic sequences, generative models hold the promise of accelerating the discovery of highly effective and highly novel and diverse AMPs.</p><p >In this Account, we describe the technical challenges and advancements in these AI-based approaches. We discuss the importance of integrating various data sources and the role of advanced algorithms in refining peptide predictions. Additionally, we highlight the future potential of AI to not only expedite the discovery process but also to uncover peptides with unprecedented properties, paving the way for next-generation antimicrobial therapies.</p><p >In conclusion, the synergy between AI and AMP discovery opens new frontiers in the fight against AMR. By harnessing the power of AI, we can design novel peptides that are both highly effective and safe, offering hope for a future where AMR is no longer a looming threat. Our paper underscores the transformative potential of AI in drug discovery, advocating for its continued in","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":"58 12","pages":"1831–1846 1831–1846"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.accounts.0c00594","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144296627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Phuong H. Le, Leo B. Zasada and Dianne J. Xiao*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":"58 11","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.accounts.5c00171","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144427723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterolanthanide Terephthalate Coordination Polymers: From the Fight against Counterfeiting to Plastic Waste Recycling.","authors":"Carole Daiguebonne, Chloé Blais, Kevin Bernot, Olivier Guillou","doi":"10.1021/acs.accounts.5c00190","DOIUrl":"10.1021/acs.accounts.5c00190","url":null,"abstract":"<p><p>ConspectusThe world's plastics production continues to grow and could triple by 2060. Unfortunately, only a small proportion of these plastics are currently recycled (around 30%). The remainder is incinerated (around 40%), causing high greenhouse gas emissions, or buried (around 30%), resulting in high levels of microplastic pollution. Ambitious national and international policies have been put in place to increase the proportion of recycled plastics, and major research efforts are underway to improve plastic recycling processes. Unfortunately, all recycling processes (chemical, physical, and biological) require batches of plastics to be recycled that are as homogeneous as possible. Rigorous waste sorting is therefore essential, and marking plastics with luminescent markers could provide a solution. It could also enable circular and short-loop recycling in which an object is recycled into an identical object.Heterolanthanide coordination polymers are particularly promising candidates for this application. They have demonstrated their effectiveness in the field of anticounterfeiting marking. However, their use in materials traceability requires other assets, such as markers with luminescence properties that are sufficiently different and sufficiently intense for them to be easily identified on a rapid sorting line, as laboratory analysis is no longer relevant for this application.To prepare such a range of compounds, it is necessary to master the mechanisms that govern luminescence properties. The choice of ligand and metal centers, crystal structure, and particle shaping all have a major influence on luminescence properties. Our group has been working on understanding these phenomena for some 20 years.Using as an example the family of heterolanthanide coordination polymers with general chemical formula [Ln₂(bdc)₃(H₂O)₄]_∞, where bdc^2- represents benzene-1,4-dicarboxylate, we wish to present here the various levers that can be used to modulate the emission colors and increase the luminescence intensity of heterolanthanide coordination polymers and describe a family of markers that can be used in the field of materials traceability. Beyond the choice of the metallic centers and of the ligands, markers can be designed in the form of core-shell particles, with an intermediate optically nonactive insulating shell that separates the core from the shell that are both made of optically active molecular alloys. Intermetallic energy transfers are therefore minimized, resulting in increased luminescence intensity and emission color modulation. In conclusion, we would like to draw up a rough sketch of what could be the markers used in the field of plastics traceability.</p>","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":" ","pages":"1801-1814"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Qidi Wang*,&nbsp;Chenglong Zhao and Marnix Wagemaker,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":"58 11","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.accounts.5c00074","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144427720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemical Strategies to Modulate and Manipulate RNA Epigenetic Modifications.","authors":"Liang Cheng","doi":"10.1021/acs.accounts.4c00844","DOIUrl":"10.1021/acs.accounts.4c00844","url":null,"abstract":"&lt;p&gt;&lt;p&gt;ConspectusRNA epigenetics has rapidly emerged as a key frontier in chemical biology, revealing that modifications to RNA bases and riboses can fine-tune essential cellular processes such as gene expression, translation, and metabolic homeostasis. Traditionally, researchers have relied on manipulating the \"writers,\" \"erasers,\" and \"readers\" of RNA modifications─&lt;i&gt;i.e.&lt;/i&gt;, protein cofactors─to alter and study these marks. Those enzyme-centric strategies, including small molecule inhibitors and CRISPR/Cas-based genetic perturbations, have been highly effective and are advancing in clinical applications. However, purely chemical approaches for installing, removing, or transforming RNA modifications without enzyme disturbance have offered distinct advantages, such as temporal control, reversibility, and bypassing compensatory biological feedback mechanisms that often arise with genetic or enzymatic inhibition. Every chemist should be concerned about RNA modifications, because they represent a striking intersection of molecular recognition, organic transformation, and cellular function. The ability to direct chemical reactivity at specific nucleosides in RNA can illuminate how individual modifications impact the overall gene regulation. Further, since improper RNA modification and damage patterns are implicated in cancer, metabolic disorders, and neurodegeneration, these chemical repair tools have potential as diagnostic and therapeutic interventions. Beyond medicine, agriculture also stands to benefit from chemical control of nucleoside-based plant hormones, possibly leading to improved crop productivity and resilience.In this &lt;i&gt;Account&lt;/i&gt;, we outline several innovative chemical strategies tailored to different classes of RNA modifications. Flavin-based bioorthogonal chemistry has enabled demethylation of &lt;i&gt;N&lt;/i&gt;&lt;sup&gt;6&lt;/sup&gt;-methyladenosine (m&lt;sup&gt;6&lt;/sup&gt;A) independent of endogenous demethylases, while oxidative bioorthogonal reactions can convert 5-methylcytidine (m&lt;sup&gt;5&lt;/sup&gt;C) into distinct formyl derivatives for labeling and sequencing. Nitrogen-oxide and photochemical routes provided access for the selective removal of the side chain of &lt;i&gt;N&lt;/i&gt;&lt;sup&gt;6&lt;/sup&gt;-isopentenyladenosine (i&lt;sup&gt;6&lt;/sup&gt;A), offering insights for both cell biology and plant hormone research. We also showcase how rationally designed small molecules can rewire complex RNA damage repair pathways, facilitating selective correction of vinyl-adduct lesions otherwise resistant to enzymatic repair. These purely chemical methods bypass the constraints of enzyme dependence, affording temporal precision (e.g., &lt;i&gt;via&lt;/i&gt; light activation) and site-selective modification or labeling of RNA. By strategically engineering reactivity, we have uncovered new epitranscriptomic phenomena, such as &lt;i&gt;in situ&lt;/i&gt; generation of non-native RNA modification, that offer fresh capabilities for cell imaging or targeted manipulation of plant callus development. Together, these discoveries sig","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":" ","pages":"1727-1741"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AI-Driven Antimicrobial Peptide Discovery: Mining and Generation","authors":"Paulina Szymczak, Wojciech Zarzecki, Jiejing Wang, Yiqian Duan, Jun Wang, Luis Pedro Coelho, Cesar de la Fuente-Nunez, Ewa Szczurek","doi":"10.1021/acs.accounts.0c00594","DOIUrl":"https://doi.org/10.1021/acs.accounts.0c00594","url":null,"abstract":"The escalating threat of antimicrobial resistance (AMR) poses a significant global health crisis, potentially surpassing cancer as a leading cause of death by 2050. Traditional antibiotic discovery methods have not kept pace with the rapidly evolving resistance mechanisms of pathogens, highlighting the urgent need for novel therapeutic strategies. In this context, antimicrobial peptides (AMPs) represent a promising class of therapeutics due to their selectivity toward bacteria and slower induction of resistance compared to classical, small molecule antibiotics. However, designing effective AMPs remains challenging because of the vast combinatorial sequence space and the need to balance efficacy with low toxicity. Addressing this issue is of paramount importance for chemists and researchers dedicated to developing next-generation antimicrobial agents.","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":"169 1","pages":""},"PeriodicalIF":18.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What is Editing?","authors":"Mark D. Levin, Richmond Sarpong, Alison E. Wendlandt","doi":"10.1021/acs.accounts.5c00268","DOIUrl":"https://doi.org/10.1021/acs.accounts.5c00268","url":null,"abstract":"Published as part of &lt;i&gt;Accounts of Chemical Research&lt;/i&gt; special issue “Skeletal and Stereochemical Editing”. Organic chemistry has an intimate connection with its applications, as synthesis remains the primary tool by which chemical space is navigated in the optimization of functional molecules. Medicinal chemists, for example, will prepare hundreds, if not thousands, of derivatives of promising lead compounds through iterative, parallel synthesis in order to identify the ideal compound to advance to the clinic. In the context of natural products, which have often proven to be valuable starting places for drug discovery, (1,2) the role of synthesis has been central, enabling the preparation of non-natural analogues inaccessible through semisynthesis by diverting from a totally synthetic route. This idea was eloquently captured by Danishefsky, who coined the term “molecular editing” to describe the synthesis of such analogues, essentially advocating for the application of medicinal chemistry principles even in targets as complex as epothilone B. (3) Szpilman and Carreira subsequently wrote an influential review which was responsible for the further proliferation of this coinage, bringing the original term into even broader circulation. (4) Recently, this term-of-art has taken on a very different valence─causing no small amount of confusion─because of a perspective shift in the role of chemical reactions in molecular optimization campaigns. (5−8) Parallel synthesis, though successful, has a fundamental mismatch with the underlying thought process that drives it, as even small changes to a target structure typically require &lt;i&gt;de novo&lt;/i&gt; synthesis. This tension has brought on a simple question: can we develop chemical reactions that represent direct analogues to common design strategies? This new movement has &lt;i&gt;also&lt;/i&gt; taken on the mantle of “molecular editing”, with distinct forms of optimization-mimicry developing into subfields in their own right: C–H functionalization, functional group interconversion, stereochemical modulation, and skeletal modification have all been encompassed under this redefined heading as flavors of &lt;i&gt;editing&lt;/i&gt;, especially when such transformations can be conducted with specificity on complex, late-stage compounds or at nontraditional sites of reactivity. (9−11) A challenge in this vernacular is that, taken at face value, the term molecular editing is synonymous with chemical reaction. It should be clear to even the most cynical reader, however, that not all reactions should be called edits. The above history is instructive here: the reactions that hew closest to the editing ideal are those whose changes are interpretable from a structure–activity relationship perspective. The starting material and product should form a matched molecular pair that a chemist could test to learn something about the landscape of their optimization. (12) The more changes made at once, the further one moves from interpretability. That i","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":"11 1","pages":""},"PeriodicalIF":18.3,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144201749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Liang Cheng*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":"58 11","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":16.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.accounts.4c00844","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144427687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}