ACS Chemical Biology最新文献

PEGylated ATP-Independent Luciferins for Noninvasive High-Sensitivity High-Speed Bioluminescence Imaging.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-23 DOI: 10.1021/acschembio.4c00601

Xiaodong Tian, Yiyu Zhang, Hui-Wang Ai

{"title":"PEGylated ATP-Independent Luciferins for Noninvasive High-Sensitivity High-Speed Bioluminescence Imaging.","authors":"Xiaodong Tian, Yiyu Zhang, Hui-Wang Ai","doi":"10.1021/acschembio.4c00601","DOIUrl":"https://doi.org/10.1021/acschembio.4c00601","url":null,"abstract":"Bioluminescence imaging (BLI) is a powerful, noninvasive imaging method for animal studies. NanoLuc luciferase and its derivatives are attractive bioluminescent reporters recognized for their efficient photon production and ATP independence. However, utilizing them for animal imaging poses notable challenges. Low substrate solubility has been a prominent problem, limiting in vivo brightness, while the susceptibility of luciferins to auto-oxidation by molecular oxygen in air increases handling complexity and poses an obstacle to obtaining consistent results. To address these issues, we developed a range of caged PEGylated luciferins with increased auto-oxidation resistance and water solubility of up to 25 mM, resulting in substantial in vivo bioluminescence increases in mouse models. This advancement has created the brightest and most sensitive luciferase-luciferin combination, enabling high-speed video-rate imaging of freely moving mice with brain-expressed luciferase. These innovative substrates offer new possibilities for investigating a wide range of biological processes and are poised to become invaluable resources for chemical, biological, and biomedical fields.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recognition of Noncanonical RNA Base Pairs Using Triplex-Forming Peptide Nucleic Acids.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-22 DOI: 10.1021/acschembio.4c00662

Sara Farshineh Saei, Vladislavs Baskevics, Martins Katkevics, Eriks Rozners

{"title":"Recognition of Noncanonical RNA Base Pairs Using Triplex-Forming Peptide Nucleic Acids.","authors":"Sara Farshineh Saei, Vladislavs Baskevics, Martins Katkevics, Eriks Rozners","doi":"10.1021/acschembio.4c00662","DOIUrl":"https://doi.org/10.1021/acschembio.4c00662","url":null,"abstract":"Noncanonical base pairs play an important role in enabling the structural and functional complexity of RNA. Molecular recognition of such motifs is challenging because of their diversity, significant deviation from the Watson-Crick structures, and dynamic behavior, resulting in alternative conformations of similar stability. Triplex-forming peptide nucleic acids (PNAs) have emerged as excellent ligands for the recognition of Watson-Crick base-paired double helical RNA. The present study extends the recognition potential of PNA to RNA helices having noncanonical GoU, AoC, and tandem GoA/AoG base pairs. The purines of the noncanonical base pairs formed M+·GoU, T·AoC, M+·GoA, and T·AoG Hoogsteen triples of similar or slightly reduced stability compared to the canonical M+·G-C and T·A-U triples. Recognition of pyrimidines was more challenging. While the P·CoA triple was only slightly less stable than P·C-G, the E nucleobase did not form a stable triple with U of the UoG wobble pair. Molecular dynamics simulations suggested the formation of expected Hoogsteen hydrogen bonds for all of the stable triples. Collectively, these results expand the scope of triple helical recognition to noncanonical structures and sequence motifs common in biologically relevant RNAs.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Breaking the Myth of Enzymatic Azoreduction.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-21 DOI: 10.1021/acschembio.4c00779

Yu-Ju Peng, Bing Xu, Steven E Rokita

{"title":"Breaking the Myth of Enzymatic Azoreduction.","authors":"Yu-Ju Peng, Bing Xu, Steven E Rokita","doi":"10.1021/acschembio.4c00779","DOIUrl":"https://doi.org/10.1021/acschembio.4c00779","url":null,"abstract":"Flavin-dependent azoreductases have been applied to a wide range of tasks from decolorizing numerous azo dyes to releasing azo-conjugated prodrugs. A general narrative reiterated in much of the literature suggests that this enzyme promotes sequential reduction of both the azo-containing substrate and its corresponding hydrazo product to release the aryl amine components while consuming two equivalents of NAD(P)H. Indeed, such aryl amines can be formed by incubation of certain azo compounds with azoreductases, but the nature of the substrates capable of this apparent azo bond lysis remained unknown. We have now prepared a set of azobenzene derivatives and characterized their turnover and products after treatment with azoreductase from Escherichia coli to discover the structural basis regulating aryl amine formation. Without resonance donation by aryl substituents, reduction ceases at the hydrazo product. This indicates that azoreductases do not act on the hydrazo bond. Instead, aryl amine formation depends on a spontaneous hydrazo bond lysis that is promoted by resonance stabilization and subsequent reduction of the quinone-like intermediate by azoreductase. Experimental and computational approaches confirm the substituent dependence of this process. With knowledge of this requirement, full release of aryl amines from azo-conjugates can now be designed and applied with confidence.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dual-Performing Vinyltetrazine for Rapid, Selective Bioconjugation and Functionalization of Cysteine Proteins.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-21 DOI: 10.1021/acschembio.4c00610

Mengyang Chang, Hang Xu, Yue Dong, Giri Gnawali, Fangchao Bi, Wei Wang

{"title":"Dual-Performing Vinyltetrazine for Rapid, Selective Bioconjugation and Functionalization of Cysteine Proteins.","authors":"Mengyang Chang, Hang Xu, Yue Dong, Giri Gnawali, Fangchao Bi, Wei Wang","doi":"10.1021/acschembio.4c00610","DOIUrl":"https://doi.org/10.1021/acschembio.4c00610","url":null,"abstract":"Although methods for Cys-specific bioconjugation and functionalization of proteins have been developed and widely utilized in biomolecule engineering and therapeutic development, reagents for this purpose are generally designed to accomplish bioconjugation only. Consequently, additional clickable groups must be attached to these reagents to accomplish functionalization. Herein, we describe a new, simple, dual-performing bioconjugation-functionalization reagent, VMeTz, which possesses an electron-withdrawing tetrazine (Tz) substituted vinyl (V) moiety to serve as both a Michael receptor for selective conjugation with Cys and a site for click with TCO derivatives to introduce functionality. Critically, VMeTz contains a methyl group that prevents the formation of multiple Tz-containing Cys-adducts. Reactions of VMeTz with Cys-containing peptides and proteins both in vitro and in live cells produce single stable Michael adducts with high selectivity. Moreover, the Cys-VMeTz peptide and protein conjugates undergo facile click reactions with TCO-functionalized reagents for labeling and protein profiling. Furthermore, VMeTz selectively activates and delivers the TCO-caged toxic substances Dox and PROTAC ARV-771 to cancer cells to produce therapeutic effects that are comparable to those of the parent drugs. Collectively, the studies demonstrate that VMeTz is a useful reagent for therapeutically significant Cys-specific protein bioconjugation and functionalization.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142870571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Photoresponsive Adenosine Derivatives for the Optical Control of Adenosine A_2A Receptors in Living Cells. 用于活细胞中腺苷 A2A 受体光学控制的光致腺苷衍生物

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-11-11 DOI: 10.1021/acschembio.4c00583

Harufumi Suzuki, Tomohiro Doura, Yuya Matsuba, Yuma Matsuoka, Tsuyoshi Araya, Hidetsugu Asada, So Iwata, Shigeki Kiyonaka

引用次数: 0

The TRIM33 Bromodomain Recognizes Histone Lysine Lactylation. TRIM33 溴odomain 可识别组蛋白赖氨酸乳化。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-11-18 DOI: 10.1021/acschembio.4c00248

Raymundo Nuñez, Paul F W Sidlowski, Erica A Steen, Sarah L Wynia-Smith, Daniel J Sprague, Robert F Keyes, Brian C Smith

{"title":"The TRIM33 Bromodomain Recognizes Histone Lysine Lactylation.","authors":"Raymundo Nuñez, Paul F W Sidlowski, Erica A Steen, Sarah L Wynia-Smith, Daniel J Sprague, Robert F Keyes, Brian C Smith","doi":"10.1021/acschembio.4c00248","DOIUrl":"10.1021/acschembio.4c00248","url":null,"abstract":"Histone lysine lactylation (Kla) regulates inflammatory gene expression in activated macrophages and mediates the polarization of inflammatory (M1) to reparative (M2) macrophages. However, the molecular mechanisms and key protein players involved in Kla-mediated transcriptional changes are unknown. As Kla is structurally similar to lysine acetylation (Kac), which is bound by bromodomains, we hypothesized that bromodomain-containing proteins bind histone Kla. Here, we screened 28 recombinantly expressed bromodomains for binding to histone Kla peptides via AlphaScreen assays. TRIM33 was the sole bromodomain tested that bound histone Kla peptides. TRIM33 attenuates inflammatory genes during late-stage macrophage activation; thus, TRIM33 provides a potential link between histone Kla and macrophage polarization. Orthogonal biophysical techniques, including isothermal titration calorimetry and protein-detected nuclear magnetic resonance, confirmed the submicromolar binding affinity of the TRIM33 bromodomain to both Kla and Kac histone post-translational modifications. Sequence alignments of human bromodomains revealed a unique glutamic acid residue within the TRIM33 binding pocket that we found confers TRIM33 specificity for binding Kla compared with other bromodomains. Molecular modeling of interactions of Kla with the TRIM33 bromodomain binding pocket and site-directed mutagenesis of glutamic acid confirmed the critical role of this residue in the selective recognition of Kla by TRIM33. Collectively, our findings implicate TRIM33, a bromodomain-containing protein, as a novel reader of histone Kla, potentially bridging the gap between histone Kla and macrophage polarization. This study enhances our understanding of the regulatory role of histone Kla in macrophage-mediated inflammation and offers insights into the underlying structural and biophysical mechanisms.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2418-2428"},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aptamer and N-Degron Ensemble (AptaGron) as a Target Protein Degradation Strategy.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-12-04 DOI: 10.1021/acschembio.4c00536

Mohammad Faysal Al Mazid, Olha Shkel, Eunteg Ryu, Jiwon Kim, Kyung Ho Shin, Yun Kyung Kim, Hyun Suk Lim, Jun-Seok Lee

引用次数: 0

Switchback RNA. Switchback RNA。

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-09-24 DOI: 10.1021/acschembio.4c00518

Bharath Raj Madhanagopal, Hannah Talbot, Arlin Rodriguez, Arun Richard Chandrasekaran

{"title":"Switchback RNA.","authors":"Bharath Raj Madhanagopal, Hannah Talbot, Arlin Rodriguez, Arun Richard Chandrasekaran","doi":"10.1021/acschembio.4c00518","DOIUrl":"10.1021/acschembio.4c00518","url":null,"abstract":"Intricately designed DNA and RNA motifs guide the assembly of robust and functional nucleic acid nanostructures. In this work, we present a globally left-handed RNA motif with two parallel strands called switchback RNA and report its assembly, biophysical, and biochemical characterization. Switchback RNA can be assembled in buffers without Mg2+, with improved thermal stability in buffers containing Mg2+, Na+, or K+. Differences in the binding of small molecules to switchback RNA and conventional RNA indicate design-based approaches for small molecule loading on RNA nanostructures. Further, the differential affinity of the two component strands in switchback or conventional duplex conformations allows for toehold-less strand displacement. Enzyme studies showed that the switchback and conventional RNA structures have similar levels of nuclease resistance. These results provide insights for employing switchback RNA as a structural motif in RNA nanotechnology. Our observation that RNA strands with switchback complementarity can form stable complexes at low magnesium concentrations encourages studies into the potential occurrence of switchback RNA in nature.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2394-2398"},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

PhOxi-seq Detects Enzyme-Dependent m²G in Multiple RNA Types.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-11-29 DOI: 10.1021/acschembio.4c00548

Marie Klimontova, Kimberley Chung Kim Chung, Han Zhang, Tony Kouzarides, Andrew J Bannister, Ryan Hili

引用次数: 0

Biosynthetic Incorporation of Non-native Aryl Acid Building Blocks into Peptide Products Using Engineered Adenylation Domains.

IF 3.5 2区生物学

ACS Chemical Biology Pub Date : 2024-12-20 Epub Date: 2024-12-02 DOI: 10.1021/acschembio.4c00663

Fumihiro Ishikawa, Maya Nohara, Akimasa Miyanaga, Satoki Kuramoto, Natsuki Miyano, Shumpei Asamizu, Fumitaka Kudo, Hiroyasu Onaka, Tadashi Eguchi, Genzoh Tanabe

{"title":"Biosynthetic Incorporation of Non-native Aryl Acid Building Blocks into Peptide Products Using Engineered Adenylation Domains.","authors":"Fumihiro Ishikawa, Maya Nohara, Akimasa Miyanaga, Satoki Kuramoto, Natsuki Miyano, Shumpei Asamizu, Fumitaka Kudo, Hiroyasu Onaka, Tadashi Eguchi, Genzoh Tanabe","doi":"10.1021/acschembio.4c00663","DOIUrl":"10.1021/acschembio.4c00663","url":null,"abstract":"Nonribosomal peptides (NRPs), one of the most widespread secondary metabolites in nature, with therapeutically significant activities, are biosynthesized by modular nonribosomal peptide synthetases (NRPSs). Aryl acids contribute to the structural diversity of NRPs as well as nonproteinogenic amino acids and keto acids. We previously confirmed that a single Asn-to-Gly substitution in the 2,3-dihydroxybenzoic acid-activating adenylation (A) domain EntE involved in enterobactin biosynthesis accepts monosubstituted benzoic acid derivatives with nitro, cyano, bromo, and iodo functionalities at the 2 or 3 positions. Here, we showed that the mutant EntE (N235G) accommodates various disubstituted benzoic acid derivatives with halogen, methyl, methoxy, nitro, and cyano functionalities at the 2 and 3 positions and monosubstituted benzoic acid with an alkyne at the 3 position. Structural analysis of the mutant EntE (N235G) with nonhydrolyzable aryl-AMP analogues using 3-chloro-2-methylbenzoic acid and 3-prop-2-ynoxybenzoic acid revealed how bulky 3-chloro-2-methylbenzoic acid and clickable 3-prop-2-ynoxybenzoic acid are recognized by enlarging the substrate-binding pocket of the enzyme. When engineered EntE mutants were coupled with enterobactin and vibriobactin biosynthetic enzymes, 3-hydroxybenzoic acid-, salicylic acid-, and 3-bromo-2-fluorobenzoic acid-containing peptides were produced as early stage intermediates, highlighting the potential of NRP biosynthetic pathway engineering for constructing diverse aryl acid-containing metabolites.","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"2569-2579"},"PeriodicalIF":3.5,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0