ACS Publications最新文献_第6页

Cell-Penetrating Cyclic and Disulfide-Rich Peptides Are Privileged Molecular Scaffolds for Intracellular Targeting.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-04-01 Epub Date: 2025-03-13 DOI: 10.1021/acs.biochem.4c00845

Sónia Troeira Henriques, Nicole Lawrence, Meng-Wei Kan, Lara R Malins, David J Craik

{"title":"Cell-Penetrating Cyclic and Disulfide-Rich Peptides Are Privileged Molecular Scaffolds for Intracellular Targeting.","authors":"Sónia Troeira Henriques, Nicole Lawrence, Meng-Wei Kan, Lara R Malins, David J Craik","doi":"10.1021/acs.biochem.4c00845","DOIUrl":"10.1021/acs.biochem.4c00845","url":null,"abstract":"Peptides that have a head-to-tail cyclic backbone tend to be more stable than linear peptides, as do peptides that contain one or more cross-linking disulfide bond. Some of these cyclic and/or disulfide rich peptides have been reported to penetrate cells. These include peptides from a wide range of natural sources, including plants, spiders, crabs, and humans. In this review we describe the structures and biophysical properties of a selected set of such peptides that have been studied in our laboratories. We further describe how they can be engineered to enhance their stability and cellular uptake, and to fine-tune selective cell entry and activity toward intracellular therapeutic targets. Examples of targets described include intracellular protein-protein interactions implicated in cancer, intracellular malarial parasites and intracellular bacterial targets. In addition to the important advances being made with these nature-inspired peptides, the rapid strides in machine learning and artificial intelligence seen over recent years promise to accelerate the use of de novo design methods to produce peptides that are able to pass through biological membranes. We describe examples where such approaches have been used to design macrocyclic peptides and peptide-drug conjugates that can penetrate cell membranes and even have significant oral bioavailability in some cases.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1437-1449"},"PeriodicalIF":2.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Impact of Cancer-Associated PKM2 Mutations on Enzyme Activity and Allosteric Regulation: Structural and Functional Insights into Metabolic Reprogramming.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-04-01 Epub Date: 2025-03-13 DOI: 10.1021/acs.biochem.5c00009

Saurabh Upadhyay, Mohit Bhardwaj, Sivakumar Prasanth Kumar, Shumayila Khan, Ashwani Kumar, Md Imtaiyaz Hassan

{"title":"Impact of Cancer-Associated PKM2 Mutations on Enzyme Activity and Allosteric Regulation: Structural and Functional Insights into Metabolic Reprogramming.","authors":"Saurabh Upadhyay, Mohit Bhardwaj, Sivakumar Prasanth Kumar, Shumayila Khan, Ashwani Kumar, Md Imtaiyaz Hassan","doi":"10.1021/acs.biochem.5c00009","DOIUrl":"10.1021/acs.biochem.5c00009","url":null,"abstract":"Mammalian pyruvate kinase M2 (PKM2) is a key regulator of glycolysis and is highly expressed in proliferative tissues including tumors. Mutations in PKM2 have been identified in various cancers, but their effects on enzyme activity and regulation are not fully understood. This study investigates the structural and functional effects of cancer-associated PKM2 mutations on enzyme kinetics, allosteric regulation, and oligomerization. Using computational modeling, X-ray crystallography, and biochemical assays, we demonstrated how these mutations impact PKM2 activity, substrate binding, and allosteric activation via fructose-1,6-bisphosphate (FBP), contributing to altered enzyme function. In this study, we characterized four cancer-associated PKM2 mutations (P403A, C474S, R516C, and L144P) using computational, structural, and biochemical approaches. Computational modeling revealed disruptions in allosteric signaling pathways, particularly affecting the communication between regulatory sites and the active site. X-ray crystallography demonstrated local conformational changes in the hinge and FBP-binding regions, leading to a shift from the active tetrameric state to a less active dimeric state, particularly in the C474S and R516C mutants. The mutants exhibited reduced maximal velocity, reduced substrate affinity, and altered activation by the allosteric activator fructose-1,6-bisphosphate (FBP). Under alkaline pH conditions, mimicking the tumor microenvironment, these mutations further destabilized the PKM2 oligomeric state, favoring the formation of lower-order species. Our findings suggest that PKM2 is highly sensitive to mutations, and these alterations may contribute to metabolic reprogramming in cancer cells by impairing its enzymatic regulation.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1463-1475"},"PeriodicalIF":2.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Chemically Engineered Peptide Efficiently Blocks Malaria Parasite Entry into Red Blood Cells.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-04-01 Epub Date: 2025-03-10 DOI: 10.1021/acs.biochem.4c00465

Anamika Biswas, Akash Narayan, Suman Sinha, Kalyaneswar Mandal

引用次数: 0

Thyroglossal duct cyst with hoarseness as the sole symptom and an intralaryngeal extension masquerading as a laryngeal mass: Clinical experience and literature review. 以声音嘶哑为唯一症状的甲状舌管囊肿和伪装成喉部肿块的咽内扩展：临床经验和文献综述。

IF 16.4 1区化学

Accounts of Chemical Research Pub Date : 2025-04-01 Epub Date: 2022-06-22 DOI: 10.1177/01455613221100030

Yang-Yang Bao, Yan-Ping Ge, Xiong-Jian Zhang, Yu Guo, Li-Bo Dai, Shui-Hong Zhou, Wei Lin

{"title":"Thyroglossal duct cyst with hoarseness as the sole symptom and an intralaryngeal extension masquerading as a laryngeal mass: Clinical experience and literature review.","authors":"Yang-Yang Bao, Yan-Ping Ge, Xiong-Jian Zhang, Yu Guo, Li-Bo Dai, Shui-Hong Zhou, Wei Lin","doi":"10.1177/01455613221100030","DOIUrl":"10.1177/01455613221100030","url":null,"abstract":"A thyroglossal duct cyst is the most common congenital disease in the neck. There are two age groups usually associated with thyroglossal duct cysts: 1-11 years in children and 30-60 years in adults. These midline neck masses are typically located anteriorly in the neck, inferior to the hyoid bone. We report an extremely rare case of an intralaryngeal thyroglossal duct cyst without a neck mass, presenting with hoarseness as the sole symptom. A 64-year-old man presented with a 3-month history of hoarseness. On physical examination, no neck mass or swelling was observed during cervical palpation. Laryngostroboscopy revealed a large submucosal mass in the right glottis and supraglottis, and mobility of the right vocal cord was restricted. Surgery was performed via an external approach to completely resect the cyst, together with the middle part of the hyoid bone. Histopathologic examination of the cyst led to a diagnosis of thyroglossal duct cyst. The patient recovered well and his voice returned to normal. Attention should be paid to the occurrence of rare types of thyroglossal duct cyst in unusual clinical sites. Adequate radiological examinations should be performed, and reading the computed tomography or magnetic resonance imaging scans carefully before surgery is important to avoid misdiagnosis.","PeriodicalId":1,"journal":{"name":"Accounts of Chemical Research","volume":" ","pages":"NP172-NP177"},"PeriodicalIF":16.4,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40179002","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}

引用次数: 0

Design of Mimetic Antibodies Targeting the SARS-CoV-2 Spike Glycoprotein Based on the GB1 Domain: A Molecular Simulation and Experimental Study.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-04-01 Epub Date: 2025-03-17 DOI: 10.1021/acs.biochem.4c00671

Anderson A E Santo, Aline Reis, Anderson A Pinheiro, Paulo I da Costa, Gustavo T Feliciano

{"title":"Design of Mimetic Antibodies Targeting the SARS-CoV-2 Spike Glycoprotein Based on the GB1 Domain: A Molecular Simulation and Experimental Study.","authors":"Anderson A E Santo, Aline Reis, Anderson A Pinheiro, Paulo I da Costa, Gustavo T Feliciano","doi":"10.1021/acs.biochem.4c00671","DOIUrl":"10.1021/acs.biochem.4c00671","url":null,"abstract":"In the context of fast and significant technological transformations, it is natural for innovative artificial intelligence (AI) methods to emerge for the design of bioactive molecules. In this study, we demonstrated that the design of mimetic antibodies (MA) can be achieved using a combination of software and algorithms traditionally employed in molecular simulation. This combination, organized as a genetic algorithm (GA), has the potential to address one of the main challenges in the design of bioactive molecules: GA convergence occurs rapidly due to the careful selection of initial populations based on intermolecular interactions at antigenic surfaces. Experimental immunoenzymatic tests prove that the GA successfully optimized the molecular recognition capacity of one of the MA. One of the significant results of this study is the discovery of new structural motifs, which can be designed in an original and innovative way based on the MA structure itself, eliminating the need for preexisting databases. Through the GA developed in this study, we demonstrated the application of a new protocol capable of guiding experimental methods in the development of new bioactive molecules.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1541-1549"},"PeriodicalIF":2.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646484","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Ionic Coating of siRNA Polyplexes with cRGD-PEG-Hyaluronic Acid To Modulate Serum Stability and In Vivo Performance.

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-04-01 Epub Date: 2025-03-18 DOI: 10.1021/acs.biochem.4c00650

Victoria C Vetter, Mina Yazdi, Irene Gialdini, Jana Pöhmerer, Johanna Seidl, Miriam Höhn, Don C Lamb, Ernst Wagner

{"title":"Ionic Coating of siRNA Polyplexes with cRGD-PEG-Hyaluronic Acid To Modulate Serum Stability and In Vivo Performance.","authors":"Victoria C Vetter, Mina Yazdi, Irene Gialdini, Jana Pöhmerer, Johanna Seidl, Miriam Höhn, Don C Lamb, Ernst Wagner","doi":"10.1021/acs.biochem.4c00650","DOIUrl":"10.1021/acs.biochem.4c00650","url":null,"abstract":"Efficient delivery of siRNA-based polyplexes to tumors remains a major challenge. Nonspecific interactions in the bloodstream, limited circulation time, and nontargeted biodistribution hamper sufficient tumor accumulation. To address these challenges, we developed an ionic hyaluronic acid (HA) coating to shield sequence-defined oligoaminoamide-based polyplexes. This coating should shield the positive polyplex surface charge, thus reducing nonspecific interactions and enhancing serum stability. Additionally, we modified the HA coating with the cyclic RGDfK (cRGD) peptide to specifically target tumor endothelial cells (TECs). Optionally, a polyethylene glycol (PEG) spacer was also introduced to improve ligand presentation on the polyplex surface. The HA-coated polyplexes exhibited favorable physicochemical properties, including a negative zeta potential and effective siRNA retention within the polyplex, which was not adversely affected by PEG or cRGD modification. In vitro analyses revealed that these polyplexes not only enhanced tumor cell association and preserved the high transfection efficiency of plain cationic polyplexes but also exhibited coating-dependent cellular internalization, as evidenced by a competitive inhibition experiment. Even in the presence of serum, the HA-coated polyplexes encapsulated siRNA effectively, exhibited suitable particle sizes, and maintained a high gene silencing efficiency. In vivo studies involving intravenous administration into Neuro2a tumor-bearing mice showed that the HA coating, particularly when modified with PEG and cRGD, significantly increased the tumor accumulation of polyplexes. HA-PEG-cRGD-shielded polyplexes exhibited significantly enhanced in vivo gene silencing in tumors compared with plain polyplexes. Collectively, our results indicate a superior performance of HA-coated polyplexes in terms of stability and cellular uptake, both in vitro and in vivo.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1509-1529"},"PeriodicalIF":2.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Correction to "N-Type Polyoxadiazole Conductive Polymer Binders Derived High-Performance Silicon Anodes Enabled by Crosslinking Metal Cations".

IF 8.3 2区材料科学

ACS Applied Materials & Interfaces Pub Date : 2025-04-01 DOI: 10.1021/acsami.5c04679

Zhaomei Sun, Jiadeng Zhu, Chen Yang, Qibao Xie, Yan Jiang, Kaixiang Wang, Mengjin Jiang

引用次数: 0

Vibrational Analysis Based on Cavity-Enhanced Raman Spectroscopy: Cyclohexane.

IF 2.7 2区化学

The Journal of Physical Chemistry A Pub Date : 2025-03-31 DOI: 10.1021/acs.jpca.4c07709

Qing-Ying Yang, Qin Yang, Yi-Fan Song, An-Wen Liu, Jin Wang, Yan Tan, Yu R Sun, Shui-Ming Hu

引用次数: 0

Cluster Structure and Ordering in the Nucleation and Growth of Binary Molecular Mixtures.

IF 2.8 2区化学

The Journal of Physical Chemistry B Pub Date : 2025-03-31 DOI: 10.1021/acs.jpcb.5c00430

Joseph Gregory Z Cabinta, Earl Adrian D R Hans, Roosevelt T Tabag, Johnrob Y Bantang, Ricky B Nellas

{"title":"Cluster Structure and Ordering in the Nucleation and Growth of Binary Molecular Mixtures.","authors":"Joseph Gregory Z Cabinta, Earl Adrian D R Hans, Roosevelt T Tabag, Johnrob Y Bantang, Ricky B Nellas","doi":"10.1021/acs.jpcb.5c00430","DOIUrl":"https://doi.org/10.1021/acs.jpcb.5c00430","url":null,"abstract":"A complete understanding of aerosol formation remains elusive due to the microscopic scale and transient occurrence of nucleation. This process is further complicated by the multicomponent nature of atmospheric nucleating systems in which the properties of conucleating compounds influence the affinity of molecules to cluster. Molecular dynamics simulations were performed to investigate homogeneous vapor-liquid nucleation and growth of six binary mixtures composed of water, n-nonane, 1-butanol, and methanol. Structural analyses were performed to understand the dynamic configurations generated from binary nuclei. Geometric structure analysis revealed that clusters were found to be more spherical with increasing cluster size, while composition analysis revealed that more miscible species had less mole fraction variability from an equimolar composition. Radial density profiling and cluster snapshots revealed structural features that were dependent on the miscibility of the nucleating pairs. Homogeneous mixing was observed in n-nonane/1-butanol and water-methanol due to their miscibility. Meanwhile, systems with partial miscibility (water/1-butanol, water/methanol, 1-butanol/methanol, n-nonane/methanol), exhibited preferential ordering into core-shell structures. In water/n-nonane, simultaneous unary nucleation was observed, leading to lens-on-sphere configuration. Microstructure analysis also revealed internal fragmentation within core-shell motifs of water/1-butanol and 1-butanol/methanol. These findings have serious implications in nucleation theories, which lead to valuable insights for the nucleation of naturally occurring multicomponent systems in the atmosphere.","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unifying the Absolute Configuration of Dibenzopyrrocoline Alkaloids with Relative Configuration Revision of Cryptowolinol and Description of Isocryptaustoline from Cryptocarya oubatchensis.

IF 3.3 2区生物学

Journal of Natural Products Pub Date : 2025-03-31 DOI: 10.1021/acs.jnatprod.4c01315

Rany B Mbeng Obame, Sidney Gallard, Sacha Gibert, Jean-François Gallard, Solenn Ferron, Blandine Séon-Méniel, Guillaume Bernadat, Mehdi A Beniddir, Pierre Le Pogam

{"title":"Unifying the Absolute Configuration of Dibenzopyrrocoline Alkaloids with Relative Configuration Revision of Cryptowolinol and Description of Isocryptaustoline from Cryptocarya oubatchensis.","authors":"Rany B Mbeng Obame, Sidney Gallard, Sacha Gibert, Jean-François Gallard, Solenn Ferron, Blandine Séon-Méniel, Guillaume Bernadat, Mehdi A Beniddir, Pierre Le Pogam","doi":"10.1021/acs.jnatprod.4c01315","DOIUrl":"https://doi.org/10.1021/acs.jnatprod.4c01315","url":null,"abstract":"Dibenzopyrrocoline alkaloids, found in lauraceous and hernandiaceous plants, have been studied since the 1950s. The absolute configuration of these alkaloids, including cryptaustoline, has been a topic of debate due to conflicting studies. Having in our laboratory some authentic samples of dibenzopyrrocoline-type Cryptocarya alkaloids, we decided to reinvestigate their absolute configuration using modern spectroscopic techniques along with TDDFT calculations. The NMR reinvestigation of the authentic sample of cryptowolinol led us to revise its relative configuration using ML-J-DP4 and DP4+ analyses. Moreover, the absolute configuration of all dibenzopyrrocoline alkaloids reported to date benefitted from a complete re-evaluation based on a comparison with TDDFT-SR and TDDFT-ECD predictions leading to a unified absolute configuration. At last, this patrimonial reinvestigation unveiled a historical sample corresponding to a heretofore unpublished dibenzopyrrocoline alkaloid, which we named isocryptaustoline. The reisolation of this molecule from the total alkaloid extract of Cryptocarya oubatchensis makes it a genuine natural product.","PeriodicalId":47,"journal":{"name":"Journal of Natural Products ","volume":" ","pages":""},"PeriodicalIF":3.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750272","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