Peptide Science最新文献_第4页

A network pharmacology approach to explore the molecular mechanism of active peptide ingredients of Carapax Trionycis on liver fibrosis 采用网络药理学方法探讨龙爪草活性肽成分抗肝纤维化的分子机制

4区生物学

Peptide Science Pub Date : 2023-10-19 DOI: 10.1002/pep2.24335

Zhibin Yan, Guangyu Zhao, Qihao Lin, Guiping Zhuang, Jiayi Zhu, Juan Jin

{"title":"A network pharmacology approach to explore the molecular mechanism of active peptide ingredients of <i>Carapax Trionycis</i> on liver fibrosis","authors":"Zhibin Yan, Guangyu Zhao, Qihao Lin, Guiping Zhuang, Jiayi Zhu, Juan Jin","doi":"10.1002/pep2.24335","DOIUrl":"https://doi.org/10.1002/pep2.24335","url":null,"abstract":"Abstract Carapax Trionycis is a traditional Chinese medicine and it has been clear that oligo‐peptides from Carapax Trionycis extract (CTP) are the main active substances for the treatment of liver diseases. However, little is known about the mechanism of CTP against liver fibrosis. Here, network pharmacology combined with molecular docking were performed to identify the in‐silico molecular mechanism and the potential targets for CTP to ameliorate liver fibrosis. We collected eight active peptides ingredients that published in public databases and predicted the targets. Liver fibrosis related genes were acquired from the GeneCards and DisGeNET platform. Then, we identified a total of 52 peptides‐liver fibrosis‐related genes. KEGG and GO enrichment analyses indicated that these targets are significantly enriched in relaxin signaling pathway, IL‐17 signaling pathway, TNF signaling pathway. We identified the top 10 genes with high centrality measures from the network by CytoHubba, including CASP3, AKT1, IL1B, MMP9, and PTGS2. The molecular docking between these hub genes and the corresponding CTP was performed in GRAMM and visualized by PyMOL. Our results provide an important reference and scientific basis for treating liver fibrosis with CTP.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"64 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135779743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Investigating the interaction of azobenzene moiety on the aromatic amino acid tryptophan 研究偶氮苯部分与芳香氨基酸色氨酸的相互作用

4区生物学

Peptide Science Pub Date : 2023-10-13 DOI: 10.1002/pep2.24334

Charnette Frederic, Gregory R. Wiedman

引用次数: 0

Bioactive peptides against angiotensin‐converting enzyme I: An in silico study 抗血管紧张素转换酶I的生物活性肽:一项计算机研究

4区生物学

Peptide Science Pub Date : 2023-09-23 DOI: 10.1002/pep2.24332

Antistio Alvíz‐Amador, Neyder Contreras‐Puentes, Johana Márquez‐Lázaro

引用次数: 0

Generation and study of antibodies against two triangular trimers derived from Aβ Aβ两种三角形三聚体抗体的生成与研究

4区生物学

Peptide Science Pub Date : 2023-09-18 DOI: 10.1002/pep2.24333

Adam G. Kreutzer, Ryan J. Malonis, Chelsea Marie T. Parrocha, Karen Tong, Gretchen Guaglianone, Jennifer T. Nguyen, Michelle N. Diab, Jonathan R. Lai, James S. Nowick

{"title":"Generation and study of antibodies against two triangular trimers derived from Aβ","authors":"Adam G. Kreutzer, Ryan J. Malonis, Chelsea Marie T. Parrocha, Karen Tong, Gretchen Guaglianone, Jennifer T. Nguyen, Michelle N. Diab, Jonathan R. Lai, James S. Nowick","doi":"10.1002/pep2.24333","DOIUrl":"https://doi.org/10.1002/pep2.24333","url":null,"abstract":"Abstract Monoclonal antibodies (mAbs) that target the β‐amyloid peptide (Aβ) are important Alzheimer's disease research tools and are now being used as Alzheimer's disease therapies. Conformation‐specific mAbs that target oligomeric and fibrillar Aβ assemblies are of particular interest, as these assemblies are associated with Alzheimer's disease pathogenesis and progression. This article reports the generation of rabbit mAbs against two different triangular trimers derived from Aβ. These antibodies are the first mAbs generated against Aβ oligomer mimics in which the high‐resolution structures of the oligomers are known. We describe the isolation of the mAbs using single B‐cell sorting of peripheral blood mononuclear cells (PBMCs) from immunized rabbits, the selectivity of the mAbs for the triangular trimers, the immunoreactivity of the mAbs with aggregated Aβ 42 , and the immunoreactivity of the mAbs in brain tissue from the 5xFAD Alzheimer's disease mouse model. The characterization of these mAbs against structurally defined trimers derived from Aβ enhances understanding of antibody‐amyloid recognition and may benefit the development of diagnostics and immunotherapies in Alzheimer's disease.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135155463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

A compositional view comparing modern biological condensates and primitive phase‐separated compartment 现代生物凝析物与原始相分离隔室的组成比较

IF 2.4 4区生物学

Peptide Science Pub Date : 2023-08-30 DOI: 10.1002/pep2.24331

Selene M. C. Cannelli, Ritvik Gupta, Tan Nguyen, Arunava Poddar, Srishti Sharma, Prachiti V. Vithole, Tony Z. Jia

{"title":"A compositional view comparing modern biological condensates and primitive phase‐separated compartment","authors":"Selene M. C. Cannelli, Ritvik Gupta, Tan Nguyen, Arunava Poddar, Srishti Sharma, Prachiti V. Vithole, Tony Z. Jia","doi":"10.1002/pep2.24331","DOIUrl":"https://doi.org/10.1002/pep2.24331","url":null,"abstract":"Liquid–liquid phase separation (LLPS) is a process that often occurs due to binding between oppositely charged biopolymers, and has gained increasing attention recently due to their ubiquity in biological systems and ability to direct essential cellular processes. However, while these discoveries in biology are recent, the field of origins of life has been investigating LLPS for nearly 100 years, ever since the first suggestions by Oparin and Haldane that primitive LLPS could have been precursors to the first cells on Earth. Since then, a significant amount of work has been done to elucidate different primitive LLPS systems that could have been relevant as protocellular models. Given the structural similarities between primitive LLPS and modern membraneless organelles, there may even be an evolutionary link between the two, although this remains a question to be answered. Nevertheless, in order to answer this, a source that compares compositional aspects of modern biological condensates and primitive LLPS is necessary. Here, we first focus on membraneless organelles composed of intrinsically disordered proteins (IDPs) and nucleic acids. Then, as a parallel, we explore primitive membraneless compartments composed of simple biopolymers such as short peptides and nucleic acids. This is followed by a discussion of how the first biomolecules on Earth may have originated, analyzing the environmental and chemical conditions that could have favored primitive LLPS processes. Finally, we directly compare composition of modern biological condensates and primitive phase‐separated compartments, further discussing the potential of primitive IDPs on early Earth, but also the evolution from membraneless to membrane‐bound cells. This review aims to provide a compositional comparison of modern and primitive phase‐separated structures in order to help researchers in both fields understand the current state of knowledge, how this knowledge evolved, and the current gaps that need to be further addressed.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44488885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

An in vitro evaluation of the biocompatibility of proline‐alanine‐serine peptides compared with polyethylene glycol and polyglycerol 脯氨酸-丙氨酸-丝氨酸肽与聚乙二醇和聚甘油生物相容性的体外评价

IF 2.4 4区生物学

Peptide Science Pub Date : 2023-08-11 DOI: 10.1002/pep2.24330

Qianyu Zhang, Hongjing Chen, Huali Chen

引用次数: 0

Theoretical study of CHYMO32 peptide obtained by in silico fragmentation of the escapin protein isolated from marine hare Aplysia californica: A prediction for antimicrobial activity 从加州海兔Aplysia californica分离的escain蛋白的计算机裂解获得CHYMO32肽的理论研究：抗菌活性的预测

IF 2.4 4区生物学

Peptide Science Pub Date : 2023-08-01 DOI: 10.1002/pep2.24329

Macley Silva Cardoso, J. M. Boeira

{"title":"Theoretical study of CHYMO32 peptide obtained by in silico fragmentation of the escapin protein isolated from marine hare Aplysia californica: A prediction for antimicrobial activity","authors":"Macley Silva Cardoso, J. M. Boeira","doi":"10.1002/pep2.24329","DOIUrl":"https://doi.org/10.1002/pep2.24329","url":null,"abstract":"The scenario involving the alarming growth of bacterial resistance has never been more worrying. Increasingly selective and sophisticated bacterial strains resistant to traditional antibiotics are a threat to the health system worldwide. Therefore, antimicrobial peptides (AMPs) represent a promising path in the fight against multidrug‐resistant pathogens. Here, using an in silico methodology, employing robust software, the present study aims to analyze the chymo32 peptide, obtained by enzymatic fragmentation of the escapin protein to test its possible antibacterial effects, correlating them with their physical–chemical nature. In this study, we used in silico predictions such as structural prediction, physicochemical properties, hemolytic activity, and prediction of activity for immunomodulation. Among the 378 peptide fragments obtained from the original protein, chymo32 was the only peptide selected in the field of screenings involving sequence length, cationicity, hydrophobicity, and prediction of antibacterial activity. The physical–chemical properties of chymo32 are promising, as well as its prediction as AMP. The immunomodulation predictions showed no immunogenic potential, which indicates greater safety in the posterior steps in vitro, also highlighting the absence of hemolytic activity, one of the main problems associated with AMPs in the therapeutic clinic.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49146729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Toward a broad‐spectrum peptide‐based inhibitor of small multidrug resistance efflux pumps 小型多药耐药外排泵广谱肽基抑制剂的研究

IF 2.4 4区生物学

Peptide Science Pub Date : 2023-07-23 DOI: 10.1002/pep2.24327

Chloe J. Mitchell, Kha M. Nguyen, C. Deber

引用次数: 0

Bicyclic peptides: Paving the road for therapeutics of the future 双环肽：为未来的治疗方法铺平道路

IF 2.4 4区生物学

Peptide Science Pub Date : 2023-07-09 DOI: 10.1002/pep2.24326

S. Ullrich, Christoph Nitsche

引用次数: 0

An in‐silico‐based study identified peptide inhibitors that can block the egression of the monkeypox virus by inhibiting the p37 protein target 一项基于计算机的研究确定了肽抑制剂，可以通过抑制p37蛋白靶点来阻断猴痘病毒的传播

IF 2.4 4区生物学

Peptide Science Pub Date : 2023-07-04 DOI: 10.1002/pep2.24325

Swati Singh, Varshita Srivastava, P. Godara, H. Banavath, Harshita Tak, Arya Nayak, D. Kumari, B. Naik, D. Prusty

{"title":"An in‐silico‐based study identified peptide inhibitors that can block the egression of the monkeypox virus by inhibiting the p37 protein target","authors":"Swati Singh, Varshita Srivastava, P. Godara, H. Banavath, Harshita Tak, Arya Nayak, D. Kumari, B. Naik, D. Prusty","doi":"10.1002/pep2.24325","DOIUrl":"https://doi.org/10.1002/pep2.24325","url":null,"abstract":"Monkeypox is a zoonotic disease caused by the Poxviridiea family virus Monkeypox. According to the Centers for Disease Control and Prevention, 70,420 monkeypox virus infections had been reported in 107 countries as of October 6, 2022. New studies have concluded that the monkeypox outbreak is caused by a strain with a unique mutation, increasing the possibility that the virus may develop resistance to current medicines by accumulating mutations in therapeutic targets. As peptide‐based therapeutics impede the drug target through multiple interactions, it may offer a better therapeutic solution to the possible drug resistance issue related to monkeypox treatment. Therefore, in this work, we screened an antiviral peptide library, the CPP site 2.0 database, against the p37 target protein using molecular docking approaches. The p37 is required for the viral pathogen's successful egression and spread. The allergenicity and physicochemical properties of the peptides were thoroughly analyzed before the molecular docking studies for selecting druggable candidates. The interactions of the peptides bearing the highest docking score were validated further by using molecular dynamics (MD) simulation studies. Our investigation revealed that two cell‐penetrating peptides of the CPP site 2.0 database might effectively prevent the egression and spread of the MPXV by inhibiting p37. Following more testing, these peptides can be explored in developing peptide‐based therapies against the MPX therapy.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43220124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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: 1