首页 > 最新文献

Peptide Science最新文献

英文 中文
Peptides and peptidomimetics as therapeutic agents for Covid-19. 作为 Covid-19 治疗药物的肽和肽拟物。
IF 1.5 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-01-01 Epub Date: 2021-10-11 DOI: 10.1002/pep2.24245
Achyut Dahal, Jafrin Jobayer Sonju, Konstantin G Kousoulas, Seetharama D Jois

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Covid-19 pandemic has caused high morbidity and mortality rates worldwide. Virus entry into cells can be blocked using several strategies, including inhibition of protein-protein interactions (PPIs) between the viral spike glycoprotein and cellular receptors, as well as blocking of spike protein conformational changes that are required for cleavage/activation and fusogenicity. The spike-mediated viral attachment and entry into cells via fusion of the viral envelope with cellular membranes involve PPIs mediated by short peptide fragments exhibiting particular secondary structures. Thus, peptides that can inhibit these PPIs may be used as potential antiviral agents preventing virus entry and spread. This review is focused on peptides and peptidomimetics as PPI modulators and protease inhibitors against SARS-CoV-2.

严重急性呼吸系统综合征冠状病毒-2(SARS-CoV-2)Covid-19大流行在全球范围内造成了很高的发病率和死亡率。可采用多种策略阻止病毒进入细胞,包括抑制病毒尖峰糖蛋白与细胞受体之间的蛋白-蛋白相互作用(PPIs),以及阻止尖峰蛋白构象变化(裂解/活化和融合所需的构象变化)。尖峰蛋白介导的病毒附着和通过病毒包膜与细胞膜融合进入细胞的过程涉及由表现出特殊二级结构的短肽片段介导的 PPI。因此,能够抑制这些 PPIs 的多肽可用作潜在的抗病毒药物,防止病毒进入和传播。这篇综述主要介绍了作为 PPI 调节剂和蛋白酶抑制剂的肽类和拟肽类药物对 SARS-CoV-2 的作用。
{"title":"Peptides and peptidomimetics as therapeutic agents for Covid-19.","authors":"Achyut Dahal, Jafrin Jobayer Sonju, Konstantin G Kousoulas, Seetharama D Jois","doi":"10.1002/pep2.24245","DOIUrl":"10.1002/pep2.24245","url":null,"abstract":"<p><p>The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Covid-19 pandemic has caused high morbidity and mortality rates worldwide. Virus entry into cells can be blocked using several strategies, including inhibition of protein-protein interactions (PPIs) between the viral spike glycoprotein and cellular receptors, as well as blocking of spike protein conformational changes that are required for cleavage/activation and fusogenicity. The spike-mediated viral attachment and entry into cells via fusion of the viral envelope with cellular membranes involve PPIs mediated by short peptide fragments exhibiting particular secondary structures. Thus, peptides that can inhibit these PPIs may be used as potential antiviral agents preventing virus entry and spread. This review is focused on peptides and peptidomimetics as PPI modulators and protease inhibitors against SARS-CoV-2.</p>","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"114 1","pages":"e24245"},"PeriodicalIF":1.5,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8646791/pdf/PEP2-114-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10594771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Issue Information 问题信息
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2022-01-01 DOI: 10.1002/pep2.24257
{"title":"Issue Information","authors":"","doi":"10.1002/pep2.24257","DOIUrl":"https://doi.org/10.1002/pep2.24257","url":null,"abstract":"","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45932856","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
Computational design of stapled peptide inhibitor against SARS‐CoV‐2 receptor binding domain 抗SARS - CoV - 2受体结合域的钉接肽抑制剂的计算设计
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-12-30 DOI: 10.1002/pep2.24267
A. Choudhury, A. Maity, S. Chakraborty, R. Chakrabarti
Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) has been the cause of millions of deaths worldwide. Despite the development and administration of different vaccines, the situation is still worrisome as the virus is constantly mutating to produce newer variants some of which are highly infectious. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic‐based treatment for COVID‐19. The gateway of the virus to the host cell is mediated by the binding of the receptor binding domain (RBD) of the virus spike protein to the angiotensin‐converting enzyme 2 (ACE2) of the human cell. Therefore, the RBD of SARS‐CoV‐2 can be used as a target to design therapeutics. The α1 helix of ACE2, which forms direct contact with the RBD surface, has been used as a template in the current study to design stapled peptide therapeutics. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD‐ACE2 binding. Analyses of the mechanistic detail reveal that a reorganization of amino acids at the RBD‐ACE2 interface produces favorable enthalpy of binding whereas conformational restriction of the free peptide reduces the loss in entropy to result higher binding affinity. The understanding of the relation of the nature of the stapling agent with their binding affinity opens up the avenue to explore stapled peptides as therapeutic against SARS‐CoV‐2.
自2019年首次发现以来,严重急性呼吸综合征冠状病毒2 (SARS - CoV - 2)已导致全球数百万人死亡。尽管开发和使用了不同的疫苗,但情况仍然令人担忧,因为病毒不断变异,产生新的变体,其中一些具有高度传染性。这就迫切需要了解感染机制,从而设计基于治疗的COVID - 19治疗方案。病毒进入宿主细胞的通道是通过病毒刺突蛋白的受体结合域(RBD)与人细胞的血管紧张素转换酶2 (ACE2)结合介导的。因此,SARS - CoV - 2的RBD可以作为设计治疗方法的靶点。ACE2的α1螺旋与RBD表面形成直接接触,在目前的研究中已被用作设计钉接肽疗法的模板。通过计算机模拟,估计了六种钉接肽与RBD结合的机理和热力学。其中,含有两种内酰胺装订剂的一种具有结合亲和力,足以克服RBD - ACE2的结合。机理分析表明,RBD - ACE2界面上氨基酸的重组产生了有利的结合焓,而自由肽的构象限制减少了熵的损失,从而产生更高的结合亲和力。了解钉接剂的性质与其结合亲和力之间的关系,为探索钉接肽治疗SARS - CoV - 2开辟了道路。
{"title":"Computational design of stapled peptide inhibitor against SARS‐CoV‐2 receptor binding domain","authors":"A. Choudhury, A. Maity, S. Chakraborty, R. Chakrabarti","doi":"10.1002/pep2.24267","DOIUrl":"https://doi.org/10.1002/pep2.24267","url":null,"abstract":"Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) has been the cause of millions of deaths worldwide. Despite the development and administration of different vaccines, the situation is still worrisome as the virus is constantly mutating to produce newer variants some of which are highly infectious. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic‐based treatment for COVID‐19. The gateway of the virus to the host cell is mediated by the binding of the receptor binding domain (RBD) of the virus spike protein to the angiotensin‐converting enzyme 2 (ACE2) of the human cell. Therefore, the RBD of SARS‐CoV‐2 can be used as a target to design therapeutics. The α1 helix of ACE2, which forms direct contact with the RBD surface, has been used as a template in the current study to design stapled peptide therapeutics. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD‐ACE2 binding. Analyses of the mechanistic detail reveal that a reorganization of amino acids at the RBD‐ACE2 interface produces favorable enthalpy of binding whereas conformational restriction of the free peptide reduces the loss in entropy to result higher binding affinity. The understanding of the relation of the nature of the stapling agent with their binding affinity opens up the avenue to explore stapled peptides as therapeutic against SARS‐CoV‐2.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"113 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80623589","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: 4
Generation of inhibitory peptides for IKKε from a kinase‐focused phage library of helix‐loop‐helix peptides 从螺旋-环-螺旋肽的激酶聚焦噬菌体文库中产生IKKε抑制肽
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-12-15 DOI: 10.1002/pep2.24253
Kousuke Mihara, Natsumi Nakajima, I. Fujii, Daisuke Fujiwara
Conformationally constrained peptides are attracting attention as peptide‐based molecular tools in chemical biology and drug discovery because of their desirable properties such as high selectivity for target binding and stability toward proteolytic enzymes. We previously reported a protein kinase–focused helix‐loop‐helix (HLH) peptide library. The library was constructed by phage display and subsequent chemical modification with adenosine that was employed as an anchor molecule binding to the ATP‐binding pocket of kinase. Here, we discovered and characterized HLH peptides that bind to and inhibit the serine/threonine protein kinase IKKε, a member of the IκB kinase (IKK) family. Screening the library against IKKε identified de novo HLH peptides binding to the kinase. One of the peptides, IKK‐05, showed a high α‐helical content and inhibited IKKε with a mixed‐inhibition mechanism with respect to ATP. The adenosine‐tethering peptide Adc‐IKK‐05 demonstrated significantly enhanced enzyme inhibition activity, indicating a bivalency effect in binding to IKKε. In addition, Adc‐IKK‐05 showed the highest inhibitory activity against IKKε of the IKK family members and other families tested. The peptides obtained in this research can be developed as molecular tools to study the biological functions of IKKε and to obtain structural insights for the design of selective IKKε inhibitors.
构象受限肽作为化学生物学和药物发现中基于肽的分子工具,由于其理想的特性,如对靶标结合的高选择性和对蛋白水解酶的稳定性,引起了人们的关注。我们之前报道了一个蛋白激酶聚焦的螺旋-环-螺旋(HLH)肽库。该文库通过噬菌体展示和随后的腺苷化学修饰构建,腺苷被用作与激酶的ATP结合口袋结合的锚定分子。在这里,我们发现并表征了与丝氨酸/苏氨酸蛋白激酶IKKε(IκB激酶(IKK)家族成员)结合并抑制其的HLH肽。筛选针对IKKε的文库鉴定了与激酶结合的从头HLH肽。其中一种肽IKK‐05显示出高α螺旋含量,并通过对ATP的混合抑制机制抑制IKKε。腺苷束缚肽Adc‐IKK‐05表现出显著增强的酶抑制活性,表明与IKKε结合的二价效应。此外,Adc‐IKK‐05对IKK家族成员和其他受试家族的IKKε表现出最高的抑制活性。本研究中获得的肽可作为研究IKKε生物学功能的分子工具,并为设计选择性IKKε抑制剂获得结构见解。
{"title":"Generation of inhibitory peptides for IKKε from a kinase‐focused phage library of helix‐loop‐helix peptides","authors":"Kousuke Mihara, Natsumi Nakajima, I. Fujii, Daisuke Fujiwara","doi":"10.1002/pep2.24253","DOIUrl":"https://doi.org/10.1002/pep2.24253","url":null,"abstract":"Conformationally constrained peptides are attracting attention as peptide‐based molecular tools in chemical biology and drug discovery because of their desirable properties such as high selectivity for target binding and stability toward proteolytic enzymes. We previously reported a protein kinase–focused helix‐loop‐helix (HLH) peptide library. The library was constructed by phage display and subsequent chemical modification with adenosine that was employed as an anchor molecule binding to the ATP‐binding pocket of kinase. Here, we discovered and characterized HLH peptides that bind to and inhibit the serine/threonine protein kinase IKKε, a member of the IκB kinase (IKK) family. Screening the library against IKKε identified de novo HLH peptides binding to the kinase. One of the peptides, IKK‐05, showed a high α‐helical content and inhibited IKKε with a mixed‐inhibition mechanism with respect to ATP. The adenosine‐tethering peptide Adc‐IKK‐05 demonstrated significantly enhanced enzyme inhibition activity, indicating a bivalency effect in binding to IKKε. In addition, Adc‐IKK‐05 showed the highest inhibitory activity against IKKε of the IKK family members and other families tested. The peptides obtained in this research can be developed as molecular tools to study the biological functions of IKKε and to obtain structural insights for the design of selective IKKε inhibitors.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46074409","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
Unambiguous characterization of PEGylation site on human amylin by two‐dimensional nuclear magnetic resonance spectroscopy 二维核磁共振波谱对人胰淀素聚乙二醇化位点的模糊表征
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-12-11 DOI: 10.1002/pep2.24252
L. M. T. Lima, T. S. Araújo, M. Almeida
Amylin is a 37‐residue peptide hormone, which is co‐secreted with insulin and prevents postprandial spikes in blood glycemia by slowing gastric emptying and promoting satiety. Amylin is prone to aggregate into oligomers and amyloid fibrils, which is related to the onset of type 2 diabetes, and hampers its use as a biopharmaceutical. To overcome the instability and extend its in vivo half‐life it has been proposed the conjugation of amylin with polyethylene glycol (PEG) at the HNζ or the HNα amines of Lys1. Here we used two‐dimensional nuclear magnetic resonance spectra aiming the unambiguous identification of the site of covalent modification on amylin. The coupling of PEG causes both a substantial decrease in the chemical exchange of their HN and alterations in the chemical shifts at both the HN and the neighborhood hydrocarbon groups including CHα, CHδ and CHε of Lys1. Additional analysis of chemical shifts indicates alteration in the HNα solvent accessibility of residues Cys2, Asn3, Ala5, Cys7, and Gln10, and confirmed the presence of oxidized Cys2 and Cys7. We believe that the methodology described here is a reference for the characterization of chemical coupling of a number of biopharmaceuticals.
胰淀素是一种37 -残基肽激素,与胰岛素共同分泌,通过减缓胃排空和促进饱腹感来防止餐后血糖升高。胰淀素容易聚集成低聚物和淀粉样原纤维,这与2型糖尿病的发病有关,并阻碍了其作为生物制药的使用。为了克服其不稳定性和延长其体内半衰期,有人提出在Lys1的HNζ或HNα胺上与聚乙二醇(PEG)偶联。本研究利用二维核磁共振波谱技术对胰淀素共价修饰位点进行了明确的鉴定。聚乙二醇的偶联导致它们的HN的化学交换显著降低,并改变了HN和邻域烃基(包括Lys1的CHα、CHδ和CHε)的化学位移。进一步的化学位移分析表明,残基Cys2、Asn3、Ala5、Cys7和Gln10的HNα溶剂可及性发生了变化,并证实了氧化Cys2和Cys7的存在。我们相信,这里所描述的方法是一个参考的化学偶联的一些生物制药的表征。
{"title":"Unambiguous characterization of PEGylation site on human amylin by two‐dimensional nuclear magnetic resonance spectroscopy","authors":"L. M. T. Lima, T. S. Araújo, M. Almeida","doi":"10.1002/pep2.24252","DOIUrl":"https://doi.org/10.1002/pep2.24252","url":null,"abstract":"Amylin is a 37‐residue peptide hormone, which is co‐secreted with insulin and prevents postprandial spikes in blood glycemia by slowing gastric emptying and promoting satiety. Amylin is prone to aggregate into oligomers and amyloid fibrils, which is related to the onset of type 2 diabetes, and hampers its use as a biopharmaceutical. To overcome the instability and extend its in vivo half‐life it has been proposed the conjugation of amylin with polyethylene glycol (PEG) at the HNζ or the HNα amines of Lys1. Here we used two‐dimensional nuclear magnetic resonance spectra aiming the unambiguous identification of the site of covalent modification on amylin. The coupling of PEG causes both a substantial decrease in the chemical exchange of their HN and alterations in the chemical shifts at both the HN and the neighborhood hydrocarbon groups including CHα, CHδ and CHε of Lys1. Additional analysis of chemical shifts indicates alteration in the HNα solvent accessibility of residues Cys2, Asn3, Ala5, Cys7, and Gln10, and confirmed the presence of oxidized Cys2 and Cys7. We believe that the methodology described here is a reference for the characterization of chemical coupling of a number of biopharmaceuticals.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48293618","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
Leucine rich repeat kinase 2 (LRRK2) peptide modulators: Recent advances and future directions 富含亮氨酸重复激酶2(LRRK2)肽调节剂:最新进展和未来方向
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-12-11 DOI: 10.1002/pep2.24251
Leah G. Helton, H. Rideout, F. Herberg, E. Kennedy
Leucine rich repeat kinase 2 (LRRK2) is the most common genetic contributor to Parkinson's disease (PD), a complex neurodegenerative disorder affecting nearly 10 million people worldwide. Pathogenic mutations within LRRK2 often induce increased kinase activity, an effect that can be abolished with many small molecule inhibitors; however, these small molecule inhibitors are currently limited by their toxicities. Given the large and complex nature of LRRK2, more recent efforts have focused on protein–protein interactions (PPIs) involving LRRK2 and how they can contribute to PD. Here, we review recently resolved structures of LRRK2 and highlight unique interfaces driving both catalytic and non‐catalytic activities. Combining new structural information with established in vitro and in vivo data clarifies the role of PPIs in driving LRRK2‐mediated disease pathogenesis. Since constrained peptides and peptidomimetics have the potential to engage with elongated, hydrophobic interfaces that were previously considered “undruggable,” they may provide a unique handle for LRRK2 targeting. Here, we discuss the use of constrained peptides and peptidomimetics to target LRRK2 as a strategy to downregulate its pathological activity.
富亮氨酸重复激酶2 (LRRK2)是帕金森病(PD)最常见的遗传因素,帕金森病是一种复杂的神经退行性疾病,影响全球近1000万人。LRRK2内的致病性突变经常诱导激酶活性增加,这一效应可以用许多小分子抑制剂消除;然而,这些小分子抑制剂目前受到其毒性的限制。鉴于LRRK2的大而复杂的性质,最近更多的研究集中在涉及LRRK2的蛋白质-蛋白质相互作用(PPIs)以及它们如何促进PD。在这里,我们回顾了最近发现的LRRK2结构,并强调了驱动催化和非催化活性的独特界面。将新的结构信息与已建立的体外和体内数据相结合,阐明了ppi在驱动LRRK2介导的疾病发病机制中的作用。由于受限肽和拟肽具有与先前被认为“不可药物”的细长疏水界面结合的潜力,它们可能为LRRK2靶向提供独特的处理方法。在这里,我们讨论了使用受限肽和肽拟物靶向LRRK2作为下调其病理活性的策略。
{"title":"Leucine rich repeat kinase 2 (LRRK2) peptide modulators: Recent advances and future directions","authors":"Leah G. Helton, H. Rideout, F. Herberg, E. Kennedy","doi":"10.1002/pep2.24251","DOIUrl":"https://doi.org/10.1002/pep2.24251","url":null,"abstract":"Leucine rich repeat kinase 2 (LRRK2) is the most common genetic contributor to Parkinson's disease (PD), a complex neurodegenerative disorder affecting nearly 10 million people worldwide. Pathogenic mutations within LRRK2 often induce increased kinase activity, an effect that can be abolished with many small molecule inhibitors; however, these small molecule inhibitors are currently limited by their toxicities. Given the large and complex nature of LRRK2, more recent efforts have focused on protein–protein interactions (PPIs) involving LRRK2 and how they can contribute to PD. Here, we review recently resolved structures of LRRK2 and highlight unique interfaces driving both catalytic and non‐catalytic activities. Combining new structural information with established in vitro and in vivo data clarifies the role of PPIs in driving LRRK2‐mediated disease pathogenesis. Since constrained peptides and peptidomimetics have the potential to engage with elongated, hydrophobic interfaces that were previously considered “undruggable,” they may provide a unique handle for LRRK2 targeting. Here, we discuss the use of constrained peptides and peptidomimetics to target LRRK2 as a strategy to downregulate its pathological activity.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44970207","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 conserved β‐bulge glycine residue facilitates folding and increases stability of the mouse α‐defensin cryptdin‐4 保守的β凸起甘氨酸残基促进小鼠α防御素密码子蛋白-4的折叠并增加其稳定性
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-11-26 DOI: 10.1002/pep2.24250
R. Clark, Thanh Huyen Phan, A. Song, A. Ouellette, A. C. Conibear, K. Rosengren
Defensins are key components of both innate and adaptive immune responses to pathogens. Cryptdins are mouse alpha‐defensins that are secreted from Paneth cells in the small intestine and have disulfide‐stabilised structures and antibacterial activities against both Gram‐positive and Gram‐negative bacteria. The folding and three‐dimensional structures of alpha‐defensins are thought to depend on a conserved glycine residue that forms a β‐bulge. Here we investigated the role of this conserved glycine at position 19 of cryptdin‐4 (Crp4) in terms of the folding, structure and stability. A Crp4 variant with D‐Ala at position 19 folded efficiently, was stabilised by a large number of hydrogen bonds, and resisted proteolysis in simulated intestinal fluid. Although a variant with L‐Ala at position 19 was able to adopt the correct fold, it showed less efficient folding and was degraded more rapidly than the D‐Ala variant. These results demonstrate the key role that glycine residues can have in folding of bioactive peptides and can provide insights to guide design of stable antimicrobial peptides that fold efficiently.
防御素是对病原体的先天免疫反应和适应性免疫反应的关键组成部分。Cryptdins是小鼠α防御素,由小肠中的Paneth细胞分泌,具有二硫化物稳定的结构和对革兰氏阳性和革兰氏阴性细菌的抗菌活性。α防御素的折叠和三维结构被认为取决于形成β凸起的保守甘氨酸残基。在这里,我们研究了密码子蛋白-4(Crp4)19位的这种保守甘氨酸在折叠、结构和稳定性方面的作用。在19位具有D‐Ala的Crp4变体有效折叠,通过大量氢键稳定,并在模拟肠液中抵抗蛋白水解。尽管在19位具有L‐Ala的变体能够采用正确的折叠,但其折叠效率较低,降解速度比D‐Ala变体更快。这些结果证明了甘氨酸残基在生物活性肽折叠中的关键作用,并为指导有效折叠的稳定抗菌肽的设计提供了见解。
{"title":"A conserved β‐bulge glycine residue facilitates folding and increases stability of the mouse α‐defensin cryptdin‐4","authors":"R. Clark, Thanh Huyen Phan, A. Song, A. Ouellette, A. C. Conibear, K. Rosengren","doi":"10.1002/pep2.24250","DOIUrl":"https://doi.org/10.1002/pep2.24250","url":null,"abstract":"Defensins are key components of both innate and adaptive immune responses to pathogens. Cryptdins are mouse alpha‐defensins that are secreted from Paneth cells in the small intestine and have disulfide‐stabilised structures and antibacterial activities against both Gram‐positive and Gram‐negative bacteria. The folding and three‐dimensional structures of alpha‐defensins are thought to depend on a conserved glycine residue that forms a β‐bulge. Here we investigated the role of this conserved glycine at position 19 of cryptdin‐4 (Crp4) in terms of the folding, structure and stability. A Crp4 variant with D‐Ala at position 19 folded efficiently, was stabilised by a large number of hydrogen bonds, and resisted proteolysis in simulated intestinal fluid. Although a variant with L‐Ala at position 19 was able to adopt the correct fold, it showed less efficient folding and was degraded more rapidly than the D‐Ala variant. These results demonstrate the key role that glycine residues can have in folding of bioactive peptides and can provide insights to guide design of stable antimicrobial peptides that fold efficiently.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44169021","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
Issue Information 问题信息
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-11-01 DOI: 10.1002/pep2.24249
{"title":"Issue Information","authors":"","doi":"10.1002/pep2.24249","DOIUrl":"https://doi.org/10.1002/pep2.24249","url":null,"abstract":"","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43601671","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
Identifying blood‐brain barrier peptides by using amino acids physicochemical properties and features fusion method 利用氨基酸理化性质和特征融合方法鉴定血脑屏障肽
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-10-28 DOI: 10.1002/pep2.24247
Hongliang Zou
Blood‐brain barrier peptides (BBPs) play a promising role in current drug study of central nervous system diseases. Hence, it is an urgent need to rapidly and accurately discriminating BBPs from non‐BBPs. Experimental approaches are the first choice, however, these methods are expensive and take a lot of time. Thus, more and more researchers focused their attention on computational models. In current work, we developed a support vector machine (SVM) based model to identify BBPs. First, amino acids physicochemical properties were employed to represent peptide sequences, and Pearson's correlation coefficient (PCC) and maximal information coefficient (MIC) were applied to extract useful information. Then, similarity network fusion algorithm was utilized to integrate these two different kinds of features. Next, Fisher algorithm was used to pick out the discriminative features. Finally, these selected features were input into SVM for distinguishing BBPs from non‐BBPs. The proposed model achieved 100.00% and 89.47% classification accuracies on training and independent datasets, respectively. Additionally, we found that pK2 (NH3) property of amino acid plays a key role in discriminating BBPs from non‐BBPs. The results showed that our proposed method is effective, and achieved a significantly improvement in identifying BBPs, as compared with the state‐of‐the‐art approach. The Matlab codes and datasets are freely available at https://figshare.com/articles/online_resource/iBBPs_zip/14723766.
血脑屏障肽(BBPs)在当前中枢神经系统疾病的药物研究中发挥着很有前途的作用。因此,迫切需要快速准确地区分BBP和非BBP。实验方法是第一选择,然而,这些方法昂贵且耗时。因此,越来越多的研究人员将注意力集中在计算模型上。在目前的工作中,我们开发了一个基于支持向量机(SVM)的模型来识别BBP。首先,利用氨基酸的理化性质来表示肽序列,并利用Pearson相关系数(PCC)和最大信息系数(MIC)来提取有用信息。然后,利用相似性网络融合算法对这两种不同的特征进行融合。接下来,使用Fisher算法来提取判别特征。最后,将这些选择的特征输入SVM,以区分BBP和非BBP。所提出的模型在训练数据集和独立数据集上分别实现了100.00%和89.47%的分类准确率。此外,我们发现氨基酸的pK2(NH3)性质在区分BBP和非BBP中起着关键作用。结果表明,与现有技术相比,我们提出的方法是有效的,并在识别BBP方面取得了显著改进。Matlab代码和数据集可在https://figshare.com/articles/online_resource/iBBPs_zip/14723766.
{"title":"Identifying blood‐brain barrier peptides by using amino acids physicochemical properties and features fusion method","authors":"Hongliang Zou","doi":"10.1002/pep2.24247","DOIUrl":"https://doi.org/10.1002/pep2.24247","url":null,"abstract":"Blood‐brain barrier peptides (BBPs) play a promising role in current drug study of central nervous system diseases. Hence, it is an urgent need to rapidly and accurately discriminating BBPs from non‐BBPs. Experimental approaches are the first choice, however, these methods are expensive and take a lot of time. Thus, more and more researchers focused their attention on computational models. In current work, we developed a support vector machine (SVM) based model to identify BBPs. First, amino acids physicochemical properties were employed to represent peptide sequences, and Pearson's correlation coefficient (PCC) and maximal information coefficient (MIC) were applied to extract useful information. Then, similarity network fusion algorithm was utilized to integrate these two different kinds of features. Next, Fisher algorithm was used to pick out the discriminative features. Finally, these selected features were input into SVM for distinguishing BBPs from non‐BBPs. The proposed model achieved 100.00% and 89.47% classification accuracies on training and independent datasets, respectively. Additionally, we found that pK2 (NH3) property of amino acid plays a key role in discriminating BBPs from non‐BBPs. The results showed that our proposed method is effective, and achieved a significantly improvement in identifying BBPs, as compared with the state‐of‐the‐art approach. The Matlab codes and datasets are freely available at https://figshare.com/articles/online_resource/iBBPs_zip/14723766.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43903161","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: 3
Antimicrobial peptides provide wider coverage for targeting drug‐resistant bacterial pathogens 抗菌肽为靶向耐药细菌病原体提供了更广泛的覆盖范围
IF 2.4 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2021-10-01 DOI: 10.1002/pep2.24246
Anna S. Amiss, S. Henriques, N. Lawrence
We need new treatment options to control bacterial infections. Bacteria use several strategies to resist drug treatment, including modification of the drug target, and adaptation to a different lifestyle, such as intracellular niches within host cells. Drugs that act on diverse targets are less likely to induce resistance in bacteria, than current antibiotics acting on a single molecular target. Antimicrobial peptides have been explored as a new class of antibiotics because they selectively kill bacteria via a mechanism that involves recognition of the negatively charged microbial surface. Furthermore, antimicrobial peptides with cell‐penetrating properties can cross host cell membranes and target bacteria in the cytosol or sequestered in vesicles. Therefore, bacteria in intracellular niches are less capable of evading treatment and the likelihood of establishing drug resistance is further reduced. This review highlights the potential of antimicrobial peptides as alternative therapeutics to target bacterial pathogens in both extracellular and intracellular environments, and to avoid acquired drug‐resistance.
我们需要新的治疗方案来控制细菌感染。细菌使用几种策略来抵抗药物治疗,包括修改药物靶点和适应不同的生活方式,例如宿主细胞内的细胞内生态位。作用于不同靶点的药物比目前作用于单一分子靶点的抗生素更不可能在细菌中引起耐药性。抗菌肽是一种新型的抗生素,它通过识别带负电荷的微生物表面来选择性地杀死细菌。此外,具有细胞穿透特性的抗菌肽可以穿过宿主细胞膜,在细胞质中或在囊泡中隔离目标细菌。因此,细胞内生态位中的细菌逃避治疗的能力较低,建立耐药性的可能性进一步降低。这篇综述强调了抗菌肽作为细胞外和细胞内环境中针对细菌病原体的替代治疗方法的潜力,并避免获得性耐药。
{"title":"Antimicrobial peptides provide wider coverage for targeting drug‐resistant bacterial pathogens","authors":"Anna S. Amiss, S. Henriques, N. Lawrence","doi":"10.1002/pep2.24246","DOIUrl":"https://doi.org/10.1002/pep2.24246","url":null,"abstract":"We need new treatment options to control bacterial infections. Bacteria use several strategies to resist drug treatment, including modification of the drug target, and adaptation to a different lifestyle, such as intracellular niches within host cells. Drugs that act on diverse targets are less likely to induce resistance in bacteria, than current antibiotics acting on a single molecular target. Antimicrobial peptides have been explored as a new class of antibiotics because they selectively kill bacteria via a mechanism that involves recognition of the negatively charged microbial surface. Furthermore, antimicrobial peptides with cell‐penetrating properties can cross host cell membranes and target bacteria in the cytosol or sequestered in vesicles. Therefore, bacteria in intracellular niches are less capable of evading treatment and the likelihood of establishing drug resistance is further reduced. This review highlights the potential of antimicrobial peptides as alternative therapeutics to target bacterial pathogens in both extracellular and intracellular environments, and to avoid acquired drug‐resistance.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45840893","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
期刊
Peptide Science
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1