Porphyromonas gingivalis and Fusobacterium nucleatum are known to contribute to a variety of tumorigenic pathways linked to the progression of oral squamous cell carcinoma (OSCC). The growing global incidence of antibiotic resistance highlights the critical need to consider the use of antimicrobial peptides (AMPs) as a viable alternative to conventional antibiotics. The current study comprehensively tested Lactobacillus sp.−derived AMPs against bacterially exacerbated OSCC. A total of 52 AMPs were obtained from various databases, and an in silico analysis determined their potent antibacterial and anticancer characteristics after a rigorous screening and pruning approach. Twelve AMPs were tested for 3D structural alignment prediction and validation, with the GH12 synthetic AMP serving as a control. These candidate peptides were thoroughly screened against six important virulence proteins of P. gingivalis and four of F. nucleatum, with the lowest energy score of the docked complexes measuring binding affinity and interactions with active residues being chosen. plpl_18 was determined as the most efficient new AMP that interacted with the virulence protein RagB of P. gingivalis and Fap2 of F. nucleatum with docking scores of −238.24 and −254.27 kcal/mol, respectively. This AMP plpl_18 was docked against selective target OSCC regulatory proteins such as cytokines, metallomatrix proteinase, MAPK, E‐cadherin, and JAK‐1 proteins. Among these proteins, it docked against matrix metalloproteinase‐9 with the highest negative docking scores of −7.5, −260.956, and −1361.9 kcal/mol using AutoDock Vina, HPEPDOCK, and ClusPro 2.0, respectively. Molecular dynamic simulation was used to perform extrapolated validation. These computational studies provide an essential foundation for anticipated laboratory and clinical investigations concerning the possibility of adapting therapeutic peptides based on probiotics to combat the proliferation of OSCC, which is accelerated by F. nucleatum and P. gingivalis.
{"title":"In Silico Prediction and Molecular Simulation of Antimicrobial Peptide Variants From Lactobacillus sp. Against Porphyromonas gingivalis and Fusobacterium nucleatum in Oral Squamous Cell Carcinoma","authors":"Zarin Taj, Indranil Chattopadhyay","doi":"10.1002/pep2.24348","DOIUrl":"https://doi.org/10.1002/pep2.24348","url":null,"abstract":"<jats:italic>Porphyromonas gingivalis</jats:italic> and <jats:italic>Fusobacterium nucleatum</jats:italic> are known to contribute to a variety of tumorigenic pathways linked to the progression of oral squamous cell carcinoma (OSCC). The growing global incidence of antibiotic resistance highlights the critical need to consider the use of antimicrobial peptides (AMPs) as a viable alternative to conventional antibiotics. The current study comprehensively tested <jats:italic>Lactobacillus</jats:italic> sp.−derived AMPs against bacterially exacerbated OSCC. A total of 52 AMPs were obtained from various databases, and an in silico analysis determined their potent antibacterial and anticancer characteristics after a rigorous screening and pruning approach. Twelve AMPs were tested for 3D structural alignment prediction and validation, with the GH12 synthetic AMP serving as a control. These candidate peptides were thoroughly screened against six important virulence proteins of <jats:italic>P. gingivalis</jats:italic> and four of <jats:italic>F. nucleatum</jats:italic>, with the lowest energy score of the docked complexes measuring binding affinity and interactions with active residues being chosen. plpl_18 was determined as the most efficient new AMP that interacted with the virulence protein RagB of <jats:italic>P. gingivalis</jats:italic> and Fap2 of <jats:italic>F. nucleatum</jats:italic> with docking scores of −238.24 and −254.27 kcal/mol, respectively. This AMP plpl_18 was docked against selective target OSCC regulatory proteins such as cytokines, metallomatrix proteinase, MAPK, E‐cadherin, and JAK‐1 proteins. Among these proteins, it docked against matrix metalloproteinase‐9 with the highest negative docking scores of −7.5, −260.956, and −1361.9 kcal/mol using AutoDock Vina, HPEPDOCK, and ClusPro 2.0, respectively. Molecular dynamic simulation was used to perform extrapolated validation. These computational studies provide an essential foundation for anticipated laboratory and clinical investigations concerning the possibility of adapting therapeutic peptides based on probiotics to combat the proliferation of OSCC, which is accelerated by <jats:italic>F. nucleatum</jats:italic> and <jats:italic>P. gingivalis</jats:italic>.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"59 Pt A 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140074690","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}
Matheus Nolasco, Douglas O. C. Mariano, Daniel C. Pimenta, Humberto Fonseca de Freitas, Samuel Silva da Rocha Pita, Alexsandro Branco
Wasps have been neglected in toxinological studies, even with their diversity of species, when compared to other groups of venomous animals such as snakes, scorpions, and spiders. Solitary wasps, such as Pepsis decorata, are known for their mechanism of total or temporary paralysis of the host. In addition, their venoms are considered sources for studies of small peptides, bioactive peptides with neural and antimicrobial activities. In this work, some oligopeptides were analyzed by de novo sequencing identifying 39 oligopeptide sequences. Some sequences were similar to proctolin, a bradykinin-potentiating peptide, and poneritoxin, one bradykinin-related peptide. As proctolin-like peptides were the major constituent in distinct experimental conditions, it was selected for further in silico studies in order to understand its possible importance as a constituent of wasp venom and whether these peptides could be of biotechnological importance. We investigate its binding mode comparing with proctolin and we further analyzed the importance of the tyrosine-leucine-glutamic acid (YLE) tripeptide-motif conservation. This experimental, an in silico approach, increased the range of compounds identified in peptide analyses proving good characterization of little-known peptidic compounds.
{"title":"Oligopeptides analysis in spiderhawk's venom (Pepsis decorata Perty, 1833, Hymenoptera: Pompilidae)","authors":"Matheus Nolasco, Douglas O. C. Mariano, Daniel C. Pimenta, Humberto Fonseca de Freitas, Samuel Silva da Rocha Pita, Alexsandro Branco","doi":"10.1002/pep2.24347","DOIUrl":"https://doi.org/10.1002/pep2.24347","url":null,"abstract":"Wasps have been neglected in toxinological studies, even with their diversity of species, when compared to other groups of venomous animals such as snakes, scorpions, and spiders. Solitary wasps, such as <i>Pepsis decorata</i>, are known for their mechanism of total or temporary paralysis of the host. In addition, their venoms are considered sources for studies of small peptides, bioactive peptides with neural and antimicrobial activities. In this work, some oligopeptides were analyzed by de novo sequencing identifying 39 oligopeptide sequences. Some sequences were similar to proctolin, a bradykinin-potentiating peptide, and poneritoxin, one bradykinin-related peptide. As proctolin-like peptides were the major constituent in distinct experimental conditions, it was selected for further in silico studies in order to understand its possible importance as a constituent of wasp venom and whether these peptides could be of biotechnological importance. We investigate its binding mode comparing with proctolin and we further analyzed the importance of the tyrosine-leucine-glutamic acid (YLE) tripeptide-motif conservation. This experimental, an in silico approach, increased the range of compounds identified in peptide analyses proving good characterization of little-known peptidic compounds.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"12 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139769841","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}
In the realm of therapeutic peptides, tremendous progress has been achieved in the last two decades. The building block of peptides that is, ‘Amino Acid’ has been modified by various chemical modifications such as side-chain alteration in linear peptides, cyclization, back-bone modification, pro-drug moiety, conjugation with heterocycles, and natural products to make peptides a foremost candidate as a therapeutic drug. Since the advent of insulin in 1922, peptides have immensely affected the development of the pharmaceutical industry giving rise to the peptide-based drug industry. In recent years, peptides having antimicrobial, antiviral, anti-tumor, anti-inflammatory, anti-aging, and antioxidant properties have developed. Also, it has now entered as a potent candidate in the field of oncology and also become a valuable tool as a radiolabeled peptide for the detection of various diseases. Generally, peptides were extracted from natural sources in the olden days, but presently work is directed towards finding alternate and sustainable ways for developing synthetic peptides. The present review covers the discussion about the historic evaluation of peptides, available effective synthetic processes, current advancements, use of bioinformatic tools, computational strategies, and the methodology to overcome the barrier for making peptides the potent candidate for the future world.
{"title":"Review on therapeutic potential of peptides: Advancements in synthesis methods, linear and cyclic peptides, and strategies for overcoming challenges","authors":"Naurin Lalani, Sunil Tivari, Vicky Jain, Yashwantsinh Jadeja","doi":"10.1002/pep2.24343","DOIUrl":"https://doi.org/10.1002/pep2.24343","url":null,"abstract":"In the realm of therapeutic peptides, tremendous progress has been achieved in the last two decades. The building block of peptides that is, ‘Amino Acid’ has been modified by various chemical modifications such as side-chain alteration in linear peptides, cyclization, back-bone modification, pro-drug moiety, conjugation with heterocycles, and natural products to make peptides a foremost candidate as a therapeutic drug. Since the advent of insulin in 1922, peptides have immensely affected the development of the pharmaceutical industry giving rise to the peptide-based drug industry. In recent years, peptides having antimicrobial, antiviral, anti-tumor, anti-inflammatory, anti-aging, and antioxidant properties have developed. Also, it has now entered as a potent candidate in the field of oncology and also become a valuable tool as a radiolabeled peptide for the detection of various diseases. Generally, peptides were extracted from natural sources in the olden days, but presently work is directed towards finding alternate and sustainable ways for developing synthetic peptides. The present review covers the discussion about the historic evaluation of peptides, available effective synthetic processes, current advancements, use of bioinformatic tools, computational strategies, and the methodology to overcome the barrier for making peptides the potent candidate for the future world.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"13 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139666748","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}
Celimar Sinézia, Tháyna Sisnande, Luis Peña Icart, Luís Maurício T. R. Lima
Amylin receptor agonism safely benefit diabetic patients, reducing the insulin requirements and glycemic excursions. Pramlintide is the triple proline human amylin analogue first used as injectable drug, but lacking physico-chemical compatibility when co-formulated with insulin. Here, we report the design and characterization of polymeric microparticles for oral delivery of pramlintide. Eudragit S100, a gastric-resistant polymer, was used in preparation of pramlintide-loaded spherical microcapsules by double emulsion and solvent evaporation technique, with approximately 66 μm ± 11 particle size, with 83.2% ± 2.7 efficiency for pramlintide entrapment and 67.6% ± 2.1 yield. Intra-venous pramlintide free in solution showed a plasmatic half-life of 6.8 min in mice. In contrast, oral delivery of acid-resistant pramlintide-loaded microparticles in mice showed a protracted release for 120 min compared to 30 min obtained for pramlintide in solution. Our data provide evidences for the potential use of the oral route in the therapeutic development of pramlintide formulations.
{"title":"Oral delivery of the amylin receptor agonist pramlintide","authors":"Celimar Sinézia, Tháyna Sisnande, Luis Peña Icart, Luís Maurício T. R. Lima","doi":"10.1002/pep2.24346","DOIUrl":"https://doi.org/10.1002/pep2.24346","url":null,"abstract":"Amylin receptor agonism safely benefit diabetic patients, reducing the insulin requirements and glycemic excursions. Pramlintide is the triple proline human amylin analogue first used as injectable drug, but lacking physico-chemical compatibility when co-formulated with insulin. Here, we report the design and characterization of polymeric microparticles for oral delivery of pramlintide. Eudragit S100, a gastric-resistant polymer, was used in preparation of pramlintide-loaded spherical microcapsules by double emulsion and solvent evaporation technique, with approximately 66 μm ± 11 particle size, with 83.2% ± 2.7 efficiency for pramlintide entrapment and 67.6% ± 2.1 yield. Intra-venous pramlintide free in solution showed a plasmatic half-life of 6.8 min in mice. In contrast, oral delivery of acid-resistant pramlintide-loaded microparticles in mice showed a protracted release for 120 min compared to 30 min obtained for pramlintide in solution. Our data provide evidences for the potential use of the oral route in the therapeutic development of pramlintide formulations.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"50 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139656258","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}
A well-established mechanism of action for managing pneumonia using Glycyrrhiza is unknown. Using network pharmacology and molecular docking simulations, we investigated the mechanism of action of Glycyrrhiza against pneumonia. To identify the targets of the active components of Glycyrrhiza from the Traditional Chinese Medicine Systems Pharmacology database, oral bioavailability and drug likeness were utilized as indicators. Pneumonia-associated genes were identified and screened from the databases. Integrated analysis was conducted to elucidate the relationship between the active components of Glycyrrhiza and intersecting genes; a comprehensive Glycyrrhiza active component-target gene relationship map was constructed. Intersecting genes underwent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses to examine their biological functions. A protein–protein interaction network map was constructed to identify hub genes. Molecular docking simulations were performed to investigate binding interactions between hub genes and their corresponding active components. Of the 96 overlapping genes, topological analysis revealed 10 hub genes. Glycyrrhiza exerts therapeutic effects through a multi-target and multipathway approach, suggesting a synergistic treatment for pneumonia. MAPK14 showed a favorable binding affinity with most of the active compounds, indicating that MAPK14 and related compounds in Glycyrrhiza have development potential.
{"title":"Network pharmacology combined with molecular docking simulations reveal the mechanism of action of Glycyrrhiza for treating pneumonia","authors":"Dongxin Yang, Zhehong Li, Yongrui Peng, Xiaofeng Zhu, Jun Gong, Cuilian Chen","doi":"10.1002/pep2.24342","DOIUrl":"https://doi.org/10.1002/pep2.24342","url":null,"abstract":"A well-established mechanism of action for managing pneumonia using <i>Glycyrrhiza</i> is unknown. Using network pharmacology and molecular docking simulations, we investigated the mechanism of action of <i>Glycyrrhiza</i> against pneumonia. To identify the targets of the active components of <i>Glycyrrhiza</i> from the Traditional Chinese Medicine Systems Pharmacology database, oral bioavailability and drug likeness were utilized as indicators. Pneumonia-associated genes were identified and screened from the databases. Integrated analysis was conducted to elucidate the relationship between the active components of <i>Glycyrrhiza</i> and intersecting genes; a comprehensive <i>Glycyrrhiza</i> active component-target gene relationship map was constructed. Intersecting genes underwent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses to examine their biological functions. A protein–protein interaction network map was constructed to identify hub genes. Molecular docking simulations were performed to investigate binding interactions between hub genes and their corresponding active components. Of the 96 overlapping genes, topological analysis revealed 10 hub genes. <i>Glycyrrhiza</i> exerts therapeutic effects through a multi-target and multipathway approach, suggesting a synergistic treatment for pneumonia. MAPK14 showed a favorable binding affinity with most of the active compounds, indicating that MAPK14 and related compounds in <i>Glycyrrhiza</i> have development potential.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"47 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139496065","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}
Cong Shibo, Yu Tong, Wang Sili, Gu Shuxiao, Qiao Yanfang, Liu Susu, Gao Pan, Meng Jingke, Chai Xinlou
This study aims to explore the molecular mechanism and potential active ingredients of Danhe granules in improving the blood lipid level of hypercholesterolemia by intestinal TICE (transintestinal cholesterol excretion) through in vivo experimental research, network pharmacology methods, and molecular docking. The diet-induced hypercholesterolemia rat model evaluated the effects of Danhe granules on fecal cholesterol levels and intestinal TICE-related protein expression in rats. Based on the experimental results, the network pharmacology method was used to predict the potential active ingredients, and the binding strength between the potential active ingredients and key targets was further confirmed by molecular docking. Danhe granules increased LDLR, ABCG5, ABCB1, and LXRα which can promote the uptake of cholesterol by intestinal cells and the excretion of cholesterol into the intestine, and then reduce the levels of serum LDL-C and TC and increase the level of fecal TC, so as to achieve the effect of treating hypercholesterolemia. The results of network pharmacology and molecular docking showed that 19 active ingredients had good binding activity with the targets. These may be the active ingredients of Danhe granules for the treatment of hypercholesterolemia. This study revealed the molecular mechanism of Danhe granules in the treatment of hypercholesterolemia via TICE, and preliminarily clarified the potential effective ingredients. It provides new ideas for the treatment of hypercholesterolemia and the development of new drugs.
{"title":"Molecular mechanism study and potential active ingredients prediction of Danhe granules in the treatment of hypercholesterolemia via TICE","authors":"Cong Shibo, Yu Tong, Wang Sili, Gu Shuxiao, Qiao Yanfang, Liu Susu, Gao Pan, Meng Jingke, Chai Xinlou","doi":"10.1002/pep2.24345","DOIUrl":"https://doi.org/10.1002/pep2.24345","url":null,"abstract":"This study aims to explore the molecular mechanism and potential active ingredients of Danhe granules in improving the blood lipid level of hypercholesterolemia by intestinal TICE (transintestinal cholesterol excretion) through in vivo experimental research, network pharmacology methods, and molecular docking. The diet-induced hypercholesterolemia rat model evaluated the effects of Danhe granules on fecal cholesterol levels and intestinal TICE-related protein expression in rats. Based on the experimental results, the network pharmacology method was used to predict the potential active ingredients, and the binding strength between the potential active ingredients and key targets was further confirmed by molecular docking. Danhe granules increased LDLR, ABCG5, ABCB1, and LXRα which can promote the uptake of cholesterol by intestinal cells and the excretion of cholesterol into the intestine, and then reduce the levels of serum LDL-C and TC and increase the level of fecal TC, so as to achieve the effect of treating hypercholesterolemia. The results of network pharmacology and molecular docking showed that 19 active ingredients had good binding activity with the targets. These may be the active ingredients of Danhe granules for the treatment of hypercholesterolemia. This study revealed the molecular mechanism of Danhe granules in the treatment of hypercholesterolemia via TICE, and preliminarily clarified the potential effective ingredients. It provides new ideas for the treatment of hypercholesterolemia and the development of new drugs.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"51 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139459578","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}
Michael A. Lee, Joseph S. Brown, Andrei Loas, Bradley L. Pentelute
Solid-phase peptide synthesis (SPPS) is widely used to produce peptides. Since its invention, the solid support has enabled the elongation of the synthetic peptide chain. As technologies have evolved, the length of peptide chains accessible with SPPS has grown to that of single-domain proteins. Resins for SPPS have advanced to improve synthesis capabilities as well. The functionalization of solid supports with polyethylene glycol (PEG) is commonly employed in a range of commercially available resins to aid in the ability to synthesize long or difficult sequences. A notable example of a widely used PEG-based solid support is ChemMatrix® resin; however, this and several similar resins have recently been discontinued. Here, we demonstrate and compare the capabilities of OctaGel™, ProTide®, and TentaGel XV® resins in synthesizing sequences ranging from peptides to single domain proteins using automated fast-flow peptide synthesis. Our studies indicate that each resin performs well for routine peptide synthesis by automated flow, whereas TentaGel XV resin showed the best performance for synthesis of difficult or long peptide sequences when comparing quality using yield, purity, and real-time UV absorbance monitoring during synthesis.
{"title":"Investigation of commercially available resins for the automated flow synthesis of difficult or long peptide sequences","authors":"Michael A. Lee, Joseph S. Brown, Andrei Loas, Bradley L. Pentelute","doi":"10.1002/pep2.24344","DOIUrl":"https://doi.org/10.1002/pep2.24344","url":null,"abstract":"Solid-phase peptide synthesis (SPPS) is widely used to produce peptides. Since its invention, the solid support has enabled the elongation of the synthetic peptide chain. As technologies have evolved, the length of peptide chains accessible with SPPS has grown to that of single-domain proteins. Resins for SPPS have advanced to improve synthesis capabilities as well. The functionalization of solid supports with polyethylene glycol (PEG) is commonly employed in a range of commercially available resins to aid in the ability to synthesize long or difficult sequences. A notable example of a widely used PEG-based solid support is ChemMatrix® resin; however, this and several similar resins have recently been discontinued. Here, we demonstrate and compare the capabilities of OctaGel™, ProTide®, and TentaGel XV® resins in synthesizing sequences ranging from peptides to single domain proteins using automated fast-flow peptide synthesis. Our studies indicate that each resin performs well for routine peptide synthesis by automated flow, whereas TentaGel XV resin showed the best performance for synthesis of difficult or long peptide sequences when comparing quality using yield, purity, and real-time UV absorbance monitoring during synthesis.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"87 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139459828","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}
Qiongqiong Ren, Zejun Fan, Rong Han, Meihui Sang, Changxing Ma, Xiaoli Zhao, Shenlin Wang
Engineered Escherichia coli (E. coli) strains have been widely used to produce isotopically labeled peptides for NMR characterization on their structures and interactions. However, production of antimicrobial peptides (AMPs) by E. coli is still challenging, because AMPs are toxic to E. coli host and would lead to cell death after induction. On the other hand, expression of short peptides in E. coli host often encounter problems of the short in vivo lifetime of the peptides, which were rapidly degraded by endogenous enzymes during expression and purification steps. This report presents a practical method for overcoming these bottlenecks to enable E. coli to express AMPs and peptides that have short in vivo lifetime. This design uses the fusion of thioredoxin tags at both the N- and C-termini of the target peptides. The steric effect of the large soluble tags at both ends of the peptide reduces peptide accessibility, thereby enhancing their in vivo stability and eliminating the toxicity associated with AMPs. The approach was validated using an AMP A3K/L7K-LAH4 (K3K7) and a membrane fusion peptide (FP), which is a segment of the spike protein of SARS-CoV-2 and functions in fusing viral membranes and host cell membranes. Fusion expression of K3K7 with a thioredoxin tag only at the N-terminal resulted in high toxicity to the host cells, leading to impaired cell growth and a failure to obtain expressed fusion protein. In contrast, the fusion proteins from both termini were successfully expressed and purified. In the case of the FP, the fusion of thioredoxin at both termini significantly enhanced its stability, protecting it from enzymatic degradation during expression and purification steps. On the contrary, the FP with thioredoxin fused only at the N-terminal was found to be unstable in E. coli host strains. As stable isotope labeling on peptide is essentially important in NMR-based structure and interaction studies, we also demonstrated that the developed approach enables efficient 15N labeling for NMR studies. This strategy may also be extended to produce other challenging peptides.
工程大肠杆菌（E. coli）菌株已被广泛用于生产同位素标记的肽，以对其结构和相互作用进行核磁共振表征。然而，用大肠杆菌生产抗菌肽（AMPs）仍然具有挑战性，因为 AMPs 对大肠杆菌宿主有毒，诱导后会导致细胞死亡。另一方面，在大肠杆菌宿主中表达短肽往往会遇到短肽在体内寿命短的问题，因为短肽在表达和纯化过程中会被内源酶迅速降解。本报告提出了一种克服这些瓶颈的实用方法，使大肠杆菌能够表达体内寿命短的 AMP 和多肽。这种设计在目标肽的 N 端和 C 端融合了硫代毒素标签。肽两端的大型可溶性标签的立体效应降低了肽的可及性，从而提高了肽在体内的稳定性，并消除了与 AMP 相关的毒性。该方法使用 AMP A3K/L7K-LAH4 (K3K7) 和膜融合肽 (FP) 进行了验证，膜融合肽是 SARS-CoV-2 的尖峰蛋白的一个片段，具有融合病毒膜和宿主细胞膜的功能。K3K7 的融合表达仅在 N 端带有硫代毒素标签，因此对宿主细胞的毒性很高，导致细胞生长受阻，无法获得表达的融合蛋白。相比之下，两个末端的融合蛋白都能成功表达和纯化。就 FP 而言，硫氧还蛋白在两个末端的融合大大提高了其稳定性，使其在表达和纯化步骤中不会被酶降解。相反，只在 N 端融合了硫氧还蛋白的 FP 在大肠杆菌宿主菌株中不稳定。在基于核磁共振的结构和相互作用研究中，肽上稳定的同位素标记非常重要，因此我们也证明了所开发的方法能够为核磁共振研究提供高效的 15N 标记。这种策略也可扩展到其他具有挑战性的多肽的制备中。
{"title":"A strategy for producing isotopically labeled peptides with antimicrobial activity or with short in vivo lifetime in Escherichia coli","authors":"Qiongqiong Ren, Zejun Fan, Rong Han, Meihui Sang, Changxing Ma, Xiaoli Zhao, Shenlin Wang","doi":"10.1002/pep2.24340","DOIUrl":"https://doi.org/10.1002/pep2.24340","url":null,"abstract":"Engineered <i>Escherichia coli</i> (<i>E. coli</i>) strains have been widely used to produce isotopically labeled peptides for NMR characterization on their structures and interactions. However, production of antimicrobial peptides (AMPs) by <i>E. coli</i> is still challenging, because AMPs are toxic to <i>E. coli</i> host and would lead to cell death after induction. On the other hand, expression of short peptides in <i>E. coli</i> host often encounter problems of the short in vivo lifetime of the peptides, which were rapidly degraded by endogenous enzymes during expression and purification steps. This report presents a practical method for overcoming these bottlenecks to enable <i>E. coli</i> to express AMPs and peptides that have short in vivo lifetime. This design uses the fusion of thioredoxin tags at both the N- and C-termini of the target peptides. The steric effect of the large soluble tags at both ends of the peptide reduces peptide accessibility, thereby enhancing their in vivo stability and eliminating the toxicity associated with AMPs. The approach was validated using an AMP A3K/L7K-LAH4 (K3K7) and a membrane fusion peptide (FP), which is a segment of the spike protein of SARS-CoV-2 and functions in fusing viral membranes and host cell membranes. Fusion expression of K3K7 with a thioredoxin tag only at the N-terminal resulted in high toxicity to the host cells, leading to impaired cell growth and a failure to obtain expressed fusion protein. In contrast, the fusion proteins from both termini were successfully expressed and purified. In the case of the FP, the fusion of thioredoxin at both termini significantly enhanced its stability, protecting it from enzymatic degradation during expression and purification steps. On the contrary, the FP with thioredoxin fused only at the N-terminal was found to be unstable in <i>E. coli</i> host strains. As stable isotope labeling on peptide is essentially important in NMR-based structure and interaction studies, we also demonstrated that the developed approach enables efficient <sup>15</sup>N labeling for NMR studies. This strategy may also be extended to produce other challenging peptides.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"16 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139459579","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}
The coronavirus 2 (SARS‐CoV‐2), a positive‐sense RNA virus that causes severe acute respiratory illness, is the cause of Coronavirus Disease 2019 (COVID‐19) and Monkeypox is a zoonotic viral disease caused by a double‐strand enveloped DNA virus, a member of the Poxviridae family under the umbrella of the Orthopoxvirus genus. These viruses have harmed global health, societal stability, and global economy prompting the development of new therapeutic options. The purpose of this study was to analyze the potency of hazelnut‐derived bioactive peptides for usage in preventive measures against SARS‐CoV‐2 and Monkeypox infections. Since SARS‐CoV‐2 entry into the host cell takes place through angiotensin‐converting enzyme (ACE) receptors, an in silico attempt was made here to analyze the previously characterized ACE‐inhibitory hazelnut peptides for their anti‐COVID potential. First of all, peptide sequences with PeptideRanker values >0.5 were determined, where 43 of 256 hazelnut peptides met this condition. BIOPEP tools were used to calculate their ACE‐inhibitory characteristics. VPHW and DENPRHF demonstrated the strongest ACE‐inhibitory activity based on BIOPEP analysis. The binding potentials of VPHW (p < 0.001) and DENPRHF (p < 0.001) peptides to ACE were statistically significant based on PepSite2 analysis. The hazelnut‐derived peptides were docked with ACE, spike proteins, SARS‐CoV‐2 proteases, host cell receptors, and Monkeypox 2022 membrane proteins using HPEPDOCK and CABS‐dock. The in silico findings pointed out potential inhibition of SARS‐CoV‐2 main protease in the host cell and Monkeypox 2022 membrane protein and demonstration of multiple bioactivities.
{"title":"In silico prediction of preventive activities of bioactive hazelnut peptides against COVID‐19 and Monkeypox 2022","authors":"Zeynep Saliha Güneş, B. Cakir, İbrahim Gülseren","doi":"10.1002/pep2.24341","DOIUrl":"https://doi.org/10.1002/pep2.24341","url":null,"abstract":"The coronavirus 2 (SARS‐CoV‐2), a positive‐sense RNA virus that causes severe acute respiratory illness, is the cause of Coronavirus Disease 2019 (COVID‐19) and Monkeypox is a zoonotic viral disease caused by a double‐strand enveloped DNA virus, a member of the Poxviridae family under the umbrella of the Orthopoxvirus genus. These viruses have harmed global health, societal stability, and global economy prompting the development of new therapeutic options. The purpose of this study was to analyze the potency of hazelnut‐derived bioactive peptides for usage in preventive measures against SARS‐CoV‐2 and Monkeypox infections. Since SARS‐CoV‐2 entry into the host cell takes place through angiotensin‐converting enzyme (ACE) receptors, an in silico attempt was made here to analyze the previously characterized ACE‐inhibitory hazelnut peptides for their anti‐COVID potential. First of all, peptide sequences with PeptideRanker values >0.5 were determined, where 43 of 256 hazelnut peptides met this condition. BIOPEP tools were used to calculate their ACE‐inhibitory characteristics. VPHW and DENPRHF demonstrated the strongest ACE‐inhibitory activity based on BIOPEP analysis. The binding potentials of VPHW (p < 0.001) and DENPRHF (p < 0.001) peptides to ACE were statistically significant based on PepSite2 analysis. The hazelnut‐derived peptides were docked with ACE, spike proteins, SARS‐CoV‐2 proteases, host cell receptors, and Monkeypox 2022 membrane proteins using HPEPDOCK and CABS‐dock. The in silico findings pointed out potential inhibition of SARS‐CoV‐2 main protease in the host cell and Monkeypox 2022 membrane protein and demonstration of multiple bioactivities.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"1 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139439501","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}
Shreya Banerjee, Sunil K. Gupta, Sunit Pal, Erode N. Prabhakaran
CisPro/transPro isomerism at the prolyl amide bond is a fundamental dynamism governing protein folding, structure, and functions. Since cisPro crystal structures are rare, the interactions influencing their structures are less understood, unlike transPro. Crystal data for the sterically hindered pivaloyl-cisProlyl amide bond (2,2-dimethyl-1-(1-pyrrolidinyl)-1-propanone, Piv-cisPro) were particularly lacking for decades. Here we introduce Piv-Pro-Xaa-OMe dipeptides which crystallize with the elusive Piv-cisPro (Xaa is Leu/Ile) and the abundant Piv-transPro (Xaa is Gly/Phe) conformers.
{"title":"Crystal structures reveal that the sterically hindered pivaloyl-cisProlyl amide bond is energetically frustrated","authors":"Shreya Banerjee, Sunil K. Gupta, Sunit Pal, Erode N. Prabhakaran","doi":"10.1002/pep2.24337","DOIUrl":"https://doi.org/10.1002/pep2.24337","url":null,"abstract":"CisPro/transPro isomerism at the prolyl amide bond is a fundamental dynamism governing protein folding, structure, and functions. Since cisPro crystal structures are rare, the interactions influencing their structures are less understood, unlike transPro. Crystal data for the sterically hindered pivaloyl-cisProlyl amide bond (2,2-dimethyl-1-(1-pyrrolidinyl)-1-propanone, Piv-cisPro) were particularly lacking for decades. Here we introduce Piv-Pro-Xaa-OMe dipeptides which crystallize with the elusive Piv-cisPro (Xaa is Leu/Ile) and the abundant Piv-transPro (Xaa is Gly/Phe) conformers.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"3 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139398069","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}
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