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Zhong G, Liu H, Deng L. Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification. Interdiscip Sci 2024:10.1007/s12539-024-00640-z. [PMID: 38972032 DOI: 10.1007/s12539-024-00640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 07/08/2024]
Abstract
The emergence of antibiotic-resistant microbes raises a pressing demand for novel alternative treatments. One promising alternative is the antimicrobial peptides (AMPs), a class of innate immunity mediators within the therapeutic peptide realm. AMPs offer salient advantages such as high specificity, cost-effective synthesis, and reduced toxicity. Although some computational methodologies have been proposed to identify potential AMPs with the rapid development of artificial intelligence techniques, there is still ample room to improve their performance. This study proposes a predictive framework which ensembles deep learning and statistical learning methods to screen peptides with antimicrobial activity. We integrate multiple LightGBM classifiers and convolution neural networks which leverages various predicted sequential, structural and physicochemical properties from their residue sequences extracted by diverse machine learning paradigms. Comparative experiments exhibit that our method outperforms other state-of-the-art approaches on an independent test dataset, in terms of representative capability measures. Besides, we analyse the discrimination quality under different varieties of attribute information and it reveals that combination of multiple features could improve prediction. In addition, a case study is carried out to illustrate the exemplary favorable identification effect. We establish a web application at http://amp.denglab.org to provide convenient usage of our proposal and make the predictive framework, source code, and datasets publicly accessible at https://github.com/researchprotein/amp .
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Affiliation(s)
- Guolun Zhong
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Hui Liu
- College of Computer and Information Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
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2
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Kanwal S, Arif R, Ahmed S, Kabir M. A novel stacking-based predictor for accurate prediction of antimicrobial peptides. J Biomol Struct Dyn 2024:1-12. [PMID: 38500243 DOI: 10.1080/07391102.2024.2329298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Antimicrobial peptides (AMPs) are gaining acceptance and support as a chief antibiotic substitute since they boost human immunity. They retain a wide range of actions and have a low risk of developing resistance, which are critical properties to the pharmaceutical industry for drug discovery. Antibiotic sensitivity, however, is an issue that affects people all around the world and has the potential to one day lead to an epidemic. As cutting-edge therapeutic agents, AMPs are also expected to cure microbial infections. In order to produce tolerable drugs, it is crucial to understand the significance of the basic architecture of AMPs. Traditional laboratory methods are expensive and time-consuming for AMPs testing and detection. Currently, bioinformatics techniques are being successfully applied to the detection of AMPs. In this study, we have developed a novel STacking-based ensemble learning framework for AntiMicrobial Peptide (STAMP) prediction. First, we constructed 84 different baseline models by using 12 different feature encoding schemes and 7 popular machine learning algorithms. Second, these baseline models were trained and employed to create a new probabilistic feature vector. Finally, based on the feature selection strategy, we determined the optimal probabilistic feature vector, which was further utilized for the construction of our stacked model. Resultantly, the STAMP predictor achieved excellent performance during cross-validation with an accuracy and Matthew's correlation coefficient of 0.930 and 0.860, respectively. The corresponding metrics during the independent test were 0.710 and 0.464, respectively. Overall, STAMP achieved a more accurate and stable performance than the baseline models and significantly outperformed the existing predictors, demonstrating the effectiveness of our proposed hybrid framework. Furthermore, STAMP is expected to assist community-wide efforts in identifying AMPs and will contribute to the development of novel therapeutic methods and drug-design for immunity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sameera Kanwal
- School of Systems and Technology, University of Management and Technology, Lahore, Pakistan
| | - Roha Arif
- School of Systems and Technology, University of Management and Technology, Lahore, Pakistan
| | - Saeed Ahmed
- School of Systems and Technology, University of Management and Technology, Lahore, Pakistan
| | - Muhammad Kabir
- School of Systems and Technology, University of Management and Technology, Lahore, Pakistan
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3
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Nakamura Y, Kulkarni NN, Takahashi T, Alimohamadi H, Dokoshi T, Liu E, Shia M, Numata T, Luo EW, Gombart AF, Yang X, Secrest P, Gordts PL, Tsimikas S, Wong GC, Gallo RL. Increased LL37 in psoriasis and other inflammatory disorders promotes LDL uptake and atherosclerosis. J Clin Invest 2024; 134:e172578. [PMID: 38194294 PMCID: PMC10904043 DOI: 10.1172/jci172578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
Patients with chronic inflammatory disorders such as psoriasis have an increased risk of cardiovascular disease and elevated levels of LL37, a cathelicidin host defense peptide that has both antimicrobial and proinflammatory properties. To explore whether LL37 could contribute to the risk of heart disease, we examined its effects on lipoprotein metabolism and show that LL37 enhanced LDL uptake in macrophages through the LDL receptor (LDLR), scavenger receptor class B member 1 (SR-B1), and CD36. This interaction led to increased cytosolic cholesterol in macrophages and changes in expression of lipid metabolism genes consistent with increased cholesterol uptake. Structure-function analysis and synchrotron small-angle x-ray scattering showed structural determinants of the LL37-LDL complex that underlie its ability to bind its receptors and promote uptake. This function of LDL uptake is unique to cathelicidins from humans and some primates and was not observed with cathelicidins from mice or rabbits. Notably, Apoe-/- mice expressing LL37 developed larger atheroma plaques than did control mice, and a positive correlation between plasma LL37 and oxidized phospholipid on apolipoprotein B (OxPL-apoB) levels was observed in individuals with cardiovascular disease. These findings provide evidence that LDL uptake can be increased via interaction with LL37 and may explain the increased risk of cardiovascular disease associated with chronic inflammatory disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Adrian F. Gombart
- Linus Pauling Institute, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | | | - Patrick Secrest
- Department of Medicine, Division of Endocrinology and Metabolism, and
| | - Philip L.S.M. Gordts
- Department of Medicine, Division of Endocrinology and Metabolism, and
- Glycobiology Research and Training Center, UCSD, La Jolla, California, USA
| | | | - Gerard C.L. Wong
- Department of Bioengineering, UCLA, Los Angeles, California, USA
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4
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Lan X, Zhong J, Huang R, Liu Y, Ma X, Li X, Zhao D, Qing G, Zhang Y, Liu L, Wang J, Ma X, Luo T, Guo W, Wang Y, Li LL, Su YX, Liang XJ. Conformation Dependent Architectures of Assembled Antimicrobial Peptides with Enhanced Antimicrobial Ability. Adv Healthc Mater 2023; 12:e2301688. [PMID: 37540835 DOI: 10.1002/adhm.202301688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/19/2023] [Indexed: 08/06/2023]
Abstract
Antimicrobial peptides (AMPs) are a developing class of natural and synthetic oligopeptides with host defense mechanisms against a broad spectrum of microorganisms. With in-depth research on the structural conformations of AMPs, synthesis or modification of peptides has shown great potential in effectively obtaining new therapeutic agents with improved physicochemical and biological properties. Notably, AMPs with self-assembled properties have gradually become a hot research topic for various biomedical applications. Compared to monomeric peptides, these peptides can exist in diverse forms (e.g., nanoparticles, nanorods, and nanofibers) and possess several advantages, such as high stability, good biocompatibility, and potent biological functions, after forming aggregates under specific conditions. In particular, the stability and antibacterial property of these AMPs can be modulated by rationally regulating the peptide sequences to promote self-assembly, leading to the reconstruction of molecular structure and spatial orientation while introducing some peptide fragments into the scaffolds. In this work, four self-assembled AMPs are developed, and the relationship between their chemical structures and antibacterial activity is explored extensively through different experiments. Importantly, the evaluation of antibacterial performance in both in vitro and in vivo studies has provided a general guide for using self-assembled AMPs in subsequent treatments for combating bacterial infections.
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Affiliation(s)
- Xinmiao Lan
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, School of Pharmaceutical Science, Capital Medical University, Beijing, 100069, China
- Discipline of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Jie Zhong
- Discipline of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, 999077, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Regina Huang
- Discipline of Periodontology, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Yuhan Liu
- Department of Stomatology, Aviation General Hospital of China Medical University and Beijing Institute of Translational Medicine, Chinese Academy of Science, Beijing, 100012, China
| | - Xiaowei Ma
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xuan Li
- Discipline of Periodontology, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Dan Zhao
- Beijing Institute of Dental Research, Beijing Stomatological Hospital, Capital Medical University, Beijing, 100069, China
| | - Guangchao Qing
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Yuxuan Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinjin Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xu Ma
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting Luo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Weisheng Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Yuji Wang
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, School of Pharmaceutical Science, Capital Medical University, Beijing, 100069, China
| | - Li-Li Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Xiong Su
- Discipline of Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, 999077, China
| | - Xing-Jie Liang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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5
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van Dijk A, Guabiraba R, Bailleul G, Schouler C, Haagsman HP, Lalmanach AC. Evolutionary diversification of defensins and cathelicidins in birds and primates. Mol Immunol 2023; 157:53-69. [PMID: 36996595 DOI: 10.1016/j.molimm.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023]
Abstract
Divergent evolution for more than 310 million years has resulted in an avian immune system that is complex and more compact than that of primates, sharing much of its structure and functions. Not surprisingly, well conserved ancient host defense molecules, such as defensins and cathelicidins, have diversified over time. In this review, we describe how evolution influenced the host defense peptides repertoire, its distribution, and the relationship between structure and biological functions. Marked features of primate and avian HDPs are linked to species-specific characteristics, biological requirements, and environmental challenge.
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6
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Savitri D, Djawad K, Hatta M, Wahyuni S, Bukhari A. Active compounds in kepok banana peel as anti-inflammatory in acne vulgaris: Review article. Ann Med Surg (Lond) 2022; 84:104868. [PMID: 36582904 PMCID: PMC9793233 DOI: 10.1016/j.amsu.2022.104868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/04/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background Acne vulgaris (AV) is a chronic inflammatory skin condition affecting the pilosebaceous units characterized by recurrent comedones, erythematous papules and pustules. The disease is benign however may produce scarring, erythema, and hyperpigmentation resulting in physical and psychological problems. Conventional therapy may reduce the symptoms of AV nevertheless, has a possibility of resistance, unwanted side effects, and has high cost. Thus, utilizing natural remedies may be a useful. Methods The data in this study were collect by search the keyword combinations of medical subject heading (mesh) of "inhibition", "antimicrobial", "banana peel", "acne vulgaris" and "antiinflammation" and relevant reference lists were manually searched in PubMed, EMBRASE and Scopus database. All relevant articles in data base above were included and narratively discussed in this review article. Objective To discuss the bioactive potential of banana peel as an inflammatory modulator in acne vulgaris. Results Banana peel contains many bioactive compounds, particularly phenolic and non-phenolic antioxidants (ascorbic acid, carotene, and cyanidin) which are pivotal in removing inflammatory products by inhibiting reactive oxygen species (ROS), protecting protease inhibitors from oxidative damage, and preventing fibroblasts degradation. Banana peel also contains anti-inflammatory agents such as trigonelline which inhibits bacterial enzymes and nucleic acid synthesis; isovanillic acid which suppresses TNF-α production; and ferulic acid which inhibits the production of proinflammatory signaling and cytokines. Conclusion Banana peel contains many bioactive compounds which demonstrate anti-inflammatory properties through several processes of the inflammatory pathway. However further research is needed to confirm this finding.
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Affiliation(s)
- Dwiana Savitri
- Doctoral Program in Medical Science, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
- Faculty of Medicine, Lambung Mangkurat University, Banjarmasin, South Kalimantan, Indonesia
| | - Khairuddin Djawad
- Department of Dermatology and Venereology, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
| | - Mochammad Hatta
- Department of Molecular Biology and Immunology, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
- Corresponding author. Molecular Biology and Immunology Laboratory, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia.
| | - Sitti Wahyuni
- Department of Parasitology, Faculty of Medicine, Hasanuddin University, Makassar, South Sulawesi, Indonesia
| | - Agussalim Bukhari
- Department of Nutrition, Faculty Medicine, Universitas Hasanuddin, Makassar, South Sulawesi, Indonesia
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7
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Zhang XJ, Zhong YQ, Ma ZY, Hu YZ, Su JG, Zhang YA. Insights into the Antibacterial Properties of Complement Peptides C3a, C4a, and C5a across Vertebrates. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:ji2101019. [PMID: 36280254 DOI: 10.4049/jimmunol.2101019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 09/30/2022] [Indexed: 02/17/2024]
Abstract
Complement peptides C3a, C4a, and C5a are important components of innate immunity in vertebrates. Although they diverged from a common ancestor, only C3a and C4a can act as antibacterial peptides in Homo sapiens, suggesting that C5a has evolved into a purely chemotactic molecule; however, the antibacterial properties of C3a, C4a, and C5a across vertebrates still require elucidation. In this article, we show that, unlike those in H. sapiens, Mus musculus C3a, C4a, and C5a all possess antibacterial activities, implying that the antibacterial properties of C3a, C4a, and C5a have evolved divergently in vertebrates. The extremely different net charge, a key factor determining the antibacterial activities of cationic antimicrobial peptides, of vertebrate C3a, C4a, and C5a supports this speculation. Moreover, the antibacterial activity of overlapping peptides covering vertebrate C3a, C4a, and C5a further strongly supports the speculation, because their activity is positively correlated with the net charge of source molecules. Notably, the structures of C3a, C4a, and C5a are conserved in vertebrates, and the inactive overlapping peptides can become antibacterial peptides if mutated to possess enough net positive charges, indicating that net charge is the only factor determining the antibacterial properties of vertebrate C3a, C4a, and C5a. More importantly, many vertebrate C3a-, C4a-, and C5a-derived peptides possess high antibacterial activities yet exhibit no hemolytic activities, suggesting the application potential in anti-infective therapy. Taken together, our findings reveal that vertebrate C3a, C4a, and C5a are all sources of antibacterial peptides that will facilitate the design of excellent peptide antibiotics.
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Affiliation(s)
- Xu-Jie Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China; and
| | - Ya-Qin Zhong
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zi-You Ma
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Ya-Zhen Hu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jian-Guo Su
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yong-An Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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8
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Injectable and self-healing double network polysaccharide hydrogel as a minimally-invasive delivery platform. Carbohydr Polym 2022; 291:119585. [DOI: 10.1016/j.carbpol.2022.119585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/20/2022] [Accepted: 05/04/2022] [Indexed: 01/29/2023]
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9
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Lv H, Yan K, Guo Y, Zou Q, Hesham AEL, Liu B. AMPpred-EL: An effective antimicrobial peptide prediction model based on ensemble learning. Comput Biol Med 2022; 146:105577. [PMID: 35576825 DOI: 10.1016/j.compbiomed.2022.105577] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 11/15/2022]
Abstract
Antimicrobial peptides (AMPs) are important for the human immune system and are currently applied in clinical trials. AMPs have been received much attention for accurate recognition. Recently, several computational methods for identifying AMPs have been proposed. However, existing methods have difficulty in accurately predicting AMPs. In this paper, we propose a novel AMP prediction method called AMPpred-EL based on an ensemble learning strategy. AMPred-EL is constructed based on ensemble learning combined with LightGBM and logistic regression. Experimental results demonstrate that AMPpred-EL outperforms several state-of-the-art methods on the benchmark datasets and then improves the efficiency performance.
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Affiliation(s)
- Hongwu Lv
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Ke Yan
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yichen Guo
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China.
| | - Abd El-Latif Hesham
- Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni-Suef, 62511, Egypt.
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, 100081, China; Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, China.
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10
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Wei DX, Zhang XW. Biosynthesis, Bioactivity, Biosafety and Applications of Antimicrobial Peptides for Human Health. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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11
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Wu J, Guo R, Chai J, Xiong W, Tian M, Lu W, Xu X. The Protective Effects of Cath-MH With Anti-Propionibacterium Acnes and Anti-Inflammation Functions on Acne Vulgaris. Front Pharmacol 2021; 12:788358. [PMID: 34955858 PMCID: PMC8696257 DOI: 10.3389/fphar.2021.788358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/08/2021] [Indexed: 12/01/2022] Open
Abstract
Acne vulgaris is a common adolescent skin condition which is mainly caused by Propionibacterium acnes overcolonization and subsequent inflammation. Our previous studies have demonstrated that Cath-MH, an antimicrobial peptide from the skin of the frog Microhyla heymonsivogt, possesses potential antimicrobial, LPS-binding, and anti-septicemic properties. However, its protective effects and potential mechanisms against acne vulgaris are still unclear. In the present study, its anti-P. acnes effects were measured by two-fold broth dilution method, agglutination assay, scanning electron microscopy and confocal laser scanning microscopy experiments. Its treatment potential for acne vulgaris was further evaluated in mice ear inoculated by P. acnes. In addition, the binding ability between Cath-MH and LTA was measured by the Circular Dichroism and antibacterial assay. Moreover, the anti-inflammatory efficiency of Cath-MH was evaluated in LTA- and LPS-induced RAW 264.7 macrophage cells. Cath-MH was found to kill P. acnes with a MIC value of about 1.56 μM by membrane disruption mechanism. It also exhibited agglutination activity against P. acnes. Cath-MH was able to bind LTA as well as LPS, inhibit LTA/LPS-stimulated TLR2/4 expression, and subsequently decreased the inflammatory response in RAW 264.7 cells. As expected, Cath-MH alleviated the formation of edema and the infiltration of inflammatory cells in acne mouse model with concurrent suppression of P. acnes growth and inflammatory cytokines expression in vivo. The potent P. acnes inhibition activity combined with powerful anti-inflammatory effect of Cath-MH indicates its potential as a novel therapeutic option for acne vulgaris.
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Affiliation(s)
- Jiena Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Ruiyin Guo
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jinwei Chai
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Weichen Xiong
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Maolin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Wancheng Lu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Xueqing Xu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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12
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Miao F, Li Y, Tai Z, Zhang Y, Gao Y, Hu M, Zhu Q. Antimicrobial Peptides: The Promising Therapeutics for Cutaneous Wound Healing. Macromol Biosci 2021; 21:e2100103. [PMID: 34405955 DOI: 10.1002/mabi.202100103] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/31/2021] [Indexed: 12/12/2022]
Abstract
Chronic wound infections have caused an increasing number of deaths and economic burden, which necessitates wound treatment options. Hitherto, the development of functional wound dressings has achieved reasonable progress. Antibacterial agents, growth factors, and miRNAs are incorporated in different wound dressings to treat various types of wounds. As an effective antimicrobial agent and emerging wound healing therapeutic, antimicrobial peptides (AMPs) have attracted significant attention. The present study focuses on the application of AMPs in wound healing and discusses the types, properties and formulation strategies of AMPs used for wound healing. In addition, the clinical trial and the current status of studies on "antimicrobial peptides and wound healing" are elaborated through bibliometrics. Also, the challenges and opportunities for further development and utilization of AMP formulations in wound healing are discussed.
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Affiliation(s)
- Fengze Miao
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.,Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai, 200443, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Ying Li
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.,Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai, 200443, China
| | - Zongguang Tai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.,Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai, 200443, China
| | - Yong Zhang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Yue Gao
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Menghong Hu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.,Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai, 200443, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China
| | - Quangang Zhu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China.,Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai, 200443, China
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13
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Zhang Y, Lin J, Zhao L, Zeng X, Liu X. A novel antibacterial peptide recognition algorithm based on BERT. Brief Bioinform 2021; 22:6284370. [PMID: 34037687 DOI: 10.1093/bib/bbab200] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/19/2021] [Accepted: 05/03/2021] [Indexed: 12/31/2022] Open
Abstract
As the best substitute for antibiotics, antimicrobial peptides (AMPs) have important research significance. Due to the high cost and difficulty of experimental methods for identifying AMPs, more and more researches are focused on using computational methods to solve this problem. Most of the existing calculation methods can identify AMPs through the sequence itself, but there is still room for improvement in recognition accuracy, and there is a problem that the constructed model cannot be universal in each dataset. The pre-training strategy has been applied to many tasks in natural language processing (NLP) and has achieved gratifying results. It also has great application prospects in the field of AMP recognition and prediction. In this paper, we apply the pre-training strategy to the model training of AMP classifiers and propose a novel recognition algorithm. Our model is constructed based on the BERT model, pre-trained with the protein data from UniProt, and then fine-tuned and evaluated on six AMP datasets with large differences. Our model is superior to the existing methods and achieves the goal of accurate identification of datasets with small sample size. We try different word segmentation methods for peptide chains and prove the influence of pre-training steps and balancing datasets on the recognition effect. We find that pre-training on a large number of diverse AMP data, followed by fine-tuning on new data, is beneficial for capturing both new data's specific features and common features between AMP sequences. Finally, we construct a new AMP dataset, on which we train a general AMP recognition model.
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Affiliation(s)
- Yue Zhang
- Xiamen University, Xiamen 361005, China
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14
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Abstract
The activity of many antibiotics depends on the initial density of cells used in bacterial growth inhibition assays. This phenomenon, termed the inoculum effect, can have important consequences for the therapeutic efficacy of the drugs, because bacterial loads vary by several orders of magnitude in clinically relevant infections. Antimicrobial peptides are a promising class of molecules in the fight against drug-resistant bacteria because they act mainly by perturbing the cell membranes rather than by inhibiting intracellular targets. Here, we report a systematic characterization of the inoculum effect for this class of antibacterial compounds. Minimum inhibitory concentration values were measured for 13 peptides (including all-D enantiomers) and peptidomimetics, covering more than seven orders of magnitude in inoculated cell density. In most cases, the inoculum effect was significant for cell densities above the standard inoculum of 5 × 105 cells/mL, while for lower densities the active concentrations remained essentially constant, with values in the micromolar range. In the case of membrane-active peptides, these data can be rationalized by considering a simple model, taking into account peptide-cell association, and hypothesizing that a threshold number of cell-bound peptide molecules is required in order to cause bacterial killing. The observed effect questions the clinical utility of activity and selectivity determinations performed at a fixed, standardized cell density. A routine evaluation of the dependence of the activity of antimicrobial peptides and peptidomimetics on the inoculum should be considered.
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15
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The Spectrum of Design Solutions for Improving the Activity-Selectivity Product of Peptide Antibiotics against Multidrug-Resistant Bacteria and Prostate Cancer PC-3 Cells. Molecules 2020; 25:molecules25153526. [PMID: 32752241 PMCID: PMC7436000 DOI: 10.3390/molecules25153526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/24/2022] Open
Abstract
The link between the antimicrobial and anticancer activity of peptides has long been studied, and the number of peptides identified with both activities has recently increased considerably. In this work, we hypothesized that designed peptides with a wide spectrum of selective antimicrobial activity will also have anticancer activity, and tested this hypothesis with newly designed peptides. The spectrum of peptides, used as partial or full design templates, ranged from cell-penetrating peptides and putative bacteriocin to those from the simplest animals (placozoans) and the Chordata phylum (anurans). We applied custom computational tools to predict amino acid substitutions, conferring the increased product of bacteriostatic activity and selectivity. Experiments confirmed that better overall performance was achieved with respect to that of initial templates. Nine of our synthesized helical peptides had excellent bactericidal activity against both standard and multidrug-resistant bacteria. These peptides were then compared to a known anticancer peptide polybia-MP1, for their ability to kill prostate cancer cells and dermal primary fibroblasts. The therapeutic index was higher for seven of our peptides, and anticancer activity stronger for all of them. In conclusion, the peptides that we designed for selective antimicrobial activity also have promising potential for anticancer applications.
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16
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Tavares TD, Antunes JC, Padrão J, Ribeiro AI, Zille A, Amorim MTP, Ferreira F, Felgueiras HP. Activity of Specialized Biomolecules against Gram-Positive and Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:E314. [PMID: 32526972 PMCID: PMC7344598 DOI: 10.3390/antibiotics9060314] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 11/24/2022] Open
Abstract
The increased resistance of bacteria against conventional pharmaceutical solutions, the antibiotics, has raised serious health concerns. This has stimulated interest in the development of bio-based therapeutics with limited resistance, namely, essential oils (EOs) or antimicrobial peptides (AMPs). This study envisaged the evaluation of the antimicrobial efficacy of selected biomolecules, namely LL37, pexiganan, tea tree oil (TTO), cinnamon leaf oil (CLO) and niaouli oil (NO), against four bacteria commonly associated to nosocomial infections: Staphylococcus aureus, Staphylococcus epidermidis, Escherichia coli and Pseudomonas aeruginosa. The antibiotic vancomycin and silver nanoparticles (AgNPs) were used as control compounds for comparison purposes. The biomolecules were initially screened for their antibacterial efficacy using the agar-diffusion test, followed by the determination of minimal inhibitory concentrations (MICs), kill-time kinetics and the evaluation of the cell morphology upon 24 h exposure. All agents were effective against the selected bacteria. Interestingly, the AgNPs required a higher concentration (4000-1250 µg/mL) to induce the same effects as the AMPs (500-7.8 µg/mL) or EOs (365.2-19.7 µg/mL). Pexiganan and CLO were the most effective biomolecules, requiring lower concentrations to kill both Gram-positive and Gram-negative bacteria (62.5-7.8 µg/mL and 39.3-19.7 µg/mL, respectively), within a short period of time (averaging 2 h 15 min for all bacteria). Most biomolecules apparently disrupted the bacteria membrane stability due to the observed cell morphology deformation and by effecting on the intracellular space. AMPs were observed to induce morphological deformations and cellular content release, while EOs were seen to split and completely envelope bacteria. Data unraveled more of the potential of these new biomolecules as replacements for the conventional antibiotics and allowed us to take a step forward in the understanding of their mechanisms of action against infection-related bacteria.
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Affiliation(s)
| | | | | | | | | | | | | | - Helena P. Felgueiras
- Centre for Textile Science and Technology (2C2T), Department of Textile Engineering, University of Minho, Campus of Azurém, 4800-058 Guimarães, Portugal; (T.D.T.); (J.C.A.); (J.P.); (A.I.R.); (A.Z.); (M.T.P.A.); (F.F.)
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17
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Abstract
Antibacterial agents are a group of materials that selectively destroy bacteria by interfering with bacterial growth or survival. With the emergence of resistance phenomenon of bacterial pathogens to current antibiotics, new drugs are frequently entering into the market along with the existing drugs, and the alternative compounds with antibacterial functions are being explored. Due to the advantages of their inherent biochemical and biophysical properties including precise targeting ability, biocompatibility, biodegradability, long blood circulation time, and low cytotoxicity, biomolecules such as peptides, carbohydrates, and nucleic acids have huge potential for the antimicrobial application and have been extensively studied in recent years. In this review, antimicrobial therapeutic agents composed of three kinds of functional biological molecules were summarized. In addition, the research progress of antibacterial mechanism, chemical modification, and nanoparticle coupling of those biomolecules were also discussed.
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18
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Su X, Xu J, Yin Y, Quan X, Zhang H. Antimicrobial peptide identification using multi-scale convolutional network. BMC Bioinformatics 2019; 20:730. [PMID: 31870282 PMCID: PMC6929291 DOI: 10.1186/s12859-019-3327-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/16/2019] [Indexed: 01/14/2023] Open
Abstract
Background Antibiotic resistance has become an increasingly serious problem in the past decades. As an alternative choice, antimicrobial peptides (AMPs) have attracted lots of attention. To identify new AMPs, machine learning methods have been commonly used. More recently, some deep learning methods have also been applied to this problem. Results In this paper, we designed a deep learning model to identify AMP sequences. We employed the embedding layer and the multi-scale convolutional network in our model. The multi-scale convolutional network, which contains multiple convolutional layers of varying filter lengths, could utilize all latent features captured by the multiple convolutional layers. To further improve the performance, we also incorporated additional information into the designed model and proposed a fusion model. Results showed that our model outperforms the state-of-the-art models on two AMP datasets and the Antimicrobial Peptide Database (APD)3 benchmark dataset. The fusion model also outperforms the state-of-the-art model on an anti-inflammatory peptides (AIPs) dataset at the accuracy. Conclusions Multi-scale convolutional network is a novel addition to existing deep neural network (DNN) models. The proposed DNN model and the modified fusion model outperform the state-of-the-art models for new AMP discovery. The source code and data are available at https://github.com/zhanglabNKU/APIN.
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Affiliation(s)
- Xin Su
- College of Artificial Intelligence, Nankai University, Tongyan Road, Tianjin, 300350, China
| | - Jing Xu
- College of Computer Science, Nankai University, Tongyan Road, Tianjin, 300350, China
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, 1400 R Street, Lincoln, NE, 68588, USA
| | - Xiongwen Quan
- College of Artificial Intelligence, Nankai University, Tongyan Road, Tianjin, 300350, China
| | - Han Zhang
- College of Artificial Intelligence, Nankai University, Tongyan Road, Tianjin, 300350, China.
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19
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Xie F, Zan Y, Zhang Y, Zheng N, Yan Q, Zhang W, Zhang H, Jin M, Chen F, Zhang X, Liu S. The cysteine protease ApdS from Streptococcus suis promotes evasion of innate immune defenses by cleaving the antimicrobial peptide cathelicidin LL-37. J Biol Chem 2019; 294:17962-17977. [PMID: 31619521 DOI: 10.1074/jbc.ra119.009441] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/11/2019] [Indexed: 12/17/2022] Open
Abstract
Streptococcus suis is a globally distributed zoonotic pathogen associated with meningitis and septicemia in humans, posing a serious threat to public health. To successfully invade and disseminate within its host, this bacterium must overcome the innate immune system. The antimicrobial peptide LL-37 impedes invading pathogens by directly perforating bacterial membranes and stimulating the immune function of neutrophils, which are the major effector cells against S. suis However, little is known about the biological relationship between S. suis and LL-37 and how this bacterium adapts to and evades LL-37-mediated immune responses. In this study by using an array of approaches, including enzyme, chemotaxis, cytokine assays, quantitative RT-PCR, and CD spectroscopy, we found that the cysteine protease ApdS from S. suis cleaves LL-37 and thereby plays a key role in the interaction between S. suis and human neutrophils. S. suis infection stimulated LL-37 production in human neutrophils, and S. suis exposure to LL-37 up-regulated ApdS protease expression in the bacterium. We observed that ApdS targets and rapidly cleaves LL-37, impairing its bactericidal activity against S. suis We attributed this effect to the decreased helical content of the secondary structure in the truncated peptide. Moreover, ApdS rescued S. suis from killing by human neutrophils and neutrophil extracellular traps because LL-37 truncation attenuated neutrophil chemotaxis and inhibited the formation of extracellular traps and the production of reactive oxygen species. Altogether, our findings reveal an immunosuppressive strategy of S. suis whereby the bacterium blunts the innate host defenses via ApdS protease-mediated LL-37 cleavage.
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Affiliation(s)
- Fang Xie
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yanan Zan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yueling Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Ning Zheng
- First Affiliated Hospital of Dalian Medical University, 116044 Dalian, China
| | - Qiulong Yan
- College of Basic Medical Science, Dalian Medical University, 116044 Dalian, China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Huihui Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Mingjie Jin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Fuguang Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xinyuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.,College of Veterinary Medicine, Inner Mongolia Agricultural University, 010018 Huhehaote, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
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20
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Veltri D, Kamath U, Shehu A. Deep learning improves antimicrobial peptide recognition. Bioinformatics 2019; 34:2740-2747. [PMID: 29590297 PMCID: PMC6084614 DOI: 10.1093/bioinformatics/bty179] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/28/2018] [Indexed: 01/09/2023] Open
Abstract
Motivation Bacterial resistance to antibiotics is a growing concern. Antimicrobial peptides (AMPs), natural components of innate immunity, are popular targets for developing new drugs. Machine learning methods are now commonly adopted by wet-laboratory researchers to screen for promising candidates. Results In this work, we utilize deep learning to recognize antimicrobial activity. We propose a neural network model with convolutional and recurrent layers that leverage primary sequence composition. Results show that the proposed model outperforms state-of-the-art classification models on a comprehensive dataset. By utilizing the embedding weights, we also present a reduced-alphabet representation and show that reasonable AMP recognition can be maintained using nine amino acid types. Availability and implementation Models and datasets are made freely available through the Antimicrobial Peptide Scanner vr.2 web server at www.ampscanner.com. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Veltri
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, Rockville, MD, USA.,Medical Science & Computing, LLC, Rockville, MD, USA
| | | | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, VA, USA.,Department of Bioengineering, George Mason University, Fairfax, VA, USA.,School of Systems Biology, George Mason University, Manassas, VA, USA
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21
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Saigo N, Izumi K, Kawano R. Electrophysiological Analysis of Antimicrobial Peptides in Diverse Species. ACS OMEGA 2019; 4:13124-13130. [PMID: 31460440 PMCID: PMC6705042 DOI: 10.1021/acsomega.9b01033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/24/2019] [Indexed: 05/25/2023]
Abstract
This study describes a technical platform that allows us to measure the pore-forming activity of antimicrobial peptides (AMPs) in the lipid bilayer and estimate antimicrobial activity. We selected six different AMPs of diverse species from urochordata to vertebrata and measured the channel current signals using a microfabricated lipid bilayer system. As a result of the electrophysiological measurements, we were able to estimate the pore-forming activity and roughly predict the antimicrobial activity although there was not a strong correlation between the pore-forming activity and the variety of species. Our method will be a unique tool for analyzing a wide variety of diverse AMPs.
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Affiliation(s)
- Naoki Saigo
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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22
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Unifying structural signature of eukaryotic α-helical host defense peptides. Proc Natl Acad Sci U S A 2019; 116:6944-6953. [PMID: 30877253 DOI: 10.1073/pnas.1819250116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Diversity of α-helical host defense peptides (αHDPs) contributes to immunity against a broad spectrum of pathogens via multiple functions. Thus, resolving common structure-function relationships among αHDPs is inherently difficult, even for artificial-intelligence-based methods that seek multifactorial trends rather than foundational principles. Here, bioinformatic and pattern recognition methods were applied to identify a unifying signature of eukaryotic αHDPs derived from amino acid sequence, biochemical, and three-dimensional properties of known αHDPs. The signature formula contains a helical domain of 12 residues with a mean hydrophobic moment of 0.50 and favoring aliphatic over aromatic hydrophobes in 18-aa windows of peptides or proteins matching its semantic definition. The holistic α-core signature subsumes existing physicochemical properties of αHDPs, and converged strongly with predictions of an independent machine-learning-based classifier recognizing sequences inducing negative Gaussian curvature in target membranes. Queries using the α-core formula identified 93% of all annotated αHDPs in proteomic databases and retrieved all major αHDP families. Synthesis and antimicrobial assays confirmed efficacies of predicted sequences having no previously known antimicrobial activity. The unifying α-core signature establishes a foundational framework for discovering and understanding αHDPs encompassing diverse structural and mechanistic variations, and affords possibilities for deterministic design of antiinfectives.
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23
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Homma K, Anbo H, Noguchi T, Fukuchi S. Both Intrinsically Disordered Regions and Structural Domains Evolve Rapidly in Immune-Related Mammalian Proteins. Int J Mol Sci 2018; 19:ijms19123860. [PMID: 30518031 PMCID: PMC6321239 DOI: 10.3390/ijms19123860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 12/01/2018] [Accepted: 12/02/2018] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic proteins consist of structural domains (SDs) and intrinsically disordered regions (IDRs), i.e., regions that by themselves do not assume unique three-dimensional structures. IDRs are generally subject to less constraint and evolve more rapidly than SDs. Proteins with a lower number of protein-to-protein interactions (PPIs) are also less constrained and tend to evolve fast. Extracellular proteins of mammals, especially immune-related extracellular proteins, on average have relatively high evolution rates. This article aims to examine if a high evolution rate in IDRs or that in SDs accounts for the rapid evolution of extracellular proteins. To this end, we classified eukaryotic proteins based on their cellular localizations and analyzed them. Moreover, we divided proteins into SDs and IDRs and calculated the respective evolution rate. Fractional IDR content is positively correlated with evolution rate. For their fractional IDR content, immune-related extracellular proteins show an aberrantly high evolution rate. IDRs evolve more rapidly than SDs in most subcellular localizations. In extracellular proteins, however, the difference is diminished. For immune-related proteins in mammals in particular, the evolution rates in SDs come close to those in IDRs. Thus high evolution rates in both IDRs and SDs account for the rapid evolution of immune-related proteins.
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Affiliation(s)
- Keiichi Homma
- Department of Life Science and Informatics, Maebashi Institute of Technology, 460-1 Kamisadori-machi, Maebashi-shi 371-0816, Japan.
| | - Hiroto Anbo
- Department of Life Science and Informatics, Maebashi Institute of Technology, 460-1 Kamisadori-machi, Maebashi-shi 371-0816, Japan.
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose-shi, Tokyo 204-8588, Japan.
| | - Satoshi Fukuchi
- Department of Life Science and Informatics, Maebashi Institute of Technology, 460-1 Kamisadori-machi, Maebashi-shi 371-0816, Japan.
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24
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Pacor S, Guida F, Xhindoli D, Benincasa M, Gennaro R, Tossi A. Effect of targeted minimal sequence variations on the structure and biological activities of the human cathelicidin LL‐37. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sabrina Pacor
- Department of Life SciencesUniversity of Trieste, Building Q, Via Giorgieri 5 Trieste 34127 Italy
| | - Filomena Guida
- Department of Life SciencesUniversity of Trieste, Building Q, Via Giorgieri 5 Trieste 34127 Italy
| | - Daniela Xhindoli
- Department of Life SciencesUniversity of Trieste, Building Q, Via Giorgieri 5 Trieste 34127 Italy
| | - Monica Benincasa
- Department of Life SciencesUniversity of Trieste, Building Q, Via Giorgieri 5 Trieste 34127 Italy
| | - Renato Gennaro
- Department of Life SciencesUniversity of Trieste, Building Q, Via Giorgieri 5 Trieste 34127 Italy
| | - Alessandro Tossi
- Department of Life SciencesUniversity of Trieste, Building Q, Via Giorgieri 5 Trieste 34127 Italy
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25
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Savini F, Bobone S, Roversi D, Mangoni ML, Stella L. From liposomes to cells: Filling the gap between physicochemical and microbiological studies of the activity and selectivity of host‐defense peptides. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24041] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Filippo Savini
- Department of Chemical Science and TechnologiesUniversity of Rome Tor VergataRome00133 Italy
| | - Sara Bobone
- Department of Chemical Science and TechnologiesUniversity of Rome Tor VergataRome00133 Italy
| | - Daniela Roversi
- Department of Chemical Science and TechnologiesUniversity of Rome Tor VergataRome00133 Italy
| | - Maria Luisa Mangoni
- Department of Biochemical Sciences, Laboratory affiliated to Pasteur Italia‐Fondazione Cenci BolognettiSapienza University of RomeRome, via degli Apuli9‐00185 Italy
| | - Lorenzo Stella
- Department of Chemical Science and TechnologiesUniversity of Rome Tor VergataRome00133 Italy
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26
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Yan M, Tian HF, Hu QM, Xiao HB. Molecular Cloning of Cathelicidin-like cDNA from Andrias davidianus. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541801012x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Mercurio FA, Di Natale C, Pirone L, Iannitti R, Marasco D, Pedone EM, Palumbo R, Leone M. The Sam-Sam interaction between Ship2 and the EphA2 receptor: design and analysis of peptide inhibitors. Sci Rep 2017; 7:17474. [PMID: 29234063 PMCID: PMC5727260 DOI: 10.1038/s41598-017-17684-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
The lipid phosphatase Ship2 represents a drug discovery target for the treatment of different diseases, including cancer. Its C-terminal sterile alpha motif domain (Ship2-Sam) associates with the Sam domain from the EphA2 receptor (EphA2-Sam). This interaction is expected to mainly induce pro-oncogenic effects in cells therefore, inhibition of the Ship2-Sam/EphA2-Sam complex may represent an innovative route to discover anti-cancer therapeutics. In the present work, we designed and analyzed several peptide sequences encompassing the interaction interface of EphA2-Sam for Ship2-Sam. Peptide conformational analyses and interaction assays with Ship2-Sam conducted through diverse techniques (CD, NMR, SPR and MST), identified a positively charged penta-amino acid native motif in EphA2-Sam, that once repeated three times in tandem, binds Ship2-Sam. NMR experiments show that the peptide targets the negatively charged binding site of Ship2-Sam for EphA2-Sam. Preliminary in vitro cell-based assays indicate that -at 50 µM concentration- it induces necrosis of PC-3 prostate cancer cells with more cytotoxic effect on cancer cells than on normal dermal fibroblasts. This work represents a pioneering study that opens further opportunities for the development of inhibitors of the Ship2-Sam/EphA2-Sam complex for therapeutic applications.
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Affiliation(s)
- Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Concetta Di Natale
- Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Luciano Pirone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Roberta Iannitti
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Daniela Marasco
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.,Department of Pharmacy, Research Centre on Bioactive Peptides (CIRPeB), University of Naples "Federico II", Via Mezzocannone 16, 80134, Naples, Italy
| | - Emilia Maria Pedone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Rosanna Palumbo
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Naples, Italy.
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28
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707535] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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Wood SE, Sinsinbar G, Gudlur S, Nallani M, Huang CF, Liedberg B, Mrksich M. A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT. Angew Chem Int Ed Engl 2017; 56:16531-16535. [DOI: 10.1002/anie.201707535] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah E. Wood
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Gaurav Sinsinbar
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Sushanth Gudlur
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Madhavan Nallani
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Che-Fan Huang
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Liedberg
- Center for Biomimetic Sensor Science; School of Materials Science & Engineering; Nanyang Technological University; 50 Nanyang Drive 637553 Singapore
| | - Milan Mrksich
- Departments of Chemistry and Biomedical Engineering; Northwestern University; 2145 Sheridan Road Evanston IL 60208 USA
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Barksdale SM, Hrifko EJ, van Hoek ML. Cathelicidin antimicrobial peptide from Alligator mississippiensis has antibacterial activity against multi-drug resistant Acinetobacter baumanii and Klebsiella pneumoniae. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 70:135-144. [PMID: 28089718 DOI: 10.1016/j.dci.2017.01.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 06/06/2023]
Abstract
Alligator mississippiensis (American alligator), a member of order Crocodilia, lives in bacteria-laden environments but is not often known to succumb to bacterial infections. Their serum has been shown to have antibacterial activity beyond that of human serum, and it is believed that this activity is partially due to cationic antimicrobial peptides (CAMPs). CAMPs are produced by many organisms as part of the innate immune system. CAMPs are attractive possible therapies against multi-drug resistant bacteria, such as those found in biofilm-infected war wounds, because they seldom cause genetic resistance in bacteria and are effective against antibiotic resistant bacteria. In this work, we identified, synthesized, and characterized a cathelicidin and two shorter fragments from the American alligator. We discovered the cathelicidin using Basic Local Alignment Search Tool (BLAST) alignment and by comparing A. mississippiensis expressed sequence tags (ESTs) with propeptide cathelicidins of other reptiles. We analyzed the structure using bioinformatics tools and circular dichroism and predicted that the full-length cathelicidin peptide has a mixed structure, with an N-terminal α-helix and a center Pro hinge. In minimal inhibitory concentration (MIC) assays, it was determined that the cathelicidin and the two shorter fragments have strong activity against multiple Gram-negative bacteria, including clinical isolates of multi-drug resistant (MDR) Acinetobacter baumannii and carbapenem-resistant Klebsiella pneumoniae. Using the ethidium bromide uptake assay, it was found that these peptides permeabilize the bacterial membrane and are less sensitive to salt inhibition than many other known CAMPs. The alligator cathelicidin peptides were not hemolytic against sheep red blood cells at 300 μg/ml and were not significantly cytotoxic against A549 human lung epithelial cells after 24 h exposure in 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays. These alligator cathelicidin peptides have activity similar to other CAMPs from reptiles such as NA-CATH. It is possible that the alligator cathelicidins play an important role in the innate immune response of A. mississippiensis, similar to LL-37 in humans. In addition, due to their activities against MDR bacteria and lack of cytotoxicity, the AM-CATH peptides could be an attractive platform for further development as a potential therapeutic.
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Affiliation(s)
| | - Evelyn J Hrifko
- College of Science, George Mason University, Manassas, VA, USA
| | - Monique L van Hoek
- School of Systems Biology, George Mason University, Manassas, VA, USA; College of Science, George Mason University, Manassas, VA, USA; National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA, USA.
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31
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Christiansen SH, Zhang X, Juul-Madsen K, Hvam ML, Vad BS, Behrens MA, Thygesen IL, Jalilian B, Pedersen JS, Howard KA, Otzen DE, Vorup-Jensen T. The random co-polymer glatiramer acetate rapidly kills primary human leukocytes through sialic-acid-dependent cell membrane damage. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:425-437. [PMID: 28064019 DOI: 10.1016/j.bbamem.2017.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/12/2016] [Accepted: 01/02/2017] [Indexed: 01/02/2023]
Abstract
The formulation glatiramer acetate (GA) is widely used in therapy of multiple sclerosis. GA consists of random copolymers of four amino acids, in ratios that produce a predominantly positive charge and an amphipathic character. With the extraordinary complexity of the drug, several pharmacological modes-of-action were suggested, but so far none, which rationalizes the cationicity and amphipathicity as part of the mode-of-action. Here, we report that GA rapidly kills primary human T lymphocytes and, less actively, monocytes. LL-37 is a cleavage product of human cathelicidin with important roles in innate immunity. It shares the positive charge and amphipathic character of GA, and, as shown here, also the ability to kill human leukocyte. The cytotoxicity of both compounds depends on sialic acid in the cell membrane. The killing was associated with the generation of CD45+ debris, derived from cell membrane deformation. Nanoparticle tracking analysis confirmed the formation of such debris, even at low GA concentrations. Electric cell-substrate impedance sensing measurements also recorded stable alterations in T lymphocytes following such treatment. LL-37 forms oligomers through weak hydrophobic contacts, which is critical for the lytic properties. In our study, SAXS showed that GA also forms this type of contacts. Taken together, our study offers new insight on the immunomodulatory mode-of-action of positively charged co-polymers. The comparison of LL-37 and GA highlights a consistent requirement of certain oligomeric and chemical properties to support cytotoxic effects of cationic polymers targeting human leukocytes.
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Affiliation(s)
- Stig Hill Christiansen
- Dept. of Biomedicine, Aarhus University, The Bartholin Building (1240), Bartholins Allé 6, DK-8000 Aarhus C, Denmark.
| | - Xianwei Zhang
- Dept. of Biomedicine, Aarhus University, The Bartholin Building (1240), Bartholins Allé 6, DK-8000 Aarhus C, Denmark.
| | - Kristian Juul-Madsen
- Dept. of Biomedicine, Aarhus University, The Bartholin Building (1240), Bartholins Allé 6, DK-8000 Aarhus C, Denmark.
| | - Michael Lykke Hvam
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - Brian Stougaard Vad
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - Manja Annette Behrens
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - Ida Lysgaard Thygesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; Dept. of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark.
| | - Babak Jalilian
- Dept. of Biomedicine, Aarhus University, The Bartholin Building (1240), Bartholins Allé 6, DK-8000 Aarhus C, Denmark.
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - Kenneth A Howard
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; The Lundbeck Foundation Nanomedicine Center for Individualized Management of Tissue Damage and Regeneration (LUNA), Aarhus University, Denmark.
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
| | - Thomas Vorup-Jensen
- Dept. of Biomedicine, Aarhus University, The Bartholin Building (1240), Bartholins Allé 6, DK-8000 Aarhus C, Denmark; Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark; The Lundbeck Foundation Nanomedicine Center for Individualized Management of Tissue Damage and Regeneration (LUNA), Aarhus University, Denmark; MEMBRANES Research Center, Aarhus University, Denmark; Center for Neurodegenerative Inflammation Prevention (NEURODIN), Aarhus University, Denmark.
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32
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Positive selection in cathelicidin host defense peptides: adaptation to exogenous pathogens or endogenous receptors? Heredity (Edinb) 2016; 118:453-465. [PMID: 27925615 PMCID: PMC5564380 DOI: 10.1038/hdy.2016.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/28/2016] [Accepted: 10/03/2016] [Indexed: 11/24/2022] Open
Abstract
The cause of adaptive protein evolution includes internal (for example, co-evolution of ligand-receptor pairs) and external (for example, adaptation to different ecological niches) mechanisms. Host defense peptides (HDPs) are a class of vertebrate-specific cationic antimicrobial peptides evolving under positive selection. Besides their antibiotic activity, HDPs also exert an effect on multiple host immune cells, thus providing an ideal model to study selective agents driving their evolution. On the basis of a combination of computational and experimental approaches, we studied the evolution of LL-37-type HDPs in mammals, the mature peptide of cathelicidin CAP18 (herein termed CAP18-MP) and investigated the driving force behind the evolution. Using codon-substitution maximum likelihood models, we analyzed CAP18-MPs in 40 species belonging to nine mammalian Orders and identified four positively selected sites (PSSs) that all are located on two terminal unordered regions of CAP18-MPs. Grafting the two positively selected regions of human or whale CAP18-MP to the α-helical scaffold of a rabbit homolog (substituting its corresponding parts) led to no alterations in antibacterial activity, spectrum and action mode. Likewise, further deletion of the two terminal regions did not alter its functional features. Evolutionary conservation analysis of mammalian FPR2, a receptor known to interact with the C-terminal positively selected region of LL-37, revealed high evolutionary variability in its ligand-binding extracellular loop domains, matching sequence diversity of the unordered regions in CAP18-MPs. This is the first report describing that the signature of positive selection of cathelicidins is not associated with their direct bactericidal activity, but rather with the evolutionary variability of their endogenous receptors.
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D'Este F, Benincasa M, Cannone G, Furlan M, Scarsini M, Volpatti D, Gennaro R, Tossi A, Skerlavaj B, Scocchi M. Antimicrobial and host cell-directed activities of Gly/Ser-rich peptides from salmonid cathelicidins. FISH & SHELLFISH IMMUNOLOGY 2016; 59:456-468. [PMID: 27818338 DOI: 10.1016/j.fsi.2016.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/28/2016] [Accepted: 11/02/2016] [Indexed: 06/06/2023]
Abstract
Cathelicidins, a major family of vertebrate antimicrobial peptides (AMPs), have a recognized role in the first line of defense against infections. They have been identified in several salmonid species, where the putative mature peptides are unusually long and rich in serine and glycine residues, often arranged in short multiple repeats (RLGGGS/RPGGGS) intercalated by hydrophobic motifs. Fragments of 24-40 residues, spanning specific motifs and conserved sequences in grayling or brown, rainbow and brook trout, were chemically synthesized and examined for antimicrobial activity against relevant Gram-positive and Gram-negative salmonid pathogens, as well as laboratory reference strains. They were not active in complete medium, but showed varying potency and activity spectra in diluted media. Bacterial membrane permeabilization also occurred only under these conditions and was indicated by rapid propidium iodide uptake in peptide-treated bacteria. However, circular dichroism analyses indicated that they did not significantly adopt ordered conformations in membrane-like environments. The peptides were not hemolytic or cytotoxic to trout cells, including freshly purified head kidney leukocytes (HKL) and the fibroblastic RTG-2 cell line. Notably, when exposed to them, HKL showed increased metabolic activity, while a growth-promoting effect was observed on RTG-2 cells, suggesting a functional interaction of salmonid cathelicidins with host cells similar to that shown by mammalian ones. The three most active peptides produced a dose-dependent increase in phagocytic uptake by HKL simultaneously stimulated with bacterial particles. The peptide STF(1-37), selected for further analyses, also enhanced phagocytic uptake in the presence of autologous serum, and increased intracellular killing of live E. coli. Furthermore, when tested on HKL in combination with the immunostimulant β-glucan, it synergistically potentiated both phagocytic uptake and the respiratory burst response, activities that play a key role in fish immunity. Collectively, these data point to a role of salmonid cathelicidins as modulators of fish microbicidal mechanisms beyond a salt-sensitive antimicrobial activity, and encourage further studies also in view of potential applications in aquaculture.
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Affiliation(s)
- Francesca D'Este
- Department of Medical and Biological Sciences, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Monica Benincasa
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Giuseppe Cannone
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Michela Furlan
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Michele Scarsini
- Department of Medical and Biological Sciences, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Donatella Volpatti
- Department of Agricultural, Food, Environmental and Animal Sciences, Via Sondrio 2/a, 33100 Udine, Italy
| | - Renato Gennaro
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Barbara Skerlavaj
- Department of Medical and Biological Sciences, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy.
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Lishko VK, Moreno B, Podolnikova NP, Ugarova TP. Identification of Human Cathelicidin Peptide LL-37 as a Ligand for Macrophage Integrin α Mβ 2 (Mac-1, CD11b/CD18) that Promotes Phagocytosis by Opsonizing Bacteria. ACTA ACUST UNITED AC 2016; 2016:39-55. [PMID: 27990411 DOI: 10.2147/rrbc.s107070] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
LL-37, a cationic antimicrobial peptide, has numerous immune-modulating effects. However, the identity of a receptor(s) mediating the responses in immune cells remains uncertain. We have recently demonstrated that LL-37 interacts with the αMI-domain of integrin αMβ2 (Mac-1), a major receptor on the surface of myeloid cells, and induces a migratory response in Mac-1-expressing monocyte/macrophages as well as activation of Mac-1 on neutrophils. Here, we show that LL-37 and its C-terminal derivative supported strong adhesion of various Mac-1-expressing cells, including HEK293 cells stably transfected with Mac-1, human U937 monocytic cells and murine IC-21 macrophages. The cell adhesion to LL-37 was partially inhibited by specific Mac-1 antagonists, including mAb against the αM integrin subunit and neutrophil inhibitory factor, and completely blocked when anti-Mac-1 antibodies were combined with heparin, suggesting that cell surface heparan sulfate proteoglycans act cooperatively with integrin Mac-1. Coating both Gram-negative and Gram-positive bacteria with LL-37 significantly potentiated their phagocytosis by macrophages, and this process was blocked by a combination of anti-Mac-1 mAb and heparin. Furthermore, phagocytosis by wild-type murine peritoneal macrophages of LL-37-coated latex beads, a model of foreign surfaces, was several fold higher than that of untreated beads. By contrast, LL-37 failed to augment phagocytosis of beads by Mac-1-deficient macrophages. These results identify LL-37 as a novel ligand for integrin Mac-1 and demonstrate that the interaction between Mac-1 on macrophages and bacteria-bound LL-37 promotes phagocytosis.
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Affiliation(s)
- Valeryi K Lishko
- Center for Metabolic and Vascular Biology, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Benjamin Moreno
- Center for Metabolic and Vascular Biology, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Nataly P Podolnikova
- Center for Metabolic and Vascular Biology, School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Tatiana P Ugarova
- Center for Metabolic and Vascular Biology, School of Life Sciences, Arizona State University, Tempe, AZ 85287
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35
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Destabilization of α-Helical Structure in Solution Improves Bactericidal Activity of Antimicrobial Peptides: Opposite Effects on Bacterial and Viral Targets. Antimicrob Agents Chemother 2016; 60:1984-91. [PMID: 26824944 PMCID: PMC4808201 DOI: 10.1128/aac.02146-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/30/2015] [Indexed: 11/20/2022] Open
Abstract
We have previously examined the mechanism of antimicrobial peptides on the outer membrane of vaccinia virus. We show here that the formulation of peptides LL37 and magainin-2B amide in polysorbate 20 (Tween 20) results in greater reductions in virus titer than formulation without detergent, and the effect is replicated by substitution of polysorbate 20 with high-ionic-strength buffer. In contrast, formulation with polysorbate 20 or high-ionic-strength buffer has the opposite effect on bactericidal activity of both peptides, resulting in lesser reductions in titer for both Gram-positive and Gram-negative bacteria. Circular dichroism spectroscopy shows that the differential action of polysorbate 20 and salt on the virucidal and bactericidal activities correlates with the α-helical content of peptide secondary structure in solution, suggesting that the virucidal and bactericidal activities are mediated through distinct mechanisms. The correlation of a defined structural feature with differential activity against a host-derived viral membrane and the membranes of both Gram-positive and Gram-negative bacteria suggests that the overall helical content in solution under physiological conditions is an important feature for consideration in the design and development of candidate peptide-based antimicrobial compounds.
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36
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Tanphaichitr N, Srakaew N, Alonzi R, Kiattiburut W, Kongmanas K, Zhi R, Li W, Baker M, Wang G, Hickling D. Potential Use of Antimicrobial Peptides as Vaginal Spermicides/Microbicides. Pharmaceuticals (Basel) 2016; 9:E13. [PMID: 26978373 PMCID: PMC4812377 DOI: 10.3390/ph9010013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/11/2022] Open
Abstract
The concurrent increases in global population and sexually transmitted infection (STI) demand a search for agents with dual spermicidal and microbicidal properties for topical vaginal application. Previous attempts to develop the surfactant spermicide, nonoxynol-9 (N-9), into a vaginal microbicide were unsuccessful largely due to its inefficiency to kill microbes. Furthermore, N-9 causes damage to the vaginal epithelium, thus accelerating microbes to enter the women's body. For this reason, antimicrobial peptides (AMPs), naturally secreted by all forms of life as part of innate immunity, deserve evaluation for their potential spermicidal effects. To date, twelve spermicidal AMPs have been described including LL-37, magainin 2 and nisin A. Human cathelicidin LL-37 is the most promising spermicidal AMP to be further developed for vaginal use for the following reasons. First, it is a human AMP naturally produced in the vagina after intercourse. Second, LL-37 exerts microbicidal effects to numerous microbes including those that cause STI. Third, its cytotoxicity is selective to sperm and not to the female reproductive tract. Furthermore, the spermicidal effects of LL-37 have been demonstrated in vivo in mice. Therefore, the availability of LL-37 as a vaginal spermicide/microbicide will empower women for self-protection against unwanted pregnancies and STI.
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Affiliation(s)
- Nongnuj Tanphaichitr
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Biochemistry, Microbiology, Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, ON, Canada.
| | - Nopparat Srakaew
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Rhea Alonzi
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Department of Biochemistry, Microbiology, Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, ON, Canada.
| | - Wongsakorn Kiattiburut
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
| | - Kessiri Kongmanas
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Division of Dengue Hemorrhagic Fever Research Unit, Office of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | - Ruina Zhi
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Key Laboratory of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, and School of Public Health, Fudan University, Shanghai 200032, China.
| | - Weihua Li
- Key Laboratory of Reproduction Regulation of NPFPC, Shanghai Institute of Planned Parenthood Research, and School of Public Health, Fudan University, Shanghai 200032, China.
| | - Mark Baker
- Reproductive Proteomics, Department of Science and Information technology, University of Newcastle, Callaghan Drive, Newcastle, NSW 2308 Australia.
| | - Guanshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495, USA.
| | - Duane Hickling
- Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, ON, Canada.
- Division of Urology, Department of Surgery, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1Y 4E9, ON, Canada.
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37
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The human cathelicidin LL-37 — A pore-forming antibacterial peptide and host-cell modulator. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:546-66. [DOI: 10.1016/j.bbamem.2015.11.003] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/30/2015] [Accepted: 11/05/2015] [Indexed: 01/12/2023]
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38
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Zhang L, Wu WKK, Gallo RL, Fang EF, Hu W, Ling TKW, Shen J, Chan RLY, Lu L, Luo XM, Li MX, Chan KM, Yu J, Wong VWS, Ng SC, Wong SH, Chan FKL, Sung JJY, Chan MTV, Cho CH. Critical Role of Antimicrobial Peptide Cathelicidin for Controlling Helicobacter pylori Survival and Infection. THE JOURNAL OF IMMUNOLOGY 2016; 196:1799-1809. [DOI: 10.4049/jimmunol.1500021] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Abstract
The antimicrobial peptide cathelicidin is critical for protection against different kinds of microbial infection. This study sought to elucidate the protective action of cathelicidin against Helicobacter pylori infection and its associated gastritis. Exogenous cathelicidin was found to inhibit H. pylori growth, destroy the bacteria biofilm, and induce morphological alterations in H. pylori membrane. Additionally, knockdown of endogenous cathelicidin in human gastric epithelial HFE-145 cells markedly increased the intracellular survival of H. pylori. Consistently, cathelicidin knockout mice exhibited stronger H. pylori colonization, higher expression of proinflammatory cytokines IL-6, IL-1β, and ICAM1, and lower expression of the anti-inflammatory cytokine IL-10 in the gastric mucosa upon H. pylori infection. In wild-type mice, H. pylori infection also stimulated gastric epithelium-derived cathelicidin production. Importantly, pretreatment with bioengineered Lactococcus lactis that actively secretes cathelicidin significantly increased mucosal cathelicidin levels and reduced H. pylori infection and the associated inflammation. Moreover, cathelicidin strengthened the barrier function of gastric mucosa by stimulating mucus synthesis. Collectively, these findings indicate that cathelicidin plays a significant role as a potential natural antibiotic for H. pylori clearance and a therapeutic agent for chronic gastritis.
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Affiliation(s)
- Lin Zhang
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- †Department of Medicine and Therapeutics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- ‡CUHK Shenzhen Research Institute, Shenzhen 518057, China
| | - William K. K. Wu
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- ‡CUHK Shenzhen Research Institute, Shenzhen 518057, China
- §Department of Anesthesia and Intensive Care, Chinese University of Hong Kong, Hong Kong, China
| | - Richard L. Gallo
- ¶Division of Dermatology, University of California, San Diego, La Jolla, CA 92093
| | - Evandro F. Fang
- ‖Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Wei Hu
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
| | - Thomas K. W. Ling
- **Department of Microbiology, Prince of Wales Hospital, Chinese University of Hong Kong, Hong Kong, China
| | - Jing Shen
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
| | - Ruby L. Y. Chan
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
| | - Lan Lu
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
| | - Xiao M. Luo
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
| | - Ming X. Li
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
| | - Kam M. Chan
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
| | - Jun Yu
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- †Department of Medicine and Therapeutics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- ‡CUHK Shenzhen Research Institute, Shenzhen 518057, China
| | - Vincent W. S. Wong
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- †Department of Medicine and Therapeutics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
| | - Siew C. Ng
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- †Department of Medicine and Therapeutics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
| | - Sunny H. Wong
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- †Department of Medicine and Therapeutics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- ‡CUHK Shenzhen Research Institute, Shenzhen 518057, China
| | - Francis K. L. Chan
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- †Department of Medicine and Therapeutics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- ‡CUHK Shenzhen Research Institute, Shenzhen 518057, China
| | - Joseph J. Y. Sung
- *Institute of Digestive Diseases and State Key Laboratory of Digestive Diseases, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- †Department of Medicine and Therapeutics, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
- ‡CUHK Shenzhen Research Institute, Shenzhen 518057, China
| | - Matthew T. V. Chan
- §Department of Anesthesia and Intensive Care, Chinese University of Hong Kong, Hong Kong, China
| | - Chi H. Cho
- #School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China; and
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Zhang X, Bajic G, Andersen GR, Christiansen SH, Vorup-Jensen T. The cationic peptide LL-37 binds Mac-1 (CD11b/CD18) with a low dissociation rate and promotes phagocytosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:471-8. [PMID: 26876535 DOI: 10.1016/j.bbapap.2016.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 12/16/2022]
Abstract
As a broad-spectrum anti-microbial peptide, LL-37 plays an important role in the innate immune system. A series of previous reports implicates LL-37 as an activator of various cell surface receptor-mediated functions, including chemotaxis in integrin CD11b/CD18 (Mac-1)-expressing cells. However, evidence is scarce concerning the direct binding of LL-37 to these receptors and investigations on the associated binding kinetics is lacking. Mac-1, a member of the β2 integrin family, is mainly expressed in myeloid leukocytes. Its critical functions include phagocytosis of complement-opsonized pathogens. Here, we report on interactions of LL-37 and its fragment FK-13 with the ligand-binding domain of Mac-1, the α-chain I domain. LL-37 bound the I-domain with an affinity comparable to the complement fragment C3d, one of the strongest known ligands for Mac-1. In cell adhesion assays both LL-37 and FK-13 supported binding by Mac-1 expressing cells, however, with LL-37-coupled surfaces supporting stronger cell adhesion than FK-13. Likewise, in phagocytosis assays with primary human monocytes both LL-37 and FK-13 enhanced uptake of particles coupled with these ligands but with a tendency towards a stronger uptake by LL-37.
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Affiliation(s)
- Xianwei Zhang
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Goran Bajic
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Gregers R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Thomas Vorup-Jensen
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark; MEMBRANES Research Center, Aarhus University, DK-8000 Aarhus C, Denmark.
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40
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Bociek K, Ferluga S, Mardirossian M, Benincasa M, Tossi A, Gennaro R, Scocchi M. Lipopolysaccharide Phosphorylation by the WaaY Kinase Affects the Susceptibility of Escherichia coli to the Human Antimicrobial Peptide LL-37. J Biol Chem 2015; 290:19933-41. [PMID: 26100635 DOI: 10.1074/jbc.m114.634758] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Indexed: 01/18/2023] Open
Abstract
The human cathelicidin LL-37 is a multifunctional host defense peptide with immunomodulatory and antimicrobial roles. It kills bacteria primarily by altering membrane barrier properties, although the exact sequence of events leading to cell lysis has not yet been completely elucidated. Random insertion mutagenesis allowed isolation of Escherichia coli mutants with altered susceptibility to LL-37, pointing to factors potentially relevant to its activity. Among these, inactivation of the waaY gene, encoding a kinase responsible for heptose II phosphorylation in the LPS inner core, leads to a phenotype with decreased susceptibility to LL-37, stemming from a reduced amount of peptide binding to the surface of the cells, and a diminished capacity to lyse membranes. This points to a specific role of the LPS inner core in guiding LL-37 to the surface of Gram-negative bacteria. Although electrostatic interactions are clearly relevant, the susceptibility of the waaY mutant to other cationic helical cathelicidins was unaffected, indicating that particular structural features or LL-37 play a role in this interaction.
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Affiliation(s)
- Karol Bociek
- From the Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Sara Ferluga
- From the Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Mario Mardirossian
- From the Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Monica Benincasa
- From the Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Alessandro Tossi
- From the Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Renato Gennaro
- From the Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Marco Scocchi
- From the Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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41
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Halldórsdóttir K, Árnason E. Trans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species. PeerJ 2015; 3:e976. [PMID: 26038731 PMCID: PMC4451034 DOI: 10.7717/peerj.976] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/05/2015] [Indexed: 12/27/2022] Open
Abstract
Natural selection, the most important force in evolution, comes in three forms. Negative purifying selection removes deleterious variation and maintains adaptations. Positive directional selection fixes beneficial variants, producing new adaptations. Balancing selection maintains variation in a population. Important mechanisms of balancing selection include heterozygote advantage, frequency-dependent advantage of rarity, and local and fluctuating episodic selection. A rare pathogen gains an advantage because host defenses are predominantly effective against prevalent types. Similarly, a rare immune variant gives its host an advantage because the prevalent pathogens cannot escape the host's apostatic defense. Due to the stochastic nature of evolution, neutral variation may accumulate on genealogical branches, but trans-species polymorphisms are rare under neutrality and are strong evidence for balancing selection. Balanced polymorphism maintains diversity at the major histocompatibility complex (MHC) in vertebrates. The Atlantic cod is missing genes for both MHC-II and CD4, vital parts of the adaptive immune system. Nevertheless, cod are healthy in their ecological niche, maintaining large populations that support major commercial fisheries. Innate immunity is of interest from an evolutionary perspective, particularly in taxa lacking adaptive immunity. Here, we analyze extensive amino acid and nucleotide polymorphisms of the cathelicidin gene family in Atlantic cod and closely related taxa. There are three major clusters, Cath1, Cath2, and Cath3, that we consider to be paralogous genes. There is extensive nucleotide and amino acid allelic variation between and within clusters. The major feature of the results is that the variation clusters by alleles and not by species in phylogenetic trees and discriminant analysis of principal components. Variation within the three groups shows trans-species polymorphism that is older than speciation and that is suggestive of balancing selection maintaining the variation. Using Bayesian and likelihood methods positive and negative selection is evident at sites in the conserved part of the genes and, to a larger extent, in the active part which also shows episodic diversifying selection, further supporting the argument for balancing selection.
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Affiliation(s)
- Katrín Halldórsdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Einar Árnason
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
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42
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Zhang XJ, Zhang XY, Zhang N, Guo X, Peng KS, Wu H, Lu LF, Wu N, Chen DD, Li S, Nie P, Zhang YA. Distinctive Structural Hallmarks and Biological Activities of the Multiple Cathelicidin Antimicrobial Peptides in a Primitive Teleost Fish. THE JOURNAL OF IMMUNOLOGY 2015; 194:4974-87. [DOI: 10.4049/jimmunol.1500182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/17/2015] [Indexed: 11/19/2022]
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43
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New aspects of the structure and mode of action of the human cathelicidin LL-37 revealed by the intrinsic probe p-cyanophenylalanine. Biochem J 2015; 465:443-57. [PMID: 25378136 DOI: 10.1042/bj20141016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The human cathelicidin peptide LL-37 is an important effector of our innate immune system and contributes to host defence with direct antimicrobial activity and immunomodulatory properties, and by stimulating wound healing. Its sequence has evolved to confer specific structural characteristics that strongly affect these biological activities, and differentiate it from orthologues of other primate species. In the present paper we report a detailed study of the folding and self-assembly of this peptide in comparison with rhesus monkey peptide RL-37, taking into account the different stages of its trajectory from bulk solution to contact with, and insertion into, biological membranes. Phenylalanine residues in different positions throughout the native sequences of LL-37 and RL-37 were systematically replaced with the non-invasive fluorescent and IR probe p-cyanophenylalanine. Steady-state and time-resolved fluorescence studies showed that LL-37, in contrast to RL-37, forms oligomers with a loose hydrophobic core in physiological solutions, which persist in the presence of biological membranes. Fourier transform IR and surface plasmon resonance studies also indicated different modes of interaction for LL-37 and RL-37 with anionic and neutral membranes. This correlated with a distinctly different mode of bacterial membrane permeabilization, as determined using a flow cytometric method involving impermeant fluorescent dyes linked to polymers of defined sizes.
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44
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Mardirossian M, Grzela R, Giglione C, Meinnel T, Gennaro R, Mergaert P, Scocchi M. The host antimicrobial peptide Bac71-35 binds to bacterial ribosomal proteins and inhibits protein synthesis. ACTA ACUST UNITED AC 2014; 21:1639-47. [PMID: 25455857 DOI: 10.1016/j.chembiol.2014.10.009] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/03/2014] [Accepted: 10/06/2014] [Indexed: 11/15/2022]
Abstract
Antimicrobial peptides (AMPs) are molecules from innate immunity with high potential as novel anti-infective agents. Most of them inactivate bacteria through pore formation or membrane barrier disruption, but others cross the membrane without damages and act inside the cells, affecting vital processes. However, little is known about their intracellular bacterial targets. Here we report that Bac71-35, a proline-rich AMP belonging to the cathelicidin family, can reach high concentrations (up to 340 μM) inside the E. coli cytoplasm. The peptide specifically and completely inhibits in vitro translation in the micromolar concentration range. Experiments of incorporation of radioactive precursors in macromolecules with E. coli cells confirmed that Bac71-35 affects specifically protein synthesis. Ribosome coprecipitation and crosslinking assays showed that the peptide interacts with ribosomes, binding to a limited subset of ribosomal proteins. Overall, these results indicate that the killing mechanism of Bac71-35 is based on a specific block of protein synthesis.
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Affiliation(s)
- Mario Mardirossian
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, Trieste 34127, Italy
| | - Renata Grzela
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Carmela Giglione
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Renato Gennaro
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, Trieste 34127, Italy
| | - Peter Mergaert
- Institut des Sciences du Végétal UPR 2355 CNRS, 1 avenue de la Terrasse Bât. 23, 91198 Gif-sur-Yvette, France
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, Trieste 34127, Italy.
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Dutta J, Ramesh S, Radebe SM, Somboro AM, de la Torre BG, Kruger HG, Essack SY, Albericio F, Govender T. Optimized Microwave Assisted Synthesis of LL37, a Cathelicidin Human Antimicrobial Peptide. Int J Pept Res Ther 2014. [DOI: 10.1007/s10989-014-9439-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Picchianti M, Russo C, Castagnini M, Biagini M, Soldaini E, Balducci E. NAD-dependent ADP-ribosylation of the human antimicrobial and immune-modulatory peptide LL-37 by ADP-ribosyltransferase-1. Innate Immun 2014; 21:314-21. [PMID: 25128692 DOI: 10.1177/1753425914536242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
LL-37 is a cationic peptide belonging to the cathelicidin family that has antimicrobial and immune-modulatory properties. Here we show that the mammalian mono-ADP-ribosyltransferase-1 (ART1), which selectively transfers the ADP-ribose moiety from NAD to arginine residues, ADP-ribosylates LL-37 in vitro. The incorporation of ADP-ribose was first observed by Western blot analysis and then confirmed by MALDI-TOF. Mass-spectrometry showed that up to four of the five arginine residues present in LL-37 could be ADP-ribosylated on the same peptide when incubated at a high NAD concentration in the presence of ART1. The attachment of negatively charged ADP-ribose moieties considerably alters the positive charge of the arginine residues thus reducing the cationicity of LL-37. The cationic nature of LL-37 is key for its ability to interact with cell membranes or negatively charged biomolecules, such as DNA, RNA, F-actin and glycosaminoglycans. Thus, the ADP-ribosylation of LL-37 is expected to have the potential to modulate LL-37 biological activities in several physiological and pathological settings.
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Affiliation(s)
- Monica Picchianti
- Novartis Vaccines and Diagnostics, Siena, Italy Department of Evolutionary Biology, University of Siena, Siena, Italy
| | - Carla Russo
- Novartis Vaccines and Diagnostics, Siena, Italy
| | | | | | | | - Enrico Balducci
- School of Biosciences and Biotechnologies, University of Camerino, Camerino, Italy
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Vipericidins: a novel family of cathelicidin-related peptides from the venom gland of South American pit vipers. Amino Acids 2014; 46:2561-71. [DOI: 10.1007/s00726-014-1801-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/27/2014] [Indexed: 10/24/2022]
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48
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Ultrastructural immunolocalization of chatelicidin-like peptides in granulocytes of normal and regenerating lizard tissues. Acta Histochem 2014; 116:363-71. [PMID: 24139311 DOI: 10.1016/j.acthis.2013.08.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 12/11/2022]
Abstract
The presence and localization of cathelicidin anti-microbial peptides in the lizard, Anolis carolinensis, were investigated by immunocytochemistry. The study showed that immunoreactivity for cathelicidins 1 and 2 was only present in large granules of heterophilic-basophilic granulocytes, rarely found in the dermis and sub-dermal muscle in normal and more frequently in wound and regenerating skin tissues or in the blood. Some immunopositive granulocytes were also observed among the keratinocytes of the wound epithelium covering the tail stump and occasionally in the regenerating epidermis of the tail. Immunolabeling for cathelicidins was also seen in low electrondense amorphous material present on the surface of the wound epidermis and on the plasma membrane of bacteria present on the surface of corneocytes of the epidermis. Immunolabeling for cathelicidins was absent in the other cell types and in control sections. The study suggests that cathelicidins are normally stored in granulocytes in the blood or in connective tissues, while keratinocytes can be stimulated to produce and possibly release these molecules only after injury or microbial invasion.
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49
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Native oligomerization determines the mode of action and biological activities of human cathelicidin LL-37. Biochem J 2014; 457:263-75. [PMID: 24117320 DOI: 10.1042/bj20131048] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
LL-37 is a multifunctional component of innate immunity, with a membrane-directed antimicrobial activity and receptor-mediated pleiotropic effects on host cells. Sequence variations in its primate orthologues suggest that two types of functional features have evolved; human LL-37-like peptides form amphipathic helical structures and self-assemble under physiological conditions, whereas rhesus RL-37-like peptides only adopt this structure in the presence of bacterial membranes. The first type of peptide has a lower and more medium-sensitive antimicrobial activity than the second type, but an increased capacity to stimulate host cells. Oligomerization strongly affects the mode of interaction with biological membranes and, consequently, both cytotoxicity and receptor-mediated activities. In the present study we explored the effects of LL-37 self-association by using obligate disulfide-linked dimers with either parallel or antiparallel orientations. These had an increased propensity to form stacked helices in bulk solution and when in contact with either anionic or neutral model membranes. The antimicrobial activity against Gram-positive or Gram-negative bacteria, as well as the cytotoxic effects on host cells, strongly depended on the type of dimerization. To investigate the extent of native oligomerization we replaced Phe5 with the photoactive residue Bpa (p-benzoyl-L-phenylalanine), which, upon UV irradiation, enabled covalent cross-linking and allowed us to assess the extent of oligomerization in both physiological solution and in model membranes.
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50
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Alibardi L. Ultrastructural immunolocalization of beta-defensin-27 in granulocytes of the dermis and wound epidermis of lizard suggests they contribute to the anti-microbial skin barrier. Anat Cell Biol 2013; 46:246-53. [PMID: 24386597 PMCID: PMC3875842 DOI: 10.5115/acb.2013.46.4.246] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/05/2012] [Accepted: 09/27/2012] [Indexed: 11/27/2022] Open
Abstract
The high resistance to infections in lizard wounds suggests that these reptiles possess effective antimicrobial peptides in their tissues. The present immunocytochemical study shows the cellular localization of beta-defensin 27 in tail tissues and in the blood, a defensin previously identified in the lizard Anolis carolinensis through biomolecular methods. Beta-defensin-27 immunoreactivity is only observed in some large granules mainly contained in heterophilic granulocytes that are sparse within the dermis of the skin or in the isolated blood. This peptide is absent in other cell types of the skin, in keratinocytes and in subdermal muscle tissue of the tail in normal conditions. Pre-corneous keratinocytes of the regenerating tail epidermis are unlabeled or show a weak labeling for the peptide only in sparse cytoplasmic areas or in the extracellular spaces among corneocytes of the wound and regenerating epidermis. The study suggests that beta-defensin 27 is normally stored in granulocytes present in the blood or in connective tissues while in the epidermis keratinocytes do not show the presence of this peptide unless these cells are stimulated from injury to produce and likely release beta-defensins.
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