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Purohit K, Reddy N, Sunna A. Exploring the Potential of Bioactive Peptides: From Natural Sources to Therapeutics. Int J Mol Sci 2024; 25:1391. [PMID: 38338676 PMCID: PMC10855437 DOI: 10.3390/ijms25031391] [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: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
Bioactive peptides, specific protein fragments with positive health effects, are gaining traction in drug development for advantages like enhanced penetration, low toxicity, and rapid clearance. This comprehensive review navigates the intricate landscape of peptide science, covering discovery to functional characterization. Beginning with a peptidomic exploration of natural sources, the review emphasizes the search for novel peptides. Extraction approaches, including enzymatic hydrolysis, microbial fermentation, and specialized methods for disulfide-linked peptides, are extensively covered. Mass spectrometric analysis techniques for data acquisition and identification, such as liquid chromatography, capillary electrophoresis, untargeted peptide analysis, and bioinformatics, are thoroughly outlined. The exploration of peptide bioactivity incorporates various methodologies, from in vitro assays to in silico techniques, including advanced approaches like phage display and cell-based assays. The review also discusses the structure-activity relationship in the context of antimicrobial peptides (AMPs), ACE-inhibitory peptides (ACEs), and antioxidative peptides (AOPs). Concluding with key findings and future research directions, this interdisciplinary review serves as a comprehensive reference, offering a holistic understanding of peptides and their potential therapeutic applications.
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Affiliation(s)
- Kruttika Purohit
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
| | - Narsimha Reddy
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
- School of Science, Parramatta Campus, Western Sydney University, Penrith, NSW 2751, Australia
| | - Anwar Sunna
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia;
- Australian Research Council Industrial Transformation Training Centre for Facilitated Advancement of Australia’s Bioactives (FAAB), Sydney, NSW 2109, Australia;
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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2
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Shao WB, Luo RS, Meng J, Lv XK, Xiang HM, Xiao WL, Zhou X, Liu LW, Wu ZB, Yang S. Engineering Phenothiazine-Based Functional Mimics of Host Defense Peptides as New Agrochemical Candidates: Design, Synthesis, and Antibacterial Evaluation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37906428 DOI: 10.1021/acs.jafc.3c03952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In the protracted "arms race" between host and plant pathogenic bacteria, host organisms have evolved powerful weapons known as host defense peptides (HDPs). However, natural HDPs are not suitable for large-scale applications; therefore, researchers have chosen to develop bespoke small-molecule functional mimics. Phenothiazine derivatives were developed as functional HDPs mimics, owing to their broad biological activity and high lipophilicity. The phenothiazine analogues designed in this study exhibited excellent in vitro bioactivity against the three Gram-negative bacteria Xanthomonas oryzae pv oryzae, Xanthomonas axonopodis pv citri, and Pseudomonas syringae pv actinidiae, with optimal EC50 values of 0.80, 0.31, and 1.91 μg/mL, respectively. Preliminary evidence suggests that compound C2 may act on bacterial cell membranes and interact with bacterial Deoxyribonucleic acid in the groove binding mode. In vivo trials showed that compound C2 was highly effective against rice leaf blight (51.97-56.69%), with activity superior to those of bismerthiazol (40.7-43.4%) and thiodiazole copper (30.2-37.1%). Our study provides strong evidence to support the development of phenothiazine derivatives into pesticide candidates.
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Affiliation(s)
- Wu-Bin Shao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Rong-Shuang Luo
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Jiao Meng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiao-Kang Lv
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Hong-Mei Xiang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Wan-Lin Xiao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Li-Wei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zhi-Bing Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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3
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García-Jacas CR, García-González LA, Martinez-Rios F, Tapia-Contreras IP, Brizuela CA. Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant? Brief Bioinform 2022; 23:6754757. [PMID: 36215083 DOI: 10.1093/bib/bbac428] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/28/2022] [Accepted: 09/02/2022] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial peptides (AMPs) have received a great deal of attention given their potential to become a plausible option to fight multi-drug resistant bacteria as well as other pathogens. Quantitative sequence-activity models (QSAMs) have been helpful to discover new AMPs because they allow to explore a large universe of peptide sequences and help reduce the number of wet lab experiments. A main aspect in the building of QSAMs based on shallow learning is to determine an optimal set of protein descriptors (features) required to discriminate between sequences with different antimicrobial activities. These features are generally handcrafted from peptide sequence datasets that are labeled with specific antimicrobial activities. However, recent developments have shown that unsupervised approaches can be used to determine features that outperform human-engineered (handcrafted) features. Thus, knowing which of these two approaches contribute to a better classification of AMPs, it is a fundamental question in order to design more accurate models. Here, we present a systematic and rigorous study to compare both types of features. Experimental outcomes show that non-handcrafted features lead to achieve better performances than handcrafted features. However, the experiments also prove that an improvement in performance is achieved when both types of features are merged. A relevance analysis reveals that non-handcrafted features have higher information content than handcrafted features, while an interaction-based importance analysis reveals that handcrafted features are more important. These findings suggest that there is complementarity between both types of features. Comparisons regarding state-of-the-art deep models show that shallow models yield better performances both when fed with non-handcrafted features alone and when fed with non-handcrafted and handcrafted features together.
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Affiliation(s)
- César R García-Jacas
- Cátedras CONACYT - Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
| | - Luis A García-González
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
| | | | - Issac P Tapia-Contreras
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
| | - Carlos A Brizuela
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
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4
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Charoenkwan P, Schaduangrat N, Lio P, Moni MA, Chumnanpuen P, Shoombuatong W. iAMAP-SCM: A Novel Computational Tool for Large-Scale Identification of Antimalarial Peptides Using Estimated Propensity Scores of Dipeptides. ACS OMEGA 2022; 7:41082-41095. [PMID: 36406571 PMCID: PMC9670693 DOI: 10.1021/acsomega.2c04465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Antimalarial peptides (AMAPs) varying in length, amino acid composition, charge, conformational structure, hydrophobicity, and amphipathicity reflect their diversity in antimalarial mechanisms. Due to the worldwide major health problem concerning antimicrobial resistance, these peptides possess great therapeutic value owing to their low incidences of drug resistance as compared to conventional antibiotics. Although well-known experimental methods are able to precisely determine the antimalarial activity of peptides, these methods are still time-consuming and costly. Thus, machine learning (ML)-based methods that are capable of identifying AMAPs rapidly by using only sequence information would be beneficial for the high-throughput identification of AMAPs. In this study, we propose the first computational model (termed iAMAP-SCM) for the large-scale identification and characterization of peptides with antimalarial activity by using only sequence information. Specifically, we employed an interpretable scoring card method (SCM) to develop iAMAP-SCM and estimate propensities of 20 amino acids and 400 dipeptides to be AMAPs in a supervised manner. Experimental results showed that iAMAP-SCM could achieve a maximum accuracy and Matthew's coefficient correlation of 0.957 and 0.834, respectively, on the independent test dataset. In addition, SCM-derived propensities of 20 amino acids and selected physicochemical properties were used to provide an understanding of the functional mechanisms of AMAPs. Finally, a user-friendly online computational platform of iAMAP-SCM is publicly available at http://pmlabstack.pythonanywhere.com/iAMAP-SCM. The iAMAP-SCM predictor is anticipated to assist experimental scientists in the high-throughput identification of potential AMAP candidates for the treatment of malaria and other clinical applications.
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Affiliation(s)
- Phasit Charoenkwan
- Modern
Management and Information Technology, College of Arts, Media and
Technology, Chiang Mai University, Chiang Mai50200, Thailand
| | - Nalini Schaduangrat
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok10700, Thailand
| | - Pietro Lio
- Department
of Computer Science and Technology, University
of Cambridge, CambridgeshireCB3 0FD, U.K.
| | - Mohammad Ali Moni
- Artificial
Intelligence & Digital Health, School of Health and Rehabilitation
Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St LuciaQLD 4072, Australia
| | - Pramote Chumnanpuen
- Department
of Zoology, Faculty of Science, Kasetsart
University, Bangkok10900, Thailand
- Omics Center
for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok10900, Thailand
| | - Watshara Shoombuatong
- Center
of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok10700, Thailand
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5
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Choi M, Cho HS, Ahn B, Prathap S, Nagasundarapandian S, Park C. Genomewide Analysis and Biological Characterization of Cathelicidins with Potent Antimicrobial Activity and Low Cytotoxicity from Three Bat Species. Antibiotics (Basel) 2022; 11:antibiotics11080989. [PMID: 35892379 PMCID: PMC9330922 DOI: 10.3390/antibiotics11080989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
Cathelicidins are potent antimicrobial peptides with broad spectrum antimicrobial activity in many vertebrates and an important component of the innate immune system. However, our understanding of the genetic variations and biological characteristics of bat cathelicidins is limited. In this study, we performed genome-level analysis of the antimicrobial peptide cathelicidins from seven bat species in the six families, listed 19 cathelicidin-like sequences, and showed that the number of functional cathelicidin genes differed among bat species. Based on the identified biochemical characteristics of bat cathelicidins, three cathelicidins, HA-CATH (from Hipposideros armiger), ML-CATH (from Myotis lucifugus), and PD-CATH (from Phyllostomus discolor), with clear antimicrobial signatures were chemically synthesized and evaluated antimicrobial activity. HA-CATH showed narrow-spectrum antibacterial activity against a panel of 12 reference bacteria, comprising 6 Gram-negative and 6 Gram-positive strains. However, ML-CATH and PD-CATH showed potent antibacterial activity against a broad spectrum of Gram-negative and Gram-positive bacteria with minimum inhibitory concentration (MIC) of 1 and 3 μg/mL, respectively, against Staphylococcus aureus. ML-CATH and PD-CATH also showed antifungal activities against Candida albicans and Cryptococcus cuniculi with MIC of 5 to 40 μg/mL, respectively, and 80% inhibition of the metabolism of Mucor hiemalis hyphae at 80 μg/mL, while displaying minimal cytotoxicity to HaCaT cells. Taken together, although the spectrum and efficacy of bat cathelicidins were species-dependent, the antimicrobial activity of ML-CATH and PD-CATH was comparable to that of other highly active cathelicidins in vertebrates while having negligible cytotoxicity to mammalian cells. ML-CATH and PD-CATH can be exploited as promising candidates for the development of antimicrobial therapeutics.
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6
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García-Jacas CR, Pinacho-Castellanos SA, García-González LA, Brizuela CA. Do deep learning models make a difference in the identification of antimicrobial peptides? Brief Bioinform 2022; 23:6563422. [PMID: 35380616 DOI: 10.1093/bib/bbac094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 12/21/2022] Open
Abstract
In the last few decades, antimicrobial peptides (AMPs) have been explored as an alternative to classical antibiotics, which in turn motivated the development of machine learning models to predict antimicrobial activities in peptides. The first generation of these predictors was filled with what is now known as shallow learning-based models. These models require the computation and selection of molecular descriptors to characterize each peptide sequence and train the models. The second generation, known as deep learning-based models, which no longer requires the explicit computation and selection of those descriptors, started to be used in the prediction task of AMPs just four years ago. The superior performance claimed by deep models regarding shallow models has created a prevalent inertia to using deep learning to identify AMPs. However, methodological flaws and/or modeling biases in the building of deep models do not support such superiority. Here, we analyze the main pitfalls that led to establish biased conclusions on the leading performance of deep models. Also, we analyze whether deep models truly contribute to achieve better predictions than shallow models by performing fair studies on different state-of-the-art benchmarking datasets. The experiments reveal that deep models do not outperform shallow models in the classification of AMPs, and that both types of models codify similar chemical information since their predictions are highly similar. Thus, according to the currently available datasets, we conclude that the use of deep learning could not be the most suitable approach to develop models to identify AMPs, mainly because shallow models achieve comparable-to-superior performances and are simpler (Ockham's razor principle). Even so, we suggest the use of deep learning only when its capabilities lead to obtaining significantly better performance gains worth the additional computational cost.
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Affiliation(s)
- César R García-Jacas
- Cátedras CONACYT - Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
| | - Sergio A Pinacho-Castellanos
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México.,Centro de Investigación y Desarrollo de Tecnología Digital (CITEDI), Instituto Politécnico Nacional (IPN), 22435 Tijuana, Baja California, México
| | - Luis A García-González
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
| | - Carlos A Brizuela
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
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7
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Ramazi S, Mohammadi N, Allahverdi A, Khalili E, Abdolmaleki P. A review on antimicrobial peptides databases and the computational tools. Database (Oxford) 2022; 2022:6550847. [PMID: 35305010 PMCID: PMC9216472 DOI: 10.1093/database/baac011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 12/29/2022]
Abstract
Antimicrobial Peptides (AMPs) have been considered as potential alternatives for infection therapeutics since antibiotic resistance has been raised as a global problem. The AMPs are a group of natural peptides that play a crucial role in the immune system in various organisms AMPs have features such as a short length and efficiency against microbes. Importantly, they have represented low toxicity in mammals which makes them potential candidates for peptide-based drugs. Nevertheless, the discovery of AMPs is accompanied by several issues which are associated with labour-intensive and time-consuming wet-lab experiments. During the last decades, numerous studies have been conducted on the investigation of AMPs, either natural or synthetic type, and relevant data are recently available in many databases. Through the advancement of computational methods, a great number of AMP data are obtained from publicly accessible databanks, which are valuable resources for mining patterns to design new models for AMP prediction. However, due to the current flaws in assessing computational methods, more interrogations are warranted for accurate evaluation/analysis. Considering the diversity of AMPs and newly reported ones, an improvement in Machine Learning algorithms are crucial. In this review, we aim to provide valuable information about different types of AMPs, their mechanism of action and a landscape of current databases and computational tools as resources to collect AMPs and beneficial tools for the prediction and design of a computational model for new active AMPs.
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Affiliation(s)
- Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| | - Neda Mohammadi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Hemmat Highway, Tehran 1449614535, Iran,Institute of Pharmacology and Toxicology, University of Bonn, Biomedical Center, Venusberg Campus 1, Bonn 53127, Germany
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
| | - Elham Khalili
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Jalal Ale Ahmad Highway, Tehran 14115-111, Iran
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8
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Kumar K, Sebastiao M, Arnold AA, Bourgault S, Warschawski DE, Marcotte I. IN SITU SOLID-STATE NMR STUDY OF ANTIMICROBIAL PEPTIDE INTERACTIONs WITH ERYTHROCYTE MEMBRANES. Biophys J 2022; 121:1512-1524. [PMID: 35278426 PMCID: PMC9072582 DOI: 10.1016/j.bpj.2022.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 11/02/2022] Open
Abstract
Antimicrobial peptides are promising therapeutic agents to mitigate the global rise of antibiotic resistance. They generally act by perturbing the bacterial cell membrane and are thus less likely to induce resistance. Because they are membrane-active molecules, it is critical to verify and understand their potential action toward eukaryotic cells to help design effective and safe drugs. In this work, we studied the interaction of two antimicrobial peptides, aurein 1.2 and caerin 1.1, with red blood cell (RBC) membranes using in situ 31P and 2H solid-state NMR (SS-NMR). We established a protocol to integrate up to 25% of deuterated fatty acids in the membranes of ghosts, which are obtained when hemoglobin is removed from RBCs. Fatty acid incorporation and the integrity of the lipid bilayer were confirmed by SS-NMR and fluorescence confocal microscopy. Leakage assays were performed to assess the lytic power of the antimicrobial peptides. The in situ perturbation of the ghost membranes by aurein 1.2 and caerin 1.1 revealed by 31P and 2H SS-NMR is consistent with membrane perturbation through a carpet mechanism for aurein 1.2, whereas caerin 1.1 acts on RBCs via pore formation. These results are compatible with fluorescence microscopy images of the ghosts. The peptides interact with eukaryotic membranes following similar mechanisms that take place in bacteria, highlighting the importance of hydrophobicity when determining such interactions. Our work bridges model membranes and in vitro studies and provides an analytical toolbox to assess drug toxicity toward eukaryotic cells.
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9
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Martell EM, González-Garcia M, Ständker L, Otero-González AJ. Host defense peptides as immunomodulators: The other side of the coin. Peptides 2021; 146:170644. [PMID: 34464592 DOI: 10.1016/j.peptides.2021.170644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022]
Abstract
Host defense peptides (HDPs) exhibit a broad range of antimicrobial and immunomodulatory activities. In this sense, both functions are like different sides of the same coin. The direct antimicrobial side was discovered first, and widely studied for the development of anti-infective therapies. In contrast, the immunomodulatory side was recognized later and in the last 20 years the interest in this field has been continuously growing. Different to their antimicrobial activities, the immunomodulatory activities of host defense peptides are more effective in vivo. They offer a great opportunity for new therapeutic applications in the fields of anti-infective therapy, chronic inflammatory diseases treatment, novel vaccine adjuvants development and anticancer immunotherapy. These immune related functions of HDPs includes chemoattraction of leukocytes, modulation of inflammation, enhancement of antigen presentation and polarization of adaptive immune responses. Our attempt with this review is to make a careful evaluation of different aspects of the less explored, but attractive immunomodulatory side of the HDP functional coin.
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Affiliation(s)
- Ernesto M Martell
- Center for Protein Studies, Faculty of Biology, Havana University, Cuba
| | | | - Ludger Ständker
- Core Facility Functional Peptidomics (CFP), Ulm University Medical Center, Ulm, Germany
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10
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Gan BH, Gaynord J, Rowe SM, Deingruber T, Spring DR. The multifaceted nature of antimicrobial peptides: current synthetic chemistry approaches and future directions. Chem Soc Rev 2021; 50:7820-7880. [PMID: 34042120 PMCID: PMC8689412 DOI: 10.1039/d0cs00729c] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Bacterial infections caused by 'superbugs' are increasing globally, and conventional antibiotics are becoming less effective against these bacteria, such that we risk entering a post-antibiotic era. In recent years, antimicrobial peptides (AMPs) have gained significant attention for their clinical potential as a new class of antibiotics to combat antimicrobial resistance. In this review, we discuss several facets of AMPs including their diversity, physicochemical properties, mechanisms of action, and effects of environmental factors on these features. This review outlines various chemical synthetic strategies that have been applied to develop novel AMPs, including chemical modifications of existing peptides, semi-synthesis, and computer-aided design. We will also highlight novel AMP structures, including hybrids, antimicrobial dendrimers and polypeptides, peptidomimetics, and AMP-drug conjugates and consider recent developments in their chemical synthesis.
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Affiliation(s)
- Bee Ha Gan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Josephine Gaynord
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Sam M Rowe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Tomas Deingruber
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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11
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Pinacho-Castellanos SA, García-Jacas CR, Gilson MK, Brizuela CA. Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J Chem Inf Model 2021; 61:3141-3157. [PMID: 34081438 DOI: 10.1021/acs.jcim.1c00251] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In the last two decades, a large number of machine-learning-based predictors for the activities of antimicrobial peptides (AMPs) have been proposed. These predictors differ from one another in the learning method and in the training and testing data sets used. Unfortunately, the training data sets present several drawbacks, such as a low representativeness regarding the experimentally validated AMP space, and duplicated peptide sequences between negative and positive data sets. These limitations give a low confidence to most of the approaches to be used in prospective studies. To address these weaknesses, we propose novel modeling and assessing data sets from the largest experimentally validated nonredundant peptide data set reported to date. From these novel data sets, alignment-free quantitative sequence-activity models (AF-QSAMs) based on Random Forest are created to identify general AMPs and their antibacterial, antifungal, antiparasitic, and antiviral functional types. An applicability domain analysis is carried out to determine the reliability of the predictions obtained, which, to the best of our knowledge, is performed for the first time for AMP recognition. A benchmarking is undertaken between the models proposed and several models from the literature that are freely available in 13 programs (ClassAMP, iAMP-2L, ADAM, MLAMP, AMPScanner v2.0, AntiFP, AMPfun, PEPred-suite, AxPEP, CAMPR3, iAMPpred, APIN, and Meta-iAVP). The models proposed are those with the best performance in all of the endpoints modeled, while most of the methods from the literature have weak-to-random predictive agreements. The models proposed are also assessed through Y-scrambling and repeated k-fold cross-validation tests, demonstrating that the outcomes obtained by them are not given by chance. Three chemometric analyses also confirmed the relevance of the peptides descriptors used in the modeling. Therefore, it can be concluded that the models built by fixing the drawbacks existing in the literature contribute to identifying antibacterial, antifungal, antiparasitic, and antiviral peptides with high effectivity and reliability. Models are freely available via the AMPDiscover tool at https://biocom-ampdiscover.cicese.mx/.
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Affiliation(s)
- Sergio A Pinacho-Castellanos
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México.,Centro de Investigación y Desarrollo de Tecnología Digital (CITEDI), Instituto Politécnico Nacional (IPN), 22435 Tijuana, Baja California, México
| | - César R García-Jacas
- Cátedras CONACYT-Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Carlos A Brizuela
- Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), 22860 Ensenada, Baja California, México
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12
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Mathur D, Kaur H, Dhall A, Sharma N, Raghava GPS. SAPdb: A database of short peptides and the corresponding nanostructures formed by self-assembly. Comput Biol Med 2021; 133:104391. [PMID: 33892308 DOI: 10.1016/j.compbiomed.2021.104391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
Abstract
Nanostructures generated by self-assembly of peptides yield nanomaterials that have many therapeutic applications, including drug delivery and biomedical engineering, due to their low cytotoxicity and higher uptake by targeted cells owing to their high affinity and specificity towards cell surface receptors. Despite the promising implications of this rapidly expanding field, there is no dedicated resource to study peptide nanostructures. This study endeavours to create a repository of short peptides, which may prove to be the best models to study ordered nanostructures formed by peptide self-assembly. SAPdb has a repertoire of 1049 entries of experimentally validated nanostructures formed by the self-assembly of small peptides. It consists of 328 tripeptides, 701 dipeptides, and 20 single amino acids with some conjugate partners. Each entry encompasses comprehensive information about the peptide, such as chemical modifications, the type of nanostructure formed, experimental conditions like pH, temperature, solvent required for the self-assembly, etc. Our analysis indicates that peptides containing aromatic amino acids favour the formation of self-assembling nanostructures. Additionally, we observed that these peptides form different nanostructures under different experimental conditions. SAPdb provides this comprehensive information in a hassle-free tabulated manner at a glance. User-friendly browsing, searching, and analysis modules have been integrated for easy data retrieval, data comparison, and examination of properties. We anticipate SAPdb to be a valuable repository for researchers engaged in the burgeoning arena of nanobiotechnology. It is freely available at https://webs.iiitd.edu.in/raghava/sapdb.
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Affiliation(s)
- Deepika Mathur
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
| | - Harpreet Kaur
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India.
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi-110020, India.
| | - Neelam Sharma
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi-110020, India.
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi-110020, India. http://webs.iiitd.edu.in/raghava/
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13
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Torres MDT, Cao J, Franco OL, Lu TK, de la Fuente-Nunez C. Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery. ACS NANO 2021; 15:2143-2164. [PMID: 33538585 PMCID: PMC8734659 DOI: 10.1021/acsnano.0c09509] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Antibiotic resistance is one of the greatest challenges of our time. This global health problem originated from a paucity of truly effective antibiotic classes and an increased incidence of multi-drug-resistant bacterial isolates in hospitals worldwide. Indeed, it has been recently estimated that 10 million people will die annually from drug-resistant infections by the year 2050. Therefore, the need to develop out-of-the-box strategies to combat antibiotic resistance is urgent. The biological world has provided natural templates, called antimicrobial peptides (AMPs), which exhibit multiple intrinsic medical properties including the targeting of bacteria. AMPs can be used as scaffolds and, via engineering, can be reconfigured for optimized potency and targetability toward drug-resistant pathogens. Here, we review the recent development of tools for the discovery, design, and production of AMPs and propose that the future of peptide drug discovery will involve the convergence of computational and synthetic biology principles.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jicong Cao
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 70790160, Brazil
- S-inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS 79117010, Brazil
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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14
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Puentes PR, Henao MC, Torres CE, Gómez SC, Gómez LA, Burgos JC, Arbeláez P, Osma JF, Muñoz-Camargo C, Reyes LH, Cruz JC. Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches. Antibiotics (Basel) 2020; 9:E854. [PMID: 33265897 PMCID: PMC7759991 DOI: 10.3390/antibiotics9120854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
One of the challenges of modern biotechnology is to find new routes to mitigate the resistance to conventional antibiotics. Antimicrobial peptides (AMPs) are an alternative type of biomolecules, naturally present in a wide variety of organisms, with the capacity to overcome the current microorganism resistance threat. Here, we reviewed our recent efforts to develop a new library of non-rationally produced AMPs that relies on bacterial genome inherent diversity and compared it with rationally designed libraries. Our approach is based on a four-stage workflow process that incorporates the interplay of recent developments in four major emerging technologies: artificial intelligence, molecular dynamics, surface-display in microorganisms, and microfluidics. Implementing this framework is challenging because to obtain reliable results, the in silico algorithms to search for candidate AMPs need to overcome issues of the state-of-the-art approaches that limit the possibilities for multi-space data distribution analyses in extremely large databases. We expect to tackle this challenge by using a recently developed classification algorithm based on deep learning models that rely on convolutional layers and gated recurrent units. This will be complemented by carefully tailored molecular dynamics simulations to elucidate specific interactions with lipid bilayers. Candidate AMPs will be recombinantly-expressed on the surface of microorganisms for further screening via different droplet-based microfluidic-based strategies to identify AMPs with the desired lytic abilities. We believe that the proposed approach opens opportunities for searching and screening bioactive peptides for other applications.
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Affiliation(s)
- Paola Ruiz Puentes
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - María C. Henao
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carlos E. Torres
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Saúl C. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Laura A. Gómez
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Juan C. Burgos
- Chemical Engineering Program, Universidad de Cartagena, Cartagena 130015, Colombia;
| | - Pablo Arbeláez
- Center for Research and Formation in Artificial Intelligence, Universidad de los Andes, Bogota DC 111711, Colombia; (P.R.P.); (P.A.)
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Johann F. Osma
- Department of Electrical and Electronic Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Carolina Muñoz-Camargo
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
| | - Luis H. Reyes
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogota DC 111711, Colombia;
| | - Juan C. Cruz
- Department of Biomedical Engineering, Universidad de los Andes, Bogota DC 111711, Colombia; (C.E.T.); (S.C.G.); (L.A.G.); (C.M.-C.)
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide 5005, Australia
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15
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Liu Y, Shi J, Tong Z, Jia Y, Yang B, Wang Z. The revitalization of antimicrobial peptides in the resistance era. Pharmacol Res 2020; 163:105276. [PMID: 33161137 DOI: 10.1016/j.phrs.2020.105276] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 01/14/2023]
Abstract
The antibiotic resistance crisis is becoming incredibly thorny due to the indiscriminate employment of antibiotics in agriculture and aquaculture, such as growth promoters, and the emergence of bacteria that are capable of enduring antibiotic treatment in an endless stream. Hence, to reverse this situation, vigorous efforts should be made in the process of identifying other alternative strategies with a lower frequency of resistance. Antimicrobial peptides (AMPs), originated from host defense peptides, are generally produced by a variety of organisms as defensive weapons to protect the host from other pathogenic bacteria. The unique ability of AMPs to control bacterial infections, as well as low propensity to acquire resistance, provides the basis for it to become one of the promising antibacterial substances. Herein, we present new insights into the biological functions, structural properties, distinct mechanisms of action of AMPs and their resistance determinants. Besides, we separately discuss natural and synthetic AMPs, including their source, screening pathway and antibacterial activity. Lastly, challenges and perspectives to identify novel potent AMPs are highlighted, which will expand our understanding of the chemical space of antimicrobials and provide a pipeline for discovering the next-generation of AMPs.
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Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009, China.
| | - Jingru Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Ziwen Tong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Yuqian Jia
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Bingqing Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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16
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Dicentracin-Like from Asian sea bass Fish and Moronecidine-Like from Hippocampus Comes: Two Candidate Antimicrobial Peptides Against Leishmanina major Infection. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10125-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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Parai D, Dey P, Mukherjee SK. Antimicrobial Peptides: An Approach to Combat Resilient Infections. Curr Drug Discov Technol 2020; 17:542-552. [PMID: 31250760 DOI: 10.2174/1570163816666190620114338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND It was apparent by the end of 1980s that the success against the threats of bacterial pathogens on public health was an illusion, with the rapid development of resistant strains more than the discovery of new drugs. As a consequence, the remedial services were in the backfoot position of being on the losing side of this never-ending evolutionary war. The quest for new antibiotics to overcome resistance problems has long been a top research priority for the researchers and the pharmaceutical industry. However, the resistance problems remain unresolved due to the abrupt misuse of antibiotics by common people, which has immensely worsened the scenario by disseminating antibiotic-resistant bacterial strains around the world. OBJECTIVE Thus, immediate action is needed to measure emerging and re-emerging microbial diseases having new resistance mechanisms and to manage their rapid spread among the common public by means of novel alternative metabolites. CONCLUSION Antimicrobial Peptides (AMPs) are short, cationic peptides evolved in a wide range of living organisms and serve as the essential part of the host innate immunity. For humans, these effector molecules either can directly kill the foreign microbes or modulate the host immune systems so that the human body could develop some resistance against the microbial infections. In this review, we discuss their history, structural classifications, modes of action, and explain their biological roles as anti-infective agents. We also scrutinize their clinical potentiality, current limitations in various developmental stages and strategies to overcome for their successful clinical applications.
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Affiliation(s)
- Debaprasad Parai
- Department of Microbiology, University of Kalyani, Kalyani, WB, India
| | - Pia Dey
- Department of Microbiology, University of Kalyani, Kalyani, WB, India
| | - Samir K Mukherjee
- Department of Microbiology, University of Kalyani, Kalyani, WB, India
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18
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Islam MO, Palit P, Shawon J, Hasan MK, Mahmud A, Mahfuz M, Ahmed T, Mondal D. Exploring novel therapeutic strategies against vivax malaria through an integrated computational investigation to inhibit the merozoite surface protein−1 of Plasmodium vivax. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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19
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Barreto-Santamaría A, Patarroyo ME, Curtidor H. Designing and optimizing new antimicrobial peptides: all targets are not the same. Crit Rev Clin Lab Sci 2019; 56:351-373. [DOI: 10.1080/10408363.2019.1631249] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Adriana Barreto-Santamaría
- Fundación Instituto de Inmunología de Colombia - FIDIC, Receptor-Ligand Department, Bogotá D.C, Colombia
- Universidad del Rosario, School of Medicine and Health Sciences, Bogotá D.C., Colombia
| | - Manuel E. Patarroyo
- Fundación Instituto de Inmunología de Colombia - FIDIC, Receptor-Ligand Department, Bogotá D.C, Colombia
- Universidad Nacional de Colombia - Bogotá, Faculty of Medicine, Bogotá D.C., Colombia
| | - Hernando Curtidor
- Fundación Instituto de Inmunología de Colombia - FIDIC, Receptor-Ligand Department, Bogotá D.C, Colombia
- Universidad del Rosario, School of Medicine and Health Sciences, Bogotá D.C., Colombia
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20
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NMR model structure of the antimicrobial peptide maximin 3. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:203-212. [DOI: 10.1007/s00249-019-01346-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/17/2022]
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21
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Haney EF, Straus SK, Hancock REW. Reassessing the Host Defense Peptide Landscape. Front Chem 2019; 7:43. [PMID: 30778385 PMCID: PMC6369191 DOI: 10.3389/fchem.2019.00043] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/15/2019] [Indexed: 12/18/2022] Open
Abstract
Current research has demonstrated that small cationic amphipathic peptides have strong potential not only as antimicrobials, but also as antibiofilm agents, immune modulators, and anti-inflammatories. Although traditionally termed antimicrobial peptides (AMPs) these additional roles have prompted a shift in terminology to use the broader term host defense peptides (HDPs) to capture the multi-functional nature of these molecules. In this review, we critically examined the role of AMPs and HDPs in infectious diseases and inflammation. It is generally accepted that HDPs are multi-faceted mediators of a wide range of biological processes, with individual activities dependent on their polypeptide sequence. In this context, we explore the concept of chemical space as it applies to HDPs and hypothesize that the various functions and activities of this class of molecule exist on independent but overlapping activity landscapes. Finally, we outline several emerging functions and roles of HDPs and highlight how an improved understanding of these processes can potentially be leveraged to more fully realize the therapeutic promise of HDPs.
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Affiliation(s)
- Evan F Haney
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Suzana K Straus
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
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22
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Wang J, Dou X, Song J, Lyu Y, Zhu X, Xu L, Li W, Shan A. Antimicrobial peptides: Promising alternatives in the post feeding antibiotic era. Med Res Rev 2018; 39:831-859. [PMID: 30353555 DOI: 10.1002/med.21542] [Citation(s) in RCA: 287] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022]
Abstract
Antimicrobial peptides (AMPs), critical components of the innate immune system, are widely distributed throughout the animal and plant kingdoms. They can protect against a broad array of infection-causing agents, such as bacteria, fungi, parasites, viruses, and tumor cells, and also exhibit immunomodulatory activity. AMPs exert antimicrobial activities primarily through mechanisms involving membrane disruption, so they have a lower likelihood of inducing drug resistance. Extensive studies on the structure-activity relationship have revealed that net charge, hydrophobicity, and amphipathicity are the most important physicochemical and structural determinants endowing AMPs with antimicrobial potency and cell selectivity. This review summarizes the recent advances in AMPs development with respect to characteristics, structure-activity relationships, functions, antimicrobial mechanisms, expression regulation, and applications in food, medicine, and animals.
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Affiliation(s)
- Jiajun Wang
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Xiujing Dou
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Jing Song
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Yinfeng Lyu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Xin Zhu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Lin Xu
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Weizhong Li
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Anshan Shan
- Institute of Animal Nutrition, Department of Animal Nutrition, Northeast Agricultural University, Harbin, China
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23
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Giovati L, Santinoli C, Mangia C, Vismarra A, Belletti S, D'Adda T, Fumarola C, Ciociola T, Bacci C, Magliani W, Polonelli L, Conti S, Kramer LH. Novel Activity of a Synthetic Decapeptide Against Toxoplasma gondii Tachyzoites. Front Microbiol 2018; 9:753. [PMID: 29731744 PMCID: PMC5920037 DOI: 10.3389/fmicb.2018.00753] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/04/2018] [Indexed: 12/31/2022] Open
Abstract
The killer peptide KP is a synthetic decapeptide derived from the sequence of the variable region of a recombinant yeast killer toxin-like microbicidal single-chain antibody. KP proved to exert significant activities against diverse microbial and viral pathogens through different mechanisms of action, but little is known of its effect on apicomplexan protozoa. The aim of the present study was to evaluate the in vitro activity of KP against Toxoplasma gondii, a globally widespread protozoan parasite of great medical interest. The effect of KP treatment and its potential mechanism of action on T. gondii were evaluated by various methods, including light microscopy, quantitative PCR, flow cytometry, confocal microscopy, and transmission electron microscopy. In the presence of KP, the number of T. gondii tachyzoites able to invade Vero cells and the parasite intracellular proliferation were significantly reduced. Morphological observation and analysis of apoptotic markers suggested that KP is able to trigger an apoptosis-like cell death in T. gondii. Overall, our results indicate that KP could be a promising candidate for the development of new anti-Toxoplasma drugs with a novel mechanism of action.
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Affiliation(s)
- Laura Giovati
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Claudia Santinoli
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Carlo Mangia
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Alice Vismarra
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Silvana Belletti
- Laboratory of Histology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Tiziana D'Adda
- Laboratory of Pathological Anatomy, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Claudia Fumarola
- Laboratory of Experimental Oncology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Tecla Ciociola
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Cristina Bacci
- Department of Veterinary Science, University of Parma, Parma, Italy
| | - Walter Magliani
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Luciano Polonelli
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Stefania Conti
- Laboratory of Microbiology and Virology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Laura H Kramer
- Department of Veterinary Science, University of Parma, Parma, Italy
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24
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Martins DB, Vieira MR, Fadel V, Santana VAC, Guerra MER, Lima ML, Tempone AG, dos Santos Cabrera MP. Membrane targeting peptides toward antileishmanial activity: Design, structural determination and mechanism of interaction. Biochim Biophys Acta Gen Subj 2017; 1861:2861-2871. [DOI: 10.1016/j.bbagen.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 08/01/2017] [Accepted: 08/01/2017] [Indexed: 01/07/2023]
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25
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Guerra MER, Fadel V, Maltarollo VG, Baldissera G, Honorio KM, Ruggiero JR, Dos Santos Cabrera MP. MD simulations and multivariate studies for modeling the antileishmanial activity of peptides. Chem Biol Drug Des 2017; 90:501-510. [PMID: 28267894 DOI: 10.1111/cbdd.12970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/29/2017] [Accepted: 02/21/2017] [Indexed: 11/30/2022]
Abstract
Leishmaniasis, a protozoan-caused disease, requires alternative treatments with minimized side-effects and less prone to resistance development. Antimicrobial peptides represent a possible choice to be developed. We report on the prospection of structural parameters of 23 helical antimicrobial and leishmanicidal peptides as a tool for modeling and predicting the activity of new peptides. This investigation is based on molecular dynamic simulations (MD) in mimetic membrane environment, as most of these peptides share the feature of interacting with phospholipid bilayers. To overcome the lack of experimental data on peptides' structures, we started simulations from designed 100% α-helices. This procedure was validated through comparisons with NMR data and the determination of the structure of Decoralin-amide. From physicochemical features and MD results, descriptors were raised and statistically related to the minimum inhibitory concentration against Leishmania by the multivariate data analysis technique. This statistical procedure confirmed five descriptors combined by different loadings in five principal components. The leishmanicidal activity depends on peptides' charge, backbone solvation, volume, and solvent-accessible surface area. The generated model possesses good predictability (q2 = 0.715, r2 = 0.898) and is indicative for the most and the least active peptides. This is a novel theoretical path for structure-activity studies combining computational methods that identify and prioritize the promising peptide candidates.
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Affiliation(s)
| | - Valmir Fadel
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
| | | | | | - Kathia Maria Honorio
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Roberto Ruggiero
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
| | - Marcia Perez Dos Santos Cabrera
- Departamento de Física, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil.,Departamento de Química e Ciências Ambientais, Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
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26
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Ghosh C, Chaubey S, Tatu U, Haldar J. Aryl-alkyl-lysines: small molecular membrane-active antiplasmodial agents. MEDCHEMCOMM 2016; 8:434-439. [PMID: 30108761 DOI: 10.1039/c6md00589f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/06/2016] [Indexed: 11/21/2022]
Abstract
Due to emerging resistance there is a steady need for new antimalarial drugs. Here, we report a new class of water soluble, non-toxic compounds, aryl-alkyl-lysines, with promising activity against the ring stage of Plasmodium falciparum. The optimal compound perturbed the plasma membrane potential and the digestive vacuole of parasites. In the murine model of malaria (Plasmodium berghei ANKA) the compound was able to increase the survival of mice by at least 5 days by an intra-peritoneal route. Further, the compounds showed no apparent toxicity to mice at the concentration tested.
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Affiliation(s)
- Chandradhish Ghosh
- Chemical biology and Medicinal Chemistry Laboratory , New Chemistry Unit , Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) , Jakkur , Bengaluru 560064 , Karnataka , India .
| | - Shweta Chaubey
- Department of Biochemistry , Indian Institute of Science , Bengaluru , India
| | - Utpal Tatu
- Department of Biochemistry , Indian Institute of Science , Bengaluru , India
| | - Jayanta Haldar
- Chemical biology and Medicinal Chemistry Laboratory , New Chemistry Unit , Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) , Jakkur , Bengaluru 560064 , Karnataka , India .
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Rhaiem RB, Houimel M. Targeting Leishmania major parasite with peptides derived from a combinatorial phage display library. Acta Trop 2016; 159:11-9. [PMID: 26995695 DOI: 10.1016/j.actatropica.2016.03.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 10/27/2022]
Abstract
Cutaneous leishmaniasis (CL) is a global problem caused by intracellular protozoan pathogens of the genus Leishmania for which there are no suitable vaccine or chemotherapy options. Thus, de novo identification of small molecules binding to the Leishmania parasites by direct screening is a promising and appropriate alternative strategy for the development of new drugs. In this study, we used a random linear hexapeptide library fused to the gene III protein of M13 filamentous bacteriophage to select binding peptides to metacyclic promastigotes from a highly virulent strain of Leishmania major (Zymodeme MON-25; MHOM/TN/94/GLC94). After four rounds of stringent selection and amplification, polyclonal and monoclonal phage-peptides directed against L. major metacyclic promastigotes were assessed by ELISA, and the optimal phage-peptides were grown individually and characterized for binding to L. major by monoclonal phage ELISA. The DNA of 42 phage-peptides clones was amplified by PCR, sequenced, and their amino acid sequences deduced. Six different peptide sequences were obtained with frequencies of occurrence ranging from 2.3% to 85.7%. The biological effect of the peptides was assessed in vitro on human monocytes infected with L. major metacyclic promastigotes, and in vivo on susceptible parasite-infected BALB/c mice. The development of cutaneous lesions in the right hind footpads of infected mice after 13 weeks post-infection showed a protection rate of 81.94% with the injected peptide P2. Moreover, Western blots revealed that the P2 peptide interacted with the major surface protease gp63, a protein of 63kDa molecular weight. Moreover, bioinformatics were used to predict the interaction between peptides and the major surface molecule of the L. major. The molecular docking showed that the P2 peptide has the minimum interaction energy and maximum shape complimentarity with the L. major gp63 active site. Our study demonstrated that the P2 peptide occurs at high frequency during the screening procedure, best inhibits L. major growth kinetics in vitro, and reduces cutaneous lesions in BALB/c mice, thus showing great promise in the development of new therapeutic molecules.
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ŞABABOĞLU E, TÜRÜTOĞLU H. HAYVANLARDA DEFENSİNLER VE ÖZELLİKLERİ. MEHMET AKIF ERSOY ÜNIVERSITESI VETERINER FAKÜLTESI DERGISI 2016. [DOI: 10.24880/maeuvfd.260788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Identification of Synthetic and Natural Host Defense Peptides with Leishmanicidal Activity. Antimicrob Agents Chemother 2016; 60:2484-91. [PMID: 26883699 DOI: 10.1128/aac.02328-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/06/2016] [Indexed: 01/05/2023] Open
Abstract
Leishmaniaparasites are a major public health problem worldwide. Effective treatment of leishmaniasis is hampered by the high incidence of adverse effects to traditional drug therapy and the emergence of resistance to current therapeutics. A vaccine is currently not available. Host defense peptides have been investigated as novel therapeutic agents against a wide range of pathogens. Here we demonstrate that the antimicrobial peptide LL-37 and the three synthetic peptides E6, L-1018, and RI-1018 exhibit leishmanicidal activity against promastigotes and intramacrophage amastigotes ofLeishmania donovaniandLeishmania major We also report that theLeishmaniaprotease/virulence factor GP63 confers protection toLeishmaniafrom the cytolytic properties of alll-form peptides (E6, L-1018, and LL-37) but not thed-form peptide RI-1018. The results suggest that RI-1018, E6, and LL-37 are promising peptides to develop further into components for antileishmanial therapy.
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Lacerda AF, Pelegrini PB, de Oliveira DM, Vasconcelos ÉAR, Grossi-de-Sá MF. Anti-parasitic Peptides from Arthropods and their Application in Drug Therapy. Front Microbiol 2016; 7:91. [PMID: 26903970 PMCID: PMC4742531 DOI: 10.3389/fmicb.2016.00091] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
Africa, Asia, and Latin America are regions highly affected by endemic diseases, such as Leishmaniasis, Malaria, and Chagas' disease. They are responsible for the death of 1000s of patients every year, as there is not yet a cure for them and the drugs used are inefficient against the pathogenic parasites. During the life cycle of some parasitic protozoa, insects become the most important host and disseminator of the diseases triggered by these microorganisms. As infected insects do not develop nocive symptoms, they can carry the parasites for long time inside their body, enabling their multiplication and life cycle completion. Eventually, parasites infect human beings after insect's transmission through their saliva and/or feces. Hence, host insects and general arthropods, which developed a way to coexist with such parasites, are a promising source for the prospection of anti-parasitic compounds, as alternative methods for the treatment of protozoa-related diseases. Among the molecules already isolated and investigated, there are proteins and peptides with high activity against parasites, able to inhibit parasite activity in different stages of development. Although, studies are still taking their first steps, initial results show new perspectives on the treatment of parasitic diseases. Therefore, in this report, we describe about peptides from host insect sources with activity against the three most endemic parasites: Leishmania sp., Plasmodium sp., and Trypanosomes. Moreover, we discuss the future application insect peptides as anti-parasitic drugs and the use of non-hosts insect transcriptomes on the prospection of novel molecules for the treatment of parasitic neglected diseases.
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Affiliation(s)
- Ariane F. Lacerda
- Plant-Pest Interaction Laboratory, PBI, Genetic Resources and Biotechnology, Brazilian Agriculture Research CorporationBrasilia, Brazil
- Post-Graduation Program in Biochemistry and Molecular Biology, Federal University of Rio Grande do NorteNatal, Brazil
| | - Patrícia B. Pelegrini
- Plant-Pest Interaction Laboratory, PBI, Genetic Resources and Biotechnology, Brazilian Agriculture Research CorporationBrasilia, Brazil
| | - Daiane M. de Oliveira
- Plant-Pest Interaction Laboratory, PBI, Genetic Resources and Biotechnology, Brazilian Agriculture Research CorporationBrasilia, Brazil
- Post-Graduation Program in Pharmaceutical Sciences, Faculty of Health Sciences, University of BrasiliaBrasilia, Brazil
| | - Érico A. R. Vasconcelos
- Plant-Pest Interaction Laboratory, PBI, Genetic Resources and Biotechnology, Brazilian Agriculture Research CorporationBrasilia, Brazil
- Department of Health Sciences, Integrated College of Educational Union’s Central PlateauGama, Brazil
| | - Maria F. Grossi-de-Sá
- Plant-Pest Interaction Laboratory, PBI, Genetic Resources and Biotechnology, Brazilian Agriculture Research CorporationBrasilia, Brazil
- Post-Graduation Program in Biochemistry and Molecular Biology, Federal University of Rio Grande do NorteNatal, Brazil
- Post-Graduation Program in Pharmaceutical Sciences, Faculty of Health Sciences, University of BrasiliaBrasilia, Brazil
- Post-Graduation Program in Genomics Science and Biotechnology, Catholic University of BrasiliaBrasilia, Brazil
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Aguilera-Mendoza L, Marrero-Ponce Y, Tellez-Ibarra R, Llorente-Quesada MT, Salgado J, Barigye SJ, Liu J. Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences. Bioinformatics 2015; 31:2553-9. [DOI: 10.1093/bioinformatics/btv180] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/24/2015] [Indexed: 12/17/2022] Open
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Mehta D, Anand P, Kumar V, Joshi A, Mathur D, Singh S, Tuknait A, Chaudhary K, Gautam SK, Gautam A, Varshney GC, Raghava GPS. ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau051. [PMID: 24923818 PMCID: PMC4054663 DOI: 10.1093/database/bau051] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
ParaPep is a repository of antiparasitic peptides, which provides comprehensive information related to experimentally validated antiparasitic peptide sequences and their structures. The data were collected and compiled from published research papers, patents and from various databases. The current release of ParaPep holds 863 entries among which 519 are unique peptides. In addition to peptides having natural amino acids, ParaPep also consists of peptides having d-amino acids and chemically modified residues. In ParaPep, most of the peptides have been evaluated for growth inhibition of various species of Plasmodium, Leishmania and Trypanosoma. We have provided comprehensive information about these peptides that include peptide sequence, chemical modifications, stereochemistry, antiparasitic activity, origin, nature of peptide, assay types, type of parasite, mode of action and hemolytic activity. Structures of peptides consisting of natural, as well as modified amino acids have been determined using state-of-the-art software, PEPstr. To facilitate users, various user-friendly web tools, for data fetching, analysis and browsing, have been integrated. We hope that ParaPep will be advantageous in designing therapeutic peptides against parasitic diseases. Database URL: http://crdd.osdd.net/raghava/parapep/
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Affiliation(s)
- Divya Mehta
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Priya Anand
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Vineet Kumar
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Anshika Joshi
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Deepika Mathur
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Sandeep Singh
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Abhishek Tuknait
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Kumardeep Chaudhary
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Shailendra K Gautam
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Ankur Gautam
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Grish C Varshney
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
| | - Gajendra P S Raghava
- Cell biology and Immunology Division and Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh-160036, India
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Campos-Salinas J, Cavazzuti A, O'Valle F, Forte-Lago I, Caro M, Beverley SM, Delgado M, Gonzalez-Rey E. Therapeutic efficacy of stable analogues of vasoactive intestinal peptide against pathogens. J Biol Chem 2014; 289:14583-99. [PMID: 24706753 DOI: 10.1074/jbc.m114.560573] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Vasoactive intestinal peptide (VIP) is an anti-inflammatory neuropeptide recently identified as a potential antimicrobial peptide. To overcome the metabolic limitations of VIP, we modified the native peptide sequence and generated two stable synthetic analogues (VIP51 and VIP51(6-30)) with better antimicrobial profiles. Herein we investigate the effects of both VIP analogues on cell viability, membrane integrity, and ultrastructure of various bacterial strains and Leishmania species. We found that the two VIP derivatives kill various non-pathogenic and pathogenic Gram-positive and Gram-negative bacteria as well as the parasite Leishmania major through a mechanism that depends on the interaction with certain components of the microbial surface, the formation of pores, and the disruption of the surface membrane. The cytotoxicity of the VIP derivatives is specific for pathogens, because they do not affect the viability of mammalian cells. Docking simulations indicate that the chemical changes made in the analogues are critical to increase their antimicrobial activities. Consequently, we found that the native VIP is less potent as an antibacterial and fails as a leishmanicidal. Noteworthy from a therapeutic point of view is that treatment with both derivatives increases the survival and reduces bacterial load and inflammation in mice with polymicrobial sepsis. Moreover, treatment with VIP51(6-30) is very effective at reducing lesion size and parasite burden in a model of cutaneous leishmaniasis. These results indicate that the VIP analogues emerge as attractive alternatives for treating drug-resistant infectious diseases and provide key insights into a rational design of novel agents against these pathogens.
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Affiliation(s)
| | - Antonio Cavazzuti
- From the Institute of Parasitology and Biomedicine, CSIC, Granada 18016, Spain
| | - Francisco O'Valle
- the Department of Pathological Anatomy, Medical School of Granada, Granada 18012, Spain
| | - Irene Forte-Lago
- From the Institute of Parasitology and Biomedicine, CSIC, Granada 18016, Spain
| | - Marta Caro
- From the Institute of Parasitology and Biomedicine, CSIC, Granada 18016, Spain
| | - Stephen M Beverley
- the Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63110, and
| | - Mario Delgado
- From the Institute of Parasitology and Biomedicine, CSIC, Granada 18016, Spain
| | - Elena Gonzalez-Rey
- From the Institute of Parasitology and Biomedicine, CSIC, Granada 18016, Spain, the Department of Biochemistry and Molecular Biology, Medical School of Seville, Seville 41009, Spain
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Haines LR. Examining the tsetse teneral phenomenon and permissiveness to trypanosome infection. Front Cell Infect Microbiol 2013; 3:84. [PMID: 24312903 PMCID: PMC3833344 DOI: 10.3389/fcimb.2013.00084] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/03/2013] [Indexed: 12/31/2022] Open
Abstract
Tsetse flies are the most important vectors of African trypanosomiasis but, surprisingly, are highly refractory to trypanosome parasite infection. In populations of wild caught flies, it is rare to find mature salivarian and mouthpart parasite infection rates exceeding 1 and 15%, respectively. This inherent refractoriness persists throughout the lifespan of the fly, although extreme starvation and suboptimal environmental conditions can cause a reversion to the susceptible phenotype. The teneral phenomenon is a phenotype unique to newly emerged, previously unfed tsetse, and is evidenced by a profound susceptibility to trypanosome infection. This susceptibility persists for only a few days post-emergence and decreases with fly age and bloodmeal acquisition. Researchers investigating trypanosome-tsetse interactions routinely exploit this phenomenon by using young, unfed (teneral) flies to naturally boost trypanosome establishment and maturation rates. A suite of factors may contribute, at least in part, to this unusual parasite permissive phenotype. These include the physical maturity of midgut barriers, the activation of immunoresponsive tissues and their effector molecules, and the role of the microflora within the midgut of the newly emerged fly. However, at present, the molecular mechanisms that underpin the teneral phenomenon still remain unknown. This review will provide a historical overview of the teneral phenomenon and will examine immune-related factors that influence, and may help us better understand, this unusual phenotype.
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Affiliation(s)
- Lee Rafuse Haines
- Department of Vector Biology, Liverpool School of Tropical Medicine Liverpool, UK
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Campos-Salinas J, Caro M, Cavazzuti A, Forte-Lago I, Beverley SM, O'Valle F, Gonzalez-Rey E. Protective role of the neuropeptide urocortin II against experimental sepsis and leishmaniasis by direct killing of pathogens. THE JOURNAL OF IMMUNOLOGY 2013; 191:6040-51. [PMID: 24249730 DOI: 10.4049/jimmunol.1301921] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We currently face an alarming resurgence in infectious diseases characterized by antimicrobial resistance and therapeutic failure. This has generated the urgent need of developing new therapeutic approaches that include agents with nontraditional modes of action. A recent interest focused on approaches based on our natural immune defenses, especially on peptides that combine innate antimicrobial activity against diverse pathogens and immunoregulatory functions. In this study, to our knowledge, we describe for the first time the antimicrobial activity of the neuropeptide urocortin II (UCNII) against a panel of Gram-positive and Gram-negative bacteria and tropical parasites of the genus Leishmania. Importantly, this cytotoxicity was selective for pathogens, because UCNII did not affect mammalian cell viability. Structurally, UCNII has a cationic and amphipathic design that resembles antimicrobial peptides. Using mutants and UCNII fragments, we determined the structural requirements for the interaction between the peptide and the surface of pathogen. Following its binding to pathogen, UCNII caused cell death through different membrane-disrupting mechanisms that involve aggregation and membrane depolarization in bacteria and pore formation in Leishmania. Noteworthily, UCNII killed the infective form of Leishmania major even inside the infected macrophages. Consequently, UCNII prevented mortality caused by polymicrobial sepsis and ameliorated pathological signs of cutaneous leishmaniasis. Besides its presence in body physical and mucosal barriers, we found that innate immune cells produce UCNII in response to infections. Therefore, UCNII could be considered as an ancient highly-conserved host peptide involved in the natural antimicrobial defense and emerge as an attractive alternative to current treatments for microbial disorders with associated drug resistances.
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Affiliation(s)
- Jenny Campos-Salinas
- Institute of Parasitology and Biomedicine "López-Neyra," Spanish National Research Council, Granada 18016, Spain
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Cellular response to Trypanosoma cruzi infection induces secretion of defensin α-1, which damages the flagellum, neutralizes trypanosome motility, and inhibits infection. Infect Immun 2013; 81:4139-48. [PMID: 23980110 DOI: 10.1128/iai.01459-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human defensins play a fundamental role in the initiation of innate immune responses to some microbial pathogens. Here we show that colonic epithelial model HCT116 cells respond to Trypanosoma cruzi infection by secreting defensin α-1, which reduces infection. We also report the early effects of defensin α-1 on invasive trypomastigotes that involve damage of the flagellar structure to inhibit parasite motility and reduce cellular infection. Short exposure of defensin α-1 to trypomastigotes shows that defensin α-1 binds to the flagellum, resulting in flagellar membrane and axoneme alterations, followed by breaking of the flagellar membrane connected to the trypanosome body, leading to detachment and release of the parasite flagellum. In addition, defensin α-1 induces a significant reduction in parasite motility in a peptide concentration-dependent manner, which is abrogated by anti-defensin α-1 IgG. Preincubation of trypomastigotes with a concentration of defensin α-1 that inhibits 50% trypanosome motility significantly reduced cellular infection by 80%. Thus, human defensin α-1 is an innate immune molecule that is secreted by HCT116 cells in response to T. cruzi infection, inhibits T. cruzi motility, and plays an important role in reducing cellular infection. This is the first report showing a novel cellular innate immune response to a human parasite by secretion of defensin α-1, which neutralizes the motility of a human parasite to reduce cellular infection. The mode of activity of human defensin α-1 against T. cruzi and its function may provide insights for the development of new antiparasitic strategies.
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Avitabile C, Netti F, Orefice G, Palmieri M, Nocerino N, Malgieri G, D'Andrea LD, Capparelli R, Fattorusso R, Romanelli A. Design, structural and functional characterization of a Temporin-1b analog active against Gram-negative bacteria. Biochim Biophys Acta Gen Subj 2013; 1830:3767-75. [PMID: 23403136 DOI: 10.1016/j.bbagen.2013.01.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 01/21/2013] [Accepted: 01/28/2013] [Indexed: 10/27/2022]
Abstract
BACKGROUND Temporins are small antimicrobial peptides secreted by the Rana temporaria showing mainly activity against Gram-positive bacteria. However, different members of the temporin family, such as Temporin B, act in synergy also against Gram-negative bacteria. With the aim to develop a peptide with a wide spectrum of antimicrobial activity we designed and analyzed a series of Temporin B analogs. METHODS Peptides were initially obtained by Ala scanning on Temporin B sequence; antimicrobial activity tests allowed to identify the TB_G6A sequence, which was further optimized by increasing the peptide positive charge (TB_KKG6A). Interactions of this active peptide with the LPS of E. coli were investigated by CD, fluorescence and NMR. RESULTS TB_KKG6A is active against Gram-positive and Gram-negative bacteria at low concentrations. The peptide strongly interacts with the LPS of Gram-negative bacteria and folds upon interaction into a kinked helix. CONCLUSION Our results show that it is possible to widen the activity spectrum of an antimicrobial peptide by subtle changes of the primary structure. TB_KKG6A, having a simple composition, a broad spectrum of antimicrobial activity and a very low hemolytic activity, is a promising candidate for the design of novel antimicrobial peptides. GENERAL SIGNIFICANCE The activity of antimicrobial peptides is strongly related to the ability of the peptide to interact and break the bacterial membrane. Our studies on TB_KKG6A indicate that efficient interactions with LPS can be achieved when the peptide is not perfectly amphipathic, since this feature seems to help the toroidal pore formation process.
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Affiliation(s)
- Concetta Avitabile
- Università di Napoli Federico II, Dipartimento delle Scienze Biologiche, Napoli, Italy
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Marr AK, McGwire BS, McMaster WR. Modes of action of Leishmanicidal antimicrobial peptides. Future Microbiol 2013; 7:1047-59. [PMID: 22953706 DOI: 10.2217/fmb.12.85] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Leishmaniasis is one of the major neglected tropical diseases of the world. It is present in 88 countries with an estimated number of 500,000 cases of visceral leishmaniasis and 1.5 million cases of cutaneous disease. No effective vaccinations are available against leishmaniasis and the efficacy of existing treatments is compromised due to the emergence of drug resistance. Thus, there is an urgent need to develop new compounds with antileishmanial activity. Antimicrobial peptides have potential as novel antileishmanial therapy, either for use alone or in combination with current drug regimens. The modes of action of these peptides against Leishmania includes: membrane disruption leading to necrotic cell death; induction of apoptosis; binding to intracellular target(s); and indirect effects via immunomodulation of host immune cells. This article reviews the mechanisms of action of antimicrobial peptides with leishmanicidal activity.
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Affiliation(s)
- Alexandra K Marr
- Immunity & Infection Research Centre, Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
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Screening of Antimicrobials from Caribbean Sea Animals and Isolation of Bactericidal Proteins from the Littoral Mollusk Cenchritis muricatus. Curr Microbiol 2012; 64:501-5. [DOI: 10.1007/s00284-012-0096-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 02/03/2012] [Indexed: 01/28/2023]
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Preet S, Bharati S, Shukla G, Koul A, Rishi P. Evaluation of amoebicidal potential of Paneth cell cryptdin-2 against Entamoeba histolytica. PLoS Negl Trop Dis 2011; 5:e1386. [PMID: 22206022 PMCID: PMC3243701 DOI: 10.1371/journal.pntd.0001386] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 09/20/2011] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Amoebiasis is a major public health problem in tropical and subtropical countries. Currently, metronidazole is the gold choice medication for the treatment of this disease. However, reports have indicated towards the possibility of development of metronidazole-resistance in Entamoeba strains in near future. In view of the emergence of this possibility, in addition to the associated side effects and mutagenic ability of the currently available anti-amoebic drugs, there is a need to explore newer therapeutics against this disease. In this context, the present study evaluated the amoebicidal potential of cryptdin-2 against E. histolytica. METHODS/PRINCIPAL FINDINGS In the present study, cryptdin-2 exhibited potent in-vitro amoebicidal activity against E. histolytica in a concentration dependent manner at a minimum amoebicidal concentration (MAC) of 4 mg/L. Scanning electron microscopy as well as phase contrast microscopic investigations of cryptdin-2 treated trophozoites revealed that the peptide was able to induce significant morphological alterations in terms of membrane wrinkling, leakage of the cytoplasmic contents and damaged plasma membrane suggesting a possible membrane dependent amoebicidal activity. N-phenyl napthylamine (NPN) uptake assay in presence of sulethal, lethal as well as twice the lethal concentrations further confirmed the membrane-dependent mode of action of cryptdin-2 and suggested that the peptide could permeabilize the plasma membrane of E. histolytica. It was also found that cryptdin-2 interfered with DNA, RNA as well as protein synthesis of E. histolytica exerting the highest effect against DNA synthesis. Thus, the macromolecular synthesis studies correlated well with the observations of membrane permeabilization studies. SIGNIFICANCE/CONCLUSIONS The amoebicidal efficacy of cryptdin-2 suggests that it may be exploited as a promising option to combat amoebiasis or, at least, may act as an adjunct to metronidazole and/or other available anti-amoebic drugs.
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Affiliation(s)
- Simran Preet
- Department of Microbiology, Basic Medical Sciences Block, Panjab University, Chandigarh, India
| | - Sanjay Bharati
- Department of Biophysics, Basic Medical Sciences Block, Panjab University, Chandigarh, India
| | - Geeta Shukla
- Department of Microbiology, Basic Medical Sciences Block, Panjab University, Chandigarh, India
| | - Ashwani Koul
- Department of Biophysics, Basic Medical Sciences Block, Panjab University, Chandigarh, India
| | - Praveen Rishi
- Department of Microbiology, Basic Medical Sciences Block, Panjab University, Chandigarh, India
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Efficacy of synthetic peptides RP-1 and AA-RP-1 against Leishmania species in vitro and in vivo. Antimicrob Agents Chemother 2011; 56:658-65. [PMID: 22123683 DOI: 10.1128/aac.05349-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Host defense peptides are naturally occurring molecules that play essential roles in innate immunity to infection. Based on prior structure-function knowledge, we tested two synthetic peptides (RP-1 and AA-RP-1) modeled on the conserved, microbicidal α-helical domain of mammalian CXCL4 platelet kinocidins. These peptides were evaluated for efficacy against Leishmania species, the causative agents of the group of diseases known as leishmaniasis. In vitro antileishmanial activity was assessed against three distinct Leishmania strains by measuring proliferation, metabolic activity and parasite viability after exposure to various concentrations of peptides. We demonstrate that micromolar concentrations of RP-1 and AA-RP-1 caused dose-dependent growth inhibition of Leishmania promastigotes. This antileishmanial activity correlated with rapid membrane disruption, as well as with a loss of mitochondrial transmembrane potential. In addition, RP-1 and AA-RP-1 demonstrated distinct and significant in vivo antileishmanial activities in a mouse model of experimental visceral leishmaniasis after intravenous administration. These results establish efficacy of RP-1 lineage synthetic peptides against Leishmania species in vitro and after intravenous administration in vivo and provide further validation of proof of concept for the development of these and related systemic anti-infective peptides targeting pathogens that are resistant to conventional antibiotics.
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Bhunia A, Saravanan R, Mohanram H, Mangoni ML, Bhattacharjya S. NMR structures and interactions of temporin-1Tl and temporin-1Tb with lipopolysaccharide micelles: mechanistic insights into outer membrane permeabilization and synergistic activity. J Biol Chem 2011; 286:24394-406. [PMID: 21586570 PMCID: PMC3129218 DOI: 10.1074/jbc.m110.189662] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 04/27/2011] [Indexed: 11/06/2022] Open
Abstract
Temporins are a group of closely related short antimicrobial peptides from frog skin. Lipopolysaccharide (LPS), the major constituent of the outer membrane of gram-negative bacteria, plays important roles in the activity of temporins. Earlier studies have found that LPS induces oligomerization of temporin-1Tb (TB) thus preventing its translocation across the outer membrane and, as a result, reduces its activity on gram-negative bacteria. On the other hand, temporin-1Tl (TL) exhibits higher activity, presumably because of lack of such oligomerization. A synergistic mechanism was proposed, involving TL and TB in overcoming the LPS-mediated barrier. Here, to gain insights into interactions of TL and TB within LPS, we investigated the structures and interactions of TL, TB, and TL+TB in LPS micelles, using NMR and fluorescence spectroscopy. In the context of LPS, TL assumes a novel antiparallel dimeric helical structure sustained by intimate packing between aromatic-aromatic and aromatic-aliphatic residues. By contrast, independent TB has populations of helical and aggregated conformations in LPS. The LPS-induced aggregated states of TB are largely destabilized in the presence of TL. Saturation transfer difference NMR studies have delineated residues of TL and TB in close contact with LPS and enhanced interactions of these two peptides with LPS, when combined together. Fluorescence resonance energy transfer and (31)P NMR have pointed out the proximity of TL and TB in LPS and conformational changes of LPS, respectively. Importantly, these results provide the first structural insights into the mode of action and synergism of antimicrobial peptides at the level of the LPS-outer membrane.
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Affiliation(s)
- Anirban Bhunia
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
| | - Rathi Saravanan
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
| | - Harini Mohanram
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
| | - Maria L. Mangoni
- the Istituto Pasteur-Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche Universita‘ La Sapienza, Piazzale Aldo Moro, 5-00185 Roma, Italy
| | - Surajit Bhattacharjya
- From the School of Biological Sciences, Division of Structural and Computational Biology, Nanyang Technological University, Singapore 637551 and
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Yeung ATY, Gellatly SL, Hancock REW. Multifunctional cationic host defence peptides and their clinical applications. Cell Mol Life Sci 2011; 68:2161-76. [PMID: 21573784 PMCID: PMC11114888 DOI: 10.1007/s00018-011-0710-x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 12/21/2022]
Abstract
With the rapid rise in the emergence of bacterial strains resistant to multiple classes of antimicrobial agents, there is an urgent need to develop novel antimicrobial therapies to combat these pathogens. Cationic host defence peptides (HDPs) and synthetic derivatives termed innate defence regulators (IDRs) represent a promising alternative approach in the treatment of microbial-related diseases. Cationic HDPs (also termed antimicrobial peptides) have emerged from their origins as nature's antibiotics and are widely distributed in organisms from insects to plants to mammals and non-mammalian vertebrates. Although their original and primary function was proposed to be direct antimicrobial activity against bacteria, fungi, parasites and/or viruses, cationic HDPs are becoming increasingly recognized as multifunctional mediators, with both antimicrobial activity and diverse immunomodulatory properties. Here we provide an overview of the antimicrobial and immunomodulatory activities of cationic HDPs, and discuss their potential application as beneficial therapeutics in overcoming infectious diseases.
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Affiliation(s)
- Amy T. Y. Yeung
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Room 232, 2259 Lower Mall Research Station, Vancouver, BC V6T 1Z4 Canada
| | - Shaan L. Gellatly
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Room 232, 2259 Lower Mall Research Station, Vancouver, BC V6T 1Z4 Canada
| | - Robert E. W. Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Room 232, 2259 Lower Mall Research Station, Vancouver, BC V6T 1Z4 Canada
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45
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Antiplasmodial properties of acyl-lysyl oligomers in culture and animal models of malaria. Antimicrob Agents Chemother 2011; 55:3803-11. [PMID: 21646484 DOI: 10.1128/aac.00129-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our previous analysis of antiplasmodial properties exhibited by dodecanoyl-based oligo-acyl-lysyls (OAKs) has outlined basic attributes implicated in potent inhibition of parasite growth and underlined the critical role of excess hydrophobicity in hemotoxicity. To dissociate hemolysis from antiplasmodial effect, we screened >50 OAKs for in vitro growth inhibition of Plasmodium falciparum strains, thus revealing the minimal requirements for antiplasmodial potency in terms of sequence and composition, as confirmed by efficacy studies in vivo. The most active sequence, dodecanoyllysyl-bis(aminooctanoyllysyl)-amide (C(12)K-2α(8)), inhibited parasite growth at submicromolar concentrations (50% inhibitory concentration [IC(50)], 0.3 ± 0.1 μM) and was devoid of hemolytic activity (<0.4% hemolysis at 150 μM). Unlike the case of dodecanoyl-based analogs, which equally affect ring and trophozoite stages of the parasite developmental cycle, the ability of various octanoyl-based OAKs to distinctively affect these stages (rings were 4- to 5-fold more sensitive) suggests a distinct antiplasmodial mechanism, nonmembranolytic to host red blood cells (RBCs). Upon intraperitoneal administration to mice, C(12)K-2α(8) demonstrated sustainable high concentrations in blood (e.g., 0.1 mM at 25 mg/kg of body weight). In Plasmodium vinckei-infected mice, C(12)K-2α(8) significantly affected parasite growth (50% effective dose [ED(50)], 22 mg/kg) but also caused mortality in 2/3 mice at high doses (50 mg/kg/day × 4).
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46
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Zucca M, Savoia D. Current developments in the therapy of protozoan infections. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2011; 5:4-10. [PMID: 21629507 PMCID: PMC3103884 DOI: 10.2174/1874104501105010004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 05/25/2010] [Accepted: 06/20/2010] [Indexed: 12/03/2022]
Abstract
Protozoan parasites cause serious human and zoonotic infections, including life-threatening diseases such as malaria, African and American trypanosomiasis, and leishmaniasis. These diseases are no more common in the developed world, but together they still threaten about 40% of the world population (WHO estimates). Mortality and morbidity are high in developing countries, and the lack of vaccines makes chemotherapy the only suitable option. However, available antiparasitic drugs are hampered by more or less marked toxic side effects and by the emergence of drug resistance. As the main prevalence of parasitic diseases occurs in the poorest areas of the world, the interest of the pharmaceutical companies in the development of new drugs has been traditionally scarce. The establishment of public-private partnerships focused on tropical diseases is changing this situation, allowing the exploitation of the technological advances that took place during the past decade related to genomics, proteomics, and in silico drug discovery approaches. These techniques allowed the identification of new molecular targets that in some cases are shared by different parasites. In this review we outline the recent developments in the fields of protease and topoisomerase inhibitors, antimicrobial and cell-penetrating peptides, and RNA interference. We also report on the rapidly developing field of new vectors (micro and nano particles, mesoporous materials) that in some cases can cross host or parasite natural barriers and, by selectively delivering new or already in use drugs to the target site, minimize dosage and side effects.
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Affiliation(s)
- Mario Zucca
- Department of Clinical and Biological Sciences, University of Torino, Italy
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47
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Arnett E, Lehrer RI, Pratikhya P, Lu W, Seveau S. Defensins enable macrophages to inhibit the intracellular proliferation of Listeria monocytogenes. Cell Microbiol 2011; 13:635-51. [DOI: 10.1111/j.1462-5822.2010.01563.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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48
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Domadia PN, Bhunia A, Ramamoorthy A, Bhattacharjya S. Structure, interactions, and antibacterial activities of MSI-594 derived mutant peptide MSI-594F5A in lipopolysaccharide micelles: role of the helical hairpin conformation in outer-membrane permeabilization. J Am Chem Soc 2010; 132:18417-28. [PMID: 21128620 DOI: 10.1021/ja1083255] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipopolysaccharide (LPS) provides a well-organized permeability barrier at the outer membrane of Gram-negative bacteria. Host defense cationic antimicrobial peptides (AMPs) need to disrupt the outer membrane before gaining access to the inner cytoplasmic membrane or intracellular targets. Several AMPs are largely inactive against Gram-negative pathogens due to the restricted permeation through the LPS layer of the outer membrane. MSI-594 (GIGKFLKKAKKGIGAVLKVLTTG) is a highly active AMP with a broad-spectrum of activities against bacteria, fungi, and virus. In the context of LPS, MSI-594 assumes a hairpin helical structure dictated by packing interactions between two helical segments. Residue Phe5 of MSI-594 has been found to be engaged in important interhelical interactions. In order to understand plausible structural and functional inter-relationship of the helical hairpin structure of MSI-594 with outer membrane permeabilization, a mutant peptide, termed MSI-594F5A, containing a replacement of Phe5 with Ala has been prepared. We have compared antibacterial activities, outer and inner membrane permeabilizations, LPS binding affinity, perturbation of LPS micelles structures by MSI-594 and MSI-594F5A peptides. Our results demonstrated that the MSI-594F5A has lower activities against Gram-negative bacteria, due to limited permeabilization through the LPS layer, however, retains Gram-positive activity, akin to MSI-594. The atomic-resolution structure of MSI-594F5A has been determined in LPS micelles by NMR spectroscopy showing an amphipathic curved helix without any packing interactions. The 3D structures, interactions, and activities of MSI-594 and its mutant MSI-594F5A in LPS provide important mechanistic insights toward the requirements of LPS specific conformations and outer membrane permeabilization by broad-spectrum antimicrobial peptides.
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Affiliation(s)
- Prerna N Domadia
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore-637551
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Mechanisms mediating bactericidal properties and conditions that enhance the potency of a broad-spectrum oligo-acyl-lysyl. Antimicrob Agents Chemother 2010; 55:688-95. [PMID: 21078924 DOI: 10.1128/aac.00666-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Previous studies have established the potential of the oligo-acyl-lysyl (OAK) concept in generating simple chemical mimics of host defense peptides (HDPs) with improved antimicrobial properties. We investigated the antibacterial properties of such an OAK, C(16(ω7))-KK-C(12)-K(amide), to obtain a better understanding of the complex mode(s) of action of cationic antibacterial peptides. The average MIC, determined against a multispecies panel of 50 strains, was 6 ± 5 μg/ml. However, although the OAK exerted an essentially dose-dependent bactericidal effect (time-kill curves typically exhibited 99% death within 2 h), marked differences in the killing rates occurred among inter- and intraspecies strains. Mechanistic comparison between equally sensitive and related strains revealed death of one strain to stem from the OAK's capacity to breach the cell membrane permeability barrier, whereas the death of the related strain resulted from the OAK's direct interference with DNA functions in vivo, without detectable membrane damage. These findings therefore support the notion that the antibacterial mechanism of action of a single HDP can vary among inter- and intraspecies strains. In addition, we present data illustrating the differential effects of environmental conditions (pH, ionic strength and temperature), on the OAK's antibacterial properties, and ultimately demonstrate potency enhancement (by orders of magnitude) through selection of optimal incubation conditions. Such attributes might be useful in a variety of antibacterial applications.
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50
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Dai T, Huang YY, Sharma SK, Hashmi JT, Kurup DB, Hamblin MR. Topical antimicrobials for burn wound infections. RECENT PATENTS ON ANTI-INFECTIVE DRUG DISCOVERY 2010; 5:124-51. [PMID: 20429870 PMCID: PMC2935806 DOI: 10.2174/157489110791233522] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 03/01/2010] [Indexed: 01/22/2023]
Abstract
Throughout most of history, serious burns occupying a large percentage of body surface area were an almost certain death sentence because of subsequent infection. A number of factors such as disruption of the skin barrier, ready availability of bacterial nutrients in the burn milieu, destruction of the vascular supply to the burned skin, and systemic disturbances lead to immunosuppression combined together to make burns particularly susceptible to infection. In the 20th century the introduction of antibiotic and antifungal drugs, the use of topical antimicrobials that could be applied to burns, and widespread adoption of early excision and grafting all helped to dramatically increase survival. However the relentless increase in microbial resistance to antibiotics and other antimicrobials has led to a renewed search for alternative approaches to prevent and combat burn infections. This review will cover patented strategies that have been issued or filed with regard to new topical agents, preparations, and methods of combating burn infections. Animal models that are used in preclinical studies are discussed. Various silver preparations (nanocrystalline and slow release) are the mainstay of many approaches but antimicrobial peptides, topical photodynamic therapy, chitosan preparations, new iodine delivery formulations, phage therapy and natural products such as honey and essential oils have all been tested. This active area of research will continue to provide new topical antimicrobials for burns that will battle against growing multidrug resistance.
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Affiliation(s)
- Tianhong Dai
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA
- Department of Dermatology, Harvard Medical School, Boston, MA
| | - Ying-Ying Huang
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA
- Department of Dermatology, Harvard Medical School, Boston, MA
- Aesthetic and Plastic Center of Guangxi Medical University, Nanning, P.R China
| | - Sulbha K. Sharma
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA
| | - Javad T. Hashmi
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA
- Department of Dermatology, Harvard Medical School, Boston, MA
| | - Divya B. Kurup
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA
| | - Michael R. Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA
- Department of Dermatology, Harvard Medical School, Boston, MA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
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