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Mehraj I, Hamid A, Gani U, Iralu N, Manzoor T, Saleem Bhat S. Combating Antimicrobial Resistance by Employing Antimicrobial Peptides: Immunomodulators and Therapeutic Agents against Infectious Diseases. ACS APPLIED BIO MATERIALS 2024; 7:2023-2035. [PMID: 38533844 DOI: 10.1021/acsabm.3c01104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The rising prevalence of multiple-drug-resistant pathogens poses a formidable challenge to conventional antimicrobial treatments. The inability of potent antibiotics to combat these "superbugs" underscores the pressing need for alternative therapeutic agents. Antimicrobial peptides (AMPs) represent an alternative class of antibiotics. AMPs are essential immunomodulatory molecules that are found in various organisms. They play a pivotal role in managing microbial ecosystems and bolstering innate immunity by targeting and eliminating invading microorganisms. AMPs also have applications in the agriculture sector by combating animal as well as plant pathogens. AMPs can be exploited for the targeted therapy of various diseases and can also be used in drug-delivery systems. They can be used in synergy with current treatments like antibiotics and can potentially lead to a lower required dosage. AMPs also have huge potential in wound healing and regenerative medicine. Developing AMP-based strategies with improved safety, specificity, and efficacy is crucial in the battle against alarming global microbial resistance. This review will explore AMPs' increasing applicability, their mode of antimicrobial activity, and various delivery systems enhancing their stability and efficacy.
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Affiliation(s)
- Insha Mehraj
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 05466, India
| | - Aflaq Hamid
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 05466, India
| | - Ubaid Gani
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 05466, India
| | - Nulevino Iralu
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 05466, India
| | - Tasaduq Manzoor
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 05466, India
| | - Sahar Saleem Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir 05466, India
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Sadek ASM, Farghaly DS, Kadada H, Mashaal A. Immunomodulatory potential of Sarcophaga argyostoma larval hemolymph as a natural alternative to berenil in treating Trypanosoma evansi in vivo. Sci Rep 2024; 14:6972. [PMID: 38521853 PMCID: PMC10960805 DOI: 10.1038/s41598-024-57113-y] [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: 02/05/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
This study compared effects of diminazene aceturate (berenil), commonly used to treat domestic animals infected with Trypanosoma evansi, with the hemolymph of Sarcophaga argyostoma larva. The hemolymph may be acting as a possible natural alternative to berenil, based on immunomodulation mediated inflammatory response. Inflammatory mediators and histopathological changes in liver, kidney, and spleen of albino mice experimentally infected with T. evansi were studied. Mice were divided into five groups: G1, uninfected, untreated (negative control); G2, T. evansi infected (positive control); G3, infected and treated with berenil; G4, infected and treated with hemolymph; G5, infected and treated with hemolymph 3 days before infection (prophylactic group). Animals in (G4) and (G5) exhibited a significant overall reduction in serum levels of IFN-γ. However, the reduction in TNF-α and IL-6 levels was more limited compared to (G2) and (G3). Notably, an elevation in IL-10 levels was observed compared to animals in other groups. Furthermore, the groups treated with hemolymph demonstrated an alleviation of T. evansi infection in contrast to the other groups. This study highlights that the administration of Sarcophaga argyostoma larval hemolymph at a dosage of 0.5 ml/kg significantly inhibited T. evansi organisms in vivo, showcasing a pronounced trypanocidal effect.
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Affiliation(s)
- Al-Shaimaa M Sadek
- Parasitology, Zoology and Entomology Department, Faculty of Science (for Girls), Al-Azhar University, Cairo, Egypt.
| | - Doaa S Farghaly
- Medical Entomology, Zoology and Entomology Department, Faculty of Science (for Girls), Al-Azhar University, Cairo, Egypt
| | - Hala Kadada
- Taxonomy, Zoology and Entomology Department, Faculty of Science (for Girls), Al-Azhar University, Cairo, Egypt
| | - Alya Mashaal
- Immunology, Zoology and Entomology Department, Faculty of Science (for Girls), Al-Azhar University, Cairo, Egypt
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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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Ribeiro R, Costa L, Pinto E, Sousa E, Fernandes C. Therapeutic Potential of Marine-Derived Cyclic Peptides as Antiparasitic Agents. Mar Drugs 2023; 21:609. [PMID: 38132930 PMCID: PMC10745025 DOI: 10.3390/md21120609] [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: 11/02/2023] [Revised: 11/18/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Parasitic diseases still compromise human health. Some of the currently available therapeutic drugs have limitations considering their adverse effects, questionable efficacy, and long treatment, which have encouraged drug resistance. There is an urgent need to find new, safe, effective, and affordable antiparasitic drugs. Marine-derived cyclic peptides have been increasingly screened as candidates for developing new drugs. Therefore, in this review, a systematic analysis of the scientific literature was performed and 25 marine-derived cyclic peptides with antiparasitic activity (1-25) were found. Antimalarial activity is the most reported (51%), followed by antileishmanial (27%) and antitrypanosomal (20%) activities. Some compounds showed promising antiparasitic activity at the nM scale, being active against various parasites. The mechanisms of action and targets for some of the compounds have been investigated, revealing different strategies against parasites.
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Affiliation(s)
- Ricardo Ribeiro
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
| | - Lia Costa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
| | - Eugénia Pinto
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
- Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
| | - Carla Fernandes
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (R.R.); (L.C.); (E.S.)
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal;
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Gao J, Dong J, Sun Z, Wang T, Guan Y, Sun Y, Qin G, Zhang X, Zhen Y. Effects of antimicrobial peptide and tributyrin on fecal microflora and blood indices of female calves. Food Sci Nutr 2023; 11:5248-5257. [PMID: 37701190 PMCID: PMC10494653 DOI: 10.1002/fsn3.3483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/15/2023] [Accepted: 05/24/2023] [Indexed: 09/14/2023] Open
Abstract
This study evaluated the effects of antimicrobial peptide (AMP) and tributyrin (TB) on dairy calves in terms of growth performance, immunity, oxidative stress, and intestinal microflora. A total of 40 female calves were divided into four treatment groups (n = 10): basal diet +0.015% essential oil, basal diet +0.03% AMP, basal diet +0.15% TB, and basal diet +0.03% AMP + 0.15% TB. AMP and TB supplementation increased the average daily gain (ADG) and weaning weight, while reducing diarrhea occurrence. Additionally, AMP and TB supplementation reduced the levels of reactive oxygen species (ROS) and malonaldehyde (MDA), while increasing superoxide dismutase (SOD) levels and serum immunoglobulin M (IgM) levels. However, the combined use of AMP and TB did not significantly affect the average daily feed intake, ADG, weaning weight, or diarrhea incidence but decreased ROS levels, while increasing SOD levels as well as MDA and IgM levels. Moreover, AMP and TG supplementation increased the relative abundance of several beneficial fiber- and mucin-degrading bacteria in the gut, in contrast to combined AMP and TB supplementation. The 16S rRNA results showed that AMP supplementation significantly increased the relative abundance of Rikenellaceae_RC9_gut_group, Ruminococcaceae_UCG-014 and [Eubacterium]_coprostanoligenes group (p < .01), and significantly decreased the relative abundance of Ruminococcaceae_UCG-005 and Christensenellaceae_R-7_group (p < .01). The TB supplementation significantly increased the abundances of Rikenellaceae_RC9_gut_group and Ruminococcaceae_UCG-005 (p < .01), and significantly decreased the relative abundances of Ruminococcaceae_UCG-014, [Eubacterium]_coprostanoligenes group and Christensenellaceae_R-7_group (p < .01). The combined use of AMP and TB significantly increased the relative abundance of Rikenellaceae_RC9_gut_group and Bacteroides (p < .01), and significantly decreased the relative abundance of Ruminococcaceae_UCG-014, [Eubacterium]_coprostanoligenes group and Christensenellaceae_R-7_group (p < .01). In summary, diets supplemented with either AMP or TB improved the intestinal microflora, growth performance, and health of weaned calves, but combined use was detrimental to calf performance.
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Affiliation(s)
- Junling Gao
- College of Animal Science and Technology, JLAU‐Borui Dairy Science and Technology R&D Center, Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunChina
| | - Jianan Dong
- College of Animal Science and Technology, JLAU‐Borui Dairy Science and Technology R&D Center, Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunChina
| | - Zhe Sun
- College of Animal Science and Technology, JLAU‐Borui Dairy Science and Technology R&D Center, Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunChina
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunChina
- College of Life Science, Jilin Agricultural UniversityChangchunChina
| | - Tao Wang
- College of Animal Science and Technology, JLAU‐Borui Dairy Science and Technology R&D Center, Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunChina
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunChina
| | - Yanling Guan
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunChina
| | - Yue Sun
- Institute of Animal Husbandry and Special Animal ScienceHeilongjiang Academy of Land Reclamation SciencesHarbinChina
| | - Guixin Qin
- College of Animal Science and Technology, JLAU‐Borui Dairy Science and Technology R&D Center, Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunChina
| | - Xuefeng Zhang
- College of Animal Science and Technology, JLAU‐Borui Dairy Science and Technology R&D Center, Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunChina
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunChina
| | - Yuguo Zhen
- College of Animal Science and Technology, JLAU‐Borui Dairy Science and Technology R&D Center, Key Laboratory of Animal Nutrition and Feed Science of Jilin Province, Key Laboratory of Animal Production Product Quality and Security Ministry of EducationJilin Agricultural UniversityChangchunChina
- Postdoctoral Scientific Research Workstation, Feed Engineering Technology Research Center of Jilin ProvinceChangchun Borui Science & Technology Co., LtdChangchunChina
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Rojas-Pirela M, Kemmerling U, Quiñones W, Michels PAM, Rojas V. Antimicrobial Peptides (AMPs): Potential Therapeutic Strategy against Trypanosomiases? Biomolecules 2023; 13:biom13040599. [PMID: 37189347 DOI: 10.3390/biom13040599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023] Open
Abstract
Trypanosomiases are a group of tropical diseases that have devastating health and socio-economic effects worldwide. In humans, these diseases are caused by the pathogenic kinetoplastids Trypanosoma brucei, causing African trypanosomiasis or sleeping sickness, and Trypanosoma cruzi, causing American trypanosomiasis or Chagas disease. Currently, these diseases lack effective treatment. This is attributed to the high toxicity and limited trypanocidal activity of registered drugs, as well as resistance development and difficulties in their administration. All this has prompted the search for new compounds that can serve as the basis for the development of treatment of these diseases. Antimicrobial peptides (AMPs) are small peptides synthesized by both prokaryotes and (unicellular and multicellular) eukaryotes, where they fulfill functions related to competition strategy with other organisms and immune defense. These AMPs can bind and induce perturbation in cell membranes, leading to permeation of molecules, alteration of morphology, disruption of cellular homeostasis, and activation of cell death. These peptides have activity against various pathogenic microorganisms, including parasitic protists. Therefore, they are being considered for new therapeutic strategies to treat some parasitic diseases. In this review, we analyze AMPs as therapeutic alternatives for the treatment of trypanosomiases, emphasizing their possible application as possible candidates for the development of future natural anti-trypanosome drugs.
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Corman HN, Ross JN, Fields FR, Shoue DA, McDowell MA, Lee SW. Rationally Designed Minimal Bioactive Domains of AS-48 Bacteriocin Homologs Possess Potent Antileishmanial Properties. Microbiol Spectr 2022; 10:e0265822. [PMID: 36342284 PMCID: PMC9769502 DOI: 10.1128/spectrum.02658-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
Leishmaniasis, a category I neglected tropical disease, is a group of diseases caused by the protozoan parasite Leishmania species with a wide range of clinical manifestations. Current treatment options can be highly toxic and expensive, with drug relapse and the emergence of resistance. Bacteriocins, antimicrobial peptides ribosomally produced by bacteria, are a relatively new avenue for potential antiprotozoal drugs. Particular interest has been focused on enterocin AS-48, with previously proven efficacy against protozoan species, including Leishmania spp. Sequential characterization of enterocin AS-48 has illustrated that antibacterial bioactivity is preserved in linearized, truncated forms; however, minimal domains of AS-48 bacteriocins have not yet been explored against protozoans. Using rational design techniques to improve membrane penetration activity, we designed peptide libraries using the minimal bioactive domain of AS-48 homologs. Stepwise changes to the charge (z), hydrophobicity (H), and hydrophobic dipole moment (μH) were achieved through lysine and tryptophan substitutions and the inversion of residues within the helical wheel, respectively. A total of 480 synthetic peptide variants were assessed for antileishmanial activity against Leishmania donovani. One hundred seventy-two peptide variants exhibited 50% inhibitory concentration (IC50) values below 20 μM against axenic amastigotes, with 60 peptide variants in the nanomolar range. Nine peptide variants exhibited potent activity against intracellular amastigotes with observed IC50 values of <4 μM and limited in vitro host cell toxicity, making them worthy of further drug development. Our work demonstrates that minimal bioactive domains of naturally existing bacteriocins can be synthetically engineered to increase membrane penetration against Leishmania spp. with minimal host cytotoxicity, holding the promise of novel, potent antileishmanial therapies. IMPORTANCE Leishmaniasis is a neglected tropical disease caused by protozoan parasites of the genus Leishmania. There are three primary clinical forms, cutaneous, mucocutaneous, and visceral, with visceral leishmaniasis being fatal if left untreated. Current drug treatments are less than ideal, especially in resource-limited areas, due to the difficult administration and treatment regimens as well as the high cost and the emergence of drug resistance. Identifying potent antileishmanial agents is of the utmost importance. We utilized rational design techniques to synthesize enterocin AS-48 and AS-48-like bacteriocin-based peptides and screened these peptides against L. donovani using a fluorescence-based phenotypic assay. Our results suggest that bacteriocins, specifically these rationally designed AS-48-like peptides, are promising leads for further development as antileishmanial drugs.
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Affiliation(s)
- Hannah N. Corman
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | - Jessica N. Ross
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | | | - Douglas A. Shoue
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | - Mary Ann McDowell
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
| | - Shaun W. Lee
- University of Notre Dame, Department of Biological Sciences, Notre Dame, Indiana, USA
- University of Notre Dame, Eck Institute for Global Health, Notre Dame, Indiana, USA
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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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9
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Muema JM, Bargul JL, Obonyo MA, Njeru SN, Matoke-Muhia D, Mutunga JM. Contemporary exploitation of natural products for arthropod-borne pathogen transmission-blocking interventions. Parasit Vectors 2022; 15:298. [PMID: 36002857 PMCID: PMC9404607 DOI: 10.1186/s13071-022-05367-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/16/2022] [Indexed: 11/26/2022] Open
Abstract
An integrated approach to innovatively counter the transmission of various arthropod-borne diseases to humans would benefit from strategies that sustainably limit onward passage of infective life cycle stages of pathogens and parasites to the insect vectors and vice versa. Aiming to accelerate the impetus towards a disease-free world amid the challenges posed by climate change, discovery, mindful exploitation and integration of active natural products in design of pathogen transmission-blocking interventions is of high priority. Herein, we provide a review of natural compounds endowed with blockade potential against transmissible forms of human pathogens reported in the last 2 decades from 2000 to 2021. Finally, we propose various translational strategies that can exploit these pathogen transmission-blocking natural products into design of novel and sustainable disease control interventions. In summary, tapping these compounds will potentially aid in integrated combat mission to reduce disease transmission trends.
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Affiliation(s)
- Jackson M Muema
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000, Nairobi, 00200, Kenya.
| | - Joel L Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000, Nairobi, 00200, Kenya.,International Centre of Insect Physiology and Ecology (Icipe), P.O. Box 30772, Nairobi, 00100, Kenya
| | - Meshack A Obonyo
- Department of Biochemistry and Molecular Biology, Egerton University, P.O. Box 536, Egerton, 20115, Kenya
| | - Sospeter N Njeru
- Centre for Traditional Medicine and Drug Research (CTMDR), Kenya Medical Research Institute (KEMRI), P.O. Box 54840, Nairobi, 00200, Kenya
| | - Damaris Matoke-Muhia
- Centre for Biotechnology Research Development (CBRD), Kenya Medical Research Institute (KEMRI), P.O. Box 54840, Nairobi, 00200, Kenya
| | - James M Mutunga
- Department of Biological Sciences, Mount Kenya University (MKU), P.O. Box 54, Thika, 01000, Kenya.,School of Engineering Design, Technology and Professional Programs, Pennsylvania State University, University Park, PA, 16802, USA
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10
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Nogrado K, Adisakwattana P, Reamtong O. Antimicrobial peptides: On future antiprotozoal and anthelminthic applications. Acta Trop 2022; 235:106665. [PMID: 36030045 DOI: 10.1016/j.actatropica.2022.106665] [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: 07/27/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
Control and elimination of parasitic diseases are nowadays further complicated by emergence of drug resistance. Drug resistance is a serious threat as there are not many effective antiparasitic drugs available. Aside from drug resistance, it is also favorable to look for alternative therapeutics that have lesser adverse effects. Antimicrobial peptides (AMPs) were found to address these issues. Some of its desirable traits are they are fast-acting, it has broad action that the pathogen will have difficulty developing resistance to, it has high specificity, and most importantly there are extensive sources such as bacteria; invertebrate and vertebrate animals as well as plants. Aside from this, AMPs are also found to modulate the immune response. This review would like to describe AMPs that have been studied for their antiparasitic activities especially on parasitic diseases that causes high mortality and exhibits drug resistance like malaria and leishmaniasis and to discuss the mechanism of action of these AMPS.
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Affiliation(s)
- Kathyleen Nogrado
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
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11
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Jiang M, Zhang R, Xia Y, Jia G, Yin Y, Wang P, Wu J, Ge R. i2APP: A Two-Step Machine Learning Framework For Antiparasitic Peptides Identification. Front Genet 2022; 13:884589. [PMID: 35571057 PMCID: PMC9091563 DOI: 10.3389/fgene.2022.884589] [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: 02/26/2022] [Accepted: 04/11/2022] [Indexed: 11/18/2022] Open
Abstract
Parasites can cause enormous damage to their hosts. Studies have shown that antiparasitic peptides can inhibit the growth and development of parasites and even kill them. Because traditional biological methods to determine the activity of antiparasitic peptides are time-consuming and costly, a method for large-scale prediction of antiparasitic peptides is urgently needed. We propose a computational approach called i2APP that can efficiently identify APPs using a two-step machine learning (ML) framework. First, in order to solve the imbalance of positive and negative samples in the training set, a random under sampling method is used to generate a balanced training data set. Then, the physical and chemical features and terminus-based features are extracted, and the first classification is performed by Light Gradient Boosting Machine (LGBM) and Support Vector Machine (SVM) to obtain 264-dimensional higher level features. These features are selected by Maximal Information Coefficient (MIC) and the features with the big MIC values are retained. Finally, the SVM algorithm is used for the second classification in the optimized feature space. Thus the prediction model i2APP is fully constructed. On independent datasets, the accuracy and AUC of i2APP are 0.913 and 0.935, respectively, which are better than the state-of-arts methods. The key idea of the proposed method is that multi-level features are extracted from peptide sequences and the higher-level features can distinguish well the APPs and non-APPs.
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Affiliation(s)
- Minchao Jiang
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Renfeng Zhang
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yixiao Xia
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Gangyong Jia
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Yuyu Yin
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
| | - Pu Wang
- Computer School, Hubei University of Arts and Science, Xiangyang, China
- *Correspondence: Pu Wang, ; Jian Wu, ; Ruiquan Ge,
| | - Jian Wu
- MyGenostics Inc., Beijing, China
- *Correspondence: Pu Wang, ; Jian Wu, ; Ruiquan Ge,
| | - Ruiquan Ge
- School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China
- *Correspondence: Pu Wang, ; Jian Wu, ; Ruiquan Ge,
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12
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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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13
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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: 30] [Impact Index Per Article: 15.0] [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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14
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Timmons PB, Hewage CM. Conformation and membrane interaction studies of the potent antimicrobial and anticancer peptide palustrin-Ca. Sci Rep 2021; 11:22468. [PMID: 34789753 PMCID: PMC8599514 DOI: 10.1038/s41598-021-01769-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/03/2021] [Indexed: 01/13/2023] Open
Abstract
Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defence peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dimensional structure in a 50/50% water/2,2,2-trifluoroethanol-\documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, and a cyclic disulfide-bridged domain at the C-terminal end of the peptide sequence, between residues 23 and 29. A molecular dynamics simulation was employed to model the peptide’s interactions with sodium dodecyl sulfate micelles, a widely used bacterial membrane-mimicking environment. Throughout the simulation, the peptide was found to maintain its \documentclass[12pt]{minimal}
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\begin{document}$$^{26}$$\end{document}26, while adopting a position parallel to the surface to micelle, which is energetically-favourable due to many hydrophobic and electrostatic contacts with the micelle.
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Affiliation(s)
- Patrick B Timmons
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland.
| | - Chandralal M Hewage
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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15
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Anti-leishmanial compounds from microbial metabolites: a promising source. Appl Microbiol Biotechnol 2021; 105:8227-8240. [PMID: 34625819 DOI: 10.1007/s00253-021-11610-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 10/20/2022]
Abstract
Leishmania is a complex disease caused by the protozoan parasites and transmitted by female phlebotomine sandfly. The disease affects some of the poorest people on earth with an estimated 700,000 to 1 million new cases annually. The current treatment for leishmaniasis is toxic, long, and limited, in view of the high resistance rate presented by the parasite, necessitating new perspectives for treatment. The discovery of new compounds with different targets can be a hope to make the treatment more efficient. Microbial metabolites and their structural analogues with enormous scaffold diversity and structural complexity have historically played a key role in drug discovery. We found thirty-nine research articles published between 1999 and 2021 in the scientific database (PubMed, Science Direct) describing microbes and their metabolites with activity against leishmanial parasites which is the focus of this review. KEY POINTS: • Leishmania affects the poorest regions of the globe • Current treatments for leishmaniasis are toxic and of limited efficacy • Microbial metabolites are potential sources of antileishmania drugs.
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16
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Zhang W, Xia E, Dai R, Tang W, Bin Y, Xia J. PredAPP: Predicting Anti-Parasitic Peptides with Undersampling and Ensemble Approaches. Interdiscip Sci 2021; 14:258-268. [PMID: 34608613 DOI: 10.1007/s12539-021-00484-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022]
Abstract
Anti-parasitic peptides (APPs) have been regarded as promising therapeutic candidate drugs against parasitic diseases. Due to the fact that the experimental techniques for identifying APPs are expensive and time-consuming, there is an urgent need to develop a computational approach to predict APPs on a large scale. In this study, we provided a computational method, termed PredAPP (Prediction of Anti-Parasitic Peptides) that could effectively identify APPs using an ensemble of well-performed machine learning (ML) classifiers. Firstly, to solve the class imbalance problem, a balanced training dataset was generated by the undersampling method. We found that the balanced dataset based on cluster centroid achieved the best performance. Then, nine groups of features and six ML algorithms were combined to generate 54 classifiers and the output of these classifiers formed 54 feature representations, and in each feature group, we selected the feature representation with best performance for classification. Finally, the selected feature representations were integrated using logistic regression algorithm to construct the prediction model PredAPP. On the independent dataset, PredAPP achieved accuracy and AUC of 0.880 and 0.922, respectively, compared to 0.739 and 0.873 of AMPfun, a state-of-the-art method to predict APPs. The web server of PredAPP is freely accessible at http://predapp.xialab.info and https://github.com/xialab-ahu/PredAPP .
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China.,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Ruyu Dai
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Wending Tang
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Yannan Bin
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China. .,Anhui Key Laboratory of Modern Biomanufacturing, Anhui University, Hefei, 230601, Anhui, China.
| | - Junfeng Xia
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China. .,State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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17
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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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18
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Lee JW, Collins JE, Wendt KL, Chakrabarti D, Cichewicz RH. Leveraging Peptaibol Biosynthetic Promiscuity for Next-Generation Antiplasmodial Therapeutics. JOURNAL OF NATURAL PRODUCTS 2021; 84:503-517. [PMID: 33565879 PMCID: PMC7941592 DOI: 10.1021/acs.jnatprod.0c01370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Malaria remains a worldwide threat, afflicting over 200 million people each year. The emergence of drug resistance against existing therapeutics threatens to destabilize global efforts aimed at controlling Plasmodium spp. parasites, which is expected to leave vast portions of humanity unprotected against the disease. To address this need, systematic testing of a fungal natural product extract library assembled through the University of Oklahoma Citizen Science Soil Collection Program has generated an initial set of bioactive extracts that exhibit potent antiplasmodial activity (EC50 < 0.30 μg/mL) and low levels of toxicity against human cells (less than 50% reduction in HepG2 growth at 25 μg/mL). Analysis of the two top-performing extracts from Trichoderma sp. and Hypocrea sp. isolates revealed both contained chemically diverse assemblages of putative peptaibol-like compounds that were responsible for their antiplasmodial actions. Purification and structure determination efforts yielded 30 new peptaibols and lipopeptaibols (1-14 and 28-43), along with 22 known metabolites (15-27 and 44-52). While several compounds displayed promising activity profiles, one of the new metabolites, harzianin NPDG I (14), stood out from the others due to its noteworthy potency (EC50 = 0.10 μM against multi-drug-resistant P. falciparum line Dd2) and absence of gross toxicity toward HepG2 at the highest concentrations tested (HepG2 EC50 > 25 μM, selectivity index > 250). The unique chemodiversity afforded by these fungal isolates serves to unlock new opportunities for translating peptaibols into a bioactive scaffold worthy of further development.
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Affiliation(s)
| | | | - Karen L. Wendt
- Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Debopam Chakrabarti
- Corresponding Authors: Robert H. Cichewicz – Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States; ; Debopam Chakrabarti – Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States;
| | - Robert H. Cichewicz
- Corresponding Authors: Robert H. Cichewicz – Natural Products Discovery Group, Institute for Natural Products Applications and Research Technologies, Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, Norman, Oklahoma 73019, United States; ; Debopam Chakrabarti – Division of Molecular Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States;
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19
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Pedron CN, Silva AF, Torres MDT, Oliveira CSD, Andrade GP, Cerchiaro G, Pinhal MAS, de la Fuente-Nunez C, Oliveira Junior VX. Net charge tuning modulates the antiplasmodial and anticancer properties of peptides derived from scorpion venom. J Pept Sci 2021; 27:e3296. [PMID: 33442881 DOI: 10.1002/psc.3296] [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: 10/03/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 11/06/2022]
Abstract
VmCT1, a linear helical antimicrobial peptide isolated from the venom of the scorpion Vaejovis mexicanus, displays broad spectrum antimicrobial activity against bacteria, fungi, and protozoa. Analogs derived from this peptide containing single Arg-substitutions have been shown to increase antimicrobial and antiparasitic activities against Trypanossoma cruzi. Here, we tested these analogs against malaria, an infectious disease caused by Plasmodium protozoa, and assessed their antitumoral properties. Specifically, we tested VmCT1 synthetic variants [Arg]3 -VmCT1-NH2 , [Arg]7 -VmCT1-NH2 , and [Arg]11 -VmCT1-NH2 , against Plasmodium gallinaceum sporozoites and MCF-7 mammary cancer cells. Our screen identified peptides [Arg]3 -VmCT1-NH2 and [Arg]7 -VmCT1-NH2 as potent antiplasmodial agents (IC50 of 0.57 and 0.51 μmol L-1 , respectively), whereas [Arg]11 -VmCT1-NH2 did not show activity against P. gallinaceum sporozoites. Interestingly, all peptides presented activity against MCF-7 and displayed lower cytotoxicity toward healthy cells. We demonstrate that increasing the net positive charge of VmCT1, through arginine substitutions, modulates the biological properties of this peptide family yielding novel antiplasmodial and antitumoral molecules.
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Affiliation(s)
- Cibele Nicolaski Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.,Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Adriana Farias Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.,Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Marcelo Der Torossian 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, PA, 19102, USA.,Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19102, USA.,Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, 19102, USA
| | | | - Gislaine Patricia Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | - Giselle Cerchiaro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | | | - 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, PA, 19102, USA.,Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19102, USA.,Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, 19102, USA
| | - Vani Xavier Oliveira Junior
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.,Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
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20
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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: 16] [Impact Index Per Article: 4.0] [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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Machine learning-guided discovery and design of non-hemolytic peptides. Sci Rep 2020; 10:16581. [PMID: 33024236 PMCID: PMC7538962 DOI: 10.1038/s41598-020-73644-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/18/2020] [Indexed: 12/13/2022] Open
Abstract
Reducing hurdles to clinical trials without compromising the therapeutic promises of peptide candidates becomes an essential step in peptide-based drug design. Machine-learning models are cost-effective and time-saving strategies used to predict biological activities from primary sequences. Their limitations lie in the diversity of peptide sequences and biological information within these models. Additional outlier detection methods are needed to set the boundaries for reliable predictions; the applicability domain. Antimicrobial peptides (AMPs) constitute an extensive library of peptides offering promising avenues against antibiotic-resistant infections. Most AMPs present in clinical trials are administrated topically due to their hemolytic toxicity. Here we developed machine learning models and outlier detection methods that ensure robust predictions for the discovery of AMPs and the design of novel peptides with reduced hemolytic activity. Our best models, gradient boosting classifiers, predicted the hemolytic nature from any peptide sequence with 95–97% accuracy. Nearly 70% of AMPs were predicted as hemolytic peptides. Applying multivariate outlier detection models, we found that 273 AMPs (~ 9%) could not be predicted reliably. Our combined approach led to the discovery of 34 high-confidence non-hemolytic natural AMPs, the de novo design of 507 non-hemolytic peptides, and the guidelines for non-hemolytic peptide design.
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Arg-substituted VmCT1 analogs reveals promising candidate for the development of new antichagasic agent. Parasitology 2020; 147:1810-1818. [PMID: 33004083 DOI: 10.1017/s0031182020001882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
VmCT1 is an antimicrobial peptide (AMP) isolated from the venom of the scorpion Vaejovis mexicanus with antimicrobial, anticancer and antimalarial activities, which the rational design with Arg-substitution has yielded AMPs with higher antimicrobial activity than VmCT1. Chagas is a neglected tropical disease, becoming the development of new antichagasic agents is urgent. Thus, we aimed to evaluate the antichagasic effect of VmCT1 and three Arg-substituted analogues, as well their action mechanism. Peptides were tested against the epimastigote, trypomastigote, amastigote forms of Trypanossoma cruzi Y strain and against LLC-MK2 mammalian cells. The mechanism of action of these peptides was evaluated by means of flow cytometry and scanning electron microscopy. VmCT1 presented activity against all three forms of T. cruzi, with EC50 against trypomastigote forms of 1.37 μmol L-1 and selectivity index (SI) of 58. [Arg]3-VmCT1, [Arg]7-VmCT1 and [Arg]11-VmCT1 also showed trypanocidal effect, but [Arg]11-VmCT1 had the best effect, being able to decrease the EC50 against trypomastigote forms to 0.8 μmol L-1 and increase SI to 175. Necrosis was cell death pathway of VmCT1, as well [Arg]7-VmCT1 and [Arg]11-VmCT1, such as observed by membrane damage in flow cytometry analyses and scanning-electron-microscopy. In conclusion, [Arg]11-VmCT1 revealed promising as a candidate for new antichagasic therapeutics.
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Yang Y, Wang C, Gao N, Lyu Y, Zhang L, Zhang S, Wang J, Shan A. A Novel Dual-Targeted α-Helical Peptide With Potent Antifungal Activity Against Fluconazole-Resistant Candida albicans Clinical Isolates. Front Microbiol 2020; 11:548620. [PMID: 33101226 PMCID: PMC7554340 DOI: 10.3389/fmicb.2020.548620] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/07/2020] [Indexed: 12/30/2022] Open
Abstract
Due to compromised immune system, fungal infection incidences have markedly increased in the last few decades. Pathogenic fungi have developed resistance to the clinically available antifungal agents. Antifungal resistance poses a great challenge to clinical treatment and has stimulated the demand for novel antifungal agents. A promising alternative to the treatment of fungal diseases is the use of antimicrobial peptides (AMPs). However, the antifungal activities of AMPs have not been fully determined. Therefore, this study aimed at designing and screening α-helical peptides with potential antifungal activities. The effects of key physicochemical parameters on antifungal activities were also investigated. A series of lengthened and residue-substituted derivatives of the template peptide KV, a hexapeptide truncated from the α-helical region of porcine myeloid antimicrobial peptide-36, were designed and synthesized. Enhancement of hydrophobicity by introducing aromatic hydrophobic amino acids (tryptophan and phenylalanine) significantly increased the efficacies of the peptides against Candida albicans strains, including fluconazole-resistant isolates. Increased hydrophobicity also elevated the toxic properties of these peptides. RF3 with moderate hydrophobicity exhibited potent anticandidal activities (GM = 6.96 μM) and modest hemolytic activities (HC10 > 64 μM). Additionally, repeated exposure to a subinhibitory concentration of RF3 did not induce resistance development. The antifungal mechanisms of RF3 were due to membrane disruptions and induction of reactive oxygen species production. Such a dual-targeted mechanism was active against drug-resistant fungi. These results show the important role of hydrophobicity and provide new insights into designing and developing antifungal peptides. Meanwhile, the successful design of RF3 highlights the potential utility of AMPs in preventing the spread of drug-resistant fungal infections.
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Affiliation(s)
- Yang Yang
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Chenxi Wang
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Nan Gao
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Yinfeng Lyu
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Licong Zhang
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Sujiang Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, College of Animal Science, Tarim University, Alar, China
| | - Jiajun Wang
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity, Institute of Animal Nutrition, Northeast Agricultural University, Harbin, China
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Pietsch F, O'Neill AJ, Ivask A, Jenssen H, Inkinen J, Kahru A, Ahonen M, Schreiber F. Selection of resistance by antimicrobial coatings in the healthcare setting. J Hosp Infect 2020; 106:115-125. [PMID: 32535196 DOI: 10.1016/j.jhin.2020.06.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022]
Abstract
Antimicrobial touch surfaces have been introduced in healthcare settings with the aim of supporting existing hygiene procedures, and to help combat the increasing threat of antimicrobial resistance. However, concerns have been raised over the potential selection pressure exerted by such surfaces, which may drive the evolution and spread of antimicrobial resistance. This review highlights studies that indicate risks associated with resistance on antimicrobial surfaces by different processes, including evolution by de-novo mutation and horizontal gene transfer, and species sorting of inherently resistant bacteria dispersed on to antimicrobial surfaces. The review focuses on antimicrobial surfaces made of copper, silver and antimicrobial peptides because of the practical application of copper and silver, and the promising characteristics of antimicrobial peptides. The available data point to a potential for resistance selection and a subsequent increase in resistant strains via cross-resistance and co-resistance conferred by metal and antibiotic resistance traits. However, translational studies describing the development of resistance to antimicrobial touch surfaces in healthcare-related environments are rare, and will be needed to assess whether and how antimicrobial surfaces lead to resistance selection in these settings. Such studies will need to consider numerous variables, including the antimicrobial concentrations present in coatings, the occurrence of biofilms on surfaces, and the humidity relevant to dry-surface environments. On-site tests on the efficacy of antimicrobial coatings should routinely evaluate the risk of selection associated with their use.
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Affiliation(s)
- F Pietsch
- Federal Institute for Materials Research and Testing, Department of Materials and Environment, Division of Biodeterioration and Reference Organisms, Berlin, Germany
| | - A J O'Neill
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - A Ivask
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - H Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - J Inkinen
- Finnish Institute for Health and Welfare, Department of Health Security, Helsinki, Finland
| | - A Kahru
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - M Ahonen
- Satakunta University of Applied Sciences, Faculty of Technology, WANDER Nordic Water and Materials Institute, Rauma, Finland.
| | - F Schreiber
- Federal Institute for Materials Research and Testing, Department of Materials and Environment, Division of Biodeterioration and Reference Organisms, Berlin, Germany.
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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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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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Bo J, Yang Y, Zheng R, Fang C, Jiang Y, Liu J, Chen M, Hong F, Bailey C, Segner H, Wang K. Antimicrobial activity and mechanisms of multiple antimicrobial peptides isolated from rockfish Sebastiscus marmoratus. FISH & SHELLFISH IMMUNOLOGY 2019; 93:1007-1017. [PMID: 31449978 DOI: 10.1016/j.fsi.2019.08.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/16/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Pathogenic disease is a major factor affecting the aquaculture of the rockfish Sebastiscus marmoratus, an important commercial species inhabiting the nearshore waters of the Western Pacific Ocean. Antimicrobial peptides (AMPs), as critical components of innate immunity, have been considered as promising antibiotic substitutes. The aims of this study were 1) to identify major AMPs in the rockfish, 2) to assess their antimicrobial activity and 3) to evaluate their potential therapeutic application. Six AMPs were identified, Hepcidin 1, liver-expressed antimicrobial peptide 2 (LEAP-2), Piscidin, Moronecidin, NK-lysin and β-defensin through analysis of the liver transcriptome of S. marmoratus. The transcriptional expression profiles of these AMPs were investigated by real-time quantitative PCR (RT-qPCR). These AMPs showed tissue-specific distribution patterns, and S. marmoratus displays a time-, dose- and tissue-dependent expression of AMPs in response to lipopolysaccharide (LPS) challenge. While the synthetic peptides of LEAP-2 and Moronecidin exerted broad-spectrum antimicrobial activity against important aquatic pathogens in vitro by directly disrupting microbial membrane, and no cytotoxicity against murine hepatic cells was observed at the effective concentrations from 5 μM to 40 μM. The existence of multiple AMPs and their distinct tissue distribution patterns and inducible expression patterns suggests a sophisticated, highly redundant, and multilevel network of antimicrobial defensive mechanisms of S. marmoratus. Therefore, S. marmoratus-derived AMPs appear to be potential therapeutic applications against pathogen infections in aquaculture.
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Affiliation(s)
- Jun Bo
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Ying Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China
| | - Ronghui Zheng
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Chao Fang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Yulu Jiang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Jie Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China
| | - Mengyun Chen
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Fukun Hong
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Christyn Bailey
- Fish Immunology and Pathology Laboratory, Animal Health Research Center (CISA-INIA), Madrid, Spain
| | - Helmut Segner
- Centre for Fish and Wildlife Health, Department of Infectious Diseases and Pathobiology, University of Bern, Bern, Switzerland
| | - Kejian Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean & Earth Science, Xiamen University, Xiamen, China.
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Sabiá Júnior EF, Menezes LFS, de Araújo IFS, Schwartz EF. Natural Occurrence in Venomous Arthropods of Antimicrobial Peptides Active against Protozoan Parasites. Toxins (Basel) 2019; 11:E563. [PMID: 31557900 PMCID: PMC6832604 DOI: 10.3390/toxins11100563] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 08/31/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Arthropoda is a phylum of invertebrates that has undergone remarkable evolutionary radiation, with a wide range of venomous animals. Arthropod venom is a complex mixture of molecules and a source of new compounds, including antimicrobial peptides (AMPs). Most AMPs affect membrane integrity and produce lethal pores in microorganisms, including protozoan pathogens, whereas others act on internal targets or by modulation of the host immune system. Protozoan parasites cause some serious life-threatening diseases among millions of people worldwide, mostly affecting the poorest in developing tropical regions. Humans can be infected with protozoan parasites belonging to the genera Trypanosoma, Leishmania, Plasmodium, and Toxoplasma, responsible for Chagas disease, human African trypanosomiasis, leishmaniasis, malaria, and toxoplasmosis. There is not yet any cure or vaccine for these illnesses, and the current antiprotozoal chemotherapeutic compounds are inefficient and toxic and have been in clinical use for decades, which increases drug resistance. In this review, we will present an overview of AMPs, the diverse modes of action of AMPs on protozoan targets, and the prospection of novel AMPs isolated from venomous arthropods with the potential to become novel clinical agents to treat protozoan-borne diseases.
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Affiliation(s)
- Elias Ferreira Sabiá Júnior
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
| | - Luis Felipe Santos Menezes
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
| | - Israel Flor Silva de Araújo
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
| | - Elisabeth Ferroni Schwartz
- Departamento de Ciências Fisiológicas, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
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Qi J, Gao R, Liu C, Shan B, Gao F, He J, Yuan M, Xie H, Jin S, Ma Y. Potential role of the antimicrobial peptide Tachyplesin III against multidrug-resistant P. aeruginosa and A. baumannii coinfection in an animal model. Infect Drug Resist 2019; 12:2865-2874. [PMID: 31576151 PMCID: PMC6765326 DOI: 10.2147/idr.s217020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/24/2019] [Indexed: 01/05/2023] Open
Abstract
Background Tachyplesin III, an antimicrobial peptide (AMP), provides protection against multidrug-resistant (MDR) bacterial infections and shows cytotoxicity to mammalian cells. Mixed bacterial infections, of which P. aeruginosa plus A. baumannii is the most common and dangerous combination, are critical contributors to the morbidity and mortality of long-term in-hospital respiratory medicine patients. Therefore, the development of effective therapeutic approaches to mixed bacterial infections is urgently needed. Methods and results In this study, we demonstrated that compared with individual infections, mixed infections with MDR bacteria P. aeruginosa and A. baumannii cause more serious diseases, with increased pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and chemokines (MCP-1/MIP-2) and reduced mouse survival. In vitro treatment with Tachyplesin III enhanced phagocytosis in a mouse alveolar macrophage cell line (MH-S). Strikingly, in vivo, Tachyplesin III demonstrated a potential role against mixed-MDR bacterial coinfection. The bacterial burden in bronchoalveolar lavage fluid (BALF) was significantly reduced in the Tachyplesin III-treated group. In addition, a systemic reduction in pro-inflammatory cytokines and decreased lung injury occurred with Tachyplesin III therapy. Conclusion Therefore, our study demonstrated that Tachyplesin III represents a potential therapeutic treatment against mixed-MDR bacterial infection in vivo, which sheds light on the development of therapeutic strategies against mixed-MDR bacterial infections.
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Affiliation(s)
- Jialong Qi
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
| | - Ruiyu Gao
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
| | - Cunbao Liu
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
| | - Bin Shan
- Department of Clinical Lab, The First Affiliated Hospital of Kunming Medical University, Kunming, People's Republic of China
| | - Fulan Gao
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
| | - Jinrong He
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
| | - Mingcui Yuan
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
| | - Hanghang Xie
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
| | - Shumei Jin
- Yunnan Institute of Materia Medica, Kunming, People's Republic of China
| | - Yanbing Ma
- Department of Molecular Immunology, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China
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30
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The effect of lysine substitutions in the biological activities of the scorpion venom peptide VmCT1. Eur J Pharm Sci 2019; 136:104952. [DOI: 10.1016/j.ejps.2019.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 12/14/2022]
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31
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Mohamed WA, Abd-Elhakim YM, Ismail SAA. Involvement of the anti-inflammatory, anti-apoptotic, and anti-secretory activity of bee venom in its therapeutic effects on acetylsalicylic acid-induced gastric ulceration in rats. Toxicology 2019; 419:11-23. [PMID: 30885738 DOI: 10.1016/j.tox.2019.03.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/21/2019] [Accepted: 03/12/2019] [Indexed: 12/11/2022]
Abstract
Acetylsalicylic acid (ASA) is the most highly consumed pharmaceutical product worldwide. Importantly, gastrointestinal ulceration due to ASA is a major complication. Hence, the present work aimed to examine, for the first time, the healing properties of bee venom (BV) in acute gastric ulceration induced by ASA. Forty adult male Sprague-Dawley rats were divided into four groups that received distilled water only, ASA (500 mg/kg BW) twice daily for 3 days, ASA for 3 days followed by BV (2 mg/kg BW) for 7 days, or ASA for 3 days followed by ranitidine hydrochloride (50 mg/kg BW) for 7 days. Haematological analysis, haemostatic evaluation, and inflammatory marker estimation were performed. Rat stomachs were collected for ulcer scoring, gene expression analysis, oxidative stress assays, histopathological and immunohistochemical examinations, and tissue eosinophil scoring. The results revealed that BV markedly decreased the ulcer index, pro-inflammatory cytokine levels, malondialdehyde levels, BAX distribution, caspase-3 expression, and tissue eosinophil levels. Additionally, significant increases in antioxidant enzymes and heat shock protein 70 localization in gastric tissue were evident following BV treatment after ASA exposure. Also, BV has been found to attenuate the haematological, haemostatic, and histopathological alterations induced by ASA. Our findings collectively indicate that the gastroprotective effect of BV against ASA-induced ulceration in rats is mediated by its antioxidant, anti-inflammatory, anti-apoptotic, and anti-secretory properties.
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Affiliation(s)
- Wafaa A Mohamed
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Yasmina M Abd-Elhakim
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt.
| | - Shimaa A A Ismail
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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32
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Antimicrobial peptides with antiprotozoal activity: current state and future perspectives. Future Med Chem 2018; 10:2569-2572. [PMID: 30499691 DOI: 10.4155/fmc-2018-0460] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Moravej H, Moravej Z, Yazdanparast M, Heiat M, Mirhosseini A, Moosazadeh Moghaddam M, Mirnejad R. Antimicrobial Peptides: Features, Action, and Their Resistance Mechanisms in Bacteria. Microb Drug Resist 2018; 24:747-767. [PMID: 29957118 DOI: 10.1089/mdr.2017.0392] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In recent years, because of increased resistance to conventional antimicrobials, many researchers have started to study the synthesis of new antibiotics to control the disease-causing effects of infectious pathogens. Antimicrobial peptides (AMPs) are among the newest antibiotics; these peptides are integral compounds in all kinds of organisms and play a significant role in microbial ecology, and critically contribute to the innate immunity of organisms by destroying invading microorganisms. Moreover, AMPs may encourage cells to produce chemokines, stimulate angiogenesis, accelerate wound healing, and influence programmed cell death in multicellular organisms. Bacteria differ in their inherent susceptibility and resistance mechanisms to these peptides when responding to the antimicrobial effects of AMPs. Generally, the development of AMP resistance mechanisms is driven by direct competition between bacterial species, and host and pathogen interactions. Several studies have shown diverse mechanisms of bacterial resistance to AMPs, for example, some bacteria produce proteases and trapping proteins; some modify cell surface charge, change membrane fluidity, and activate efflux pumps; and some species make use of biofilms and exopolymers, and develop sensing systems by selective gene expression. A closer understanding of bacterial resistance mechanisms may help in developing novel therapeutic approaches for the treatment of infections caused by pathogenic organisms that are successful in developing extensive resistance to AMPs. Based on these observations, this review discusses the properties of AMPs, their targeting mechanisms, and bacterial resistance mechanisms against AMPs.
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Affiliation(s)
- Hoda Moravej
- 1 Molecular Biology Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences , Tehran, Iran
| | - Zahra Moravej
- 2 Department of Hepatitis and AIDS, Pasteur Institute of Iran , Tehran, Iran
| | - Maryam Yazdanparast
- 3 Department of Pharmacology, Experimental Medicine Research Center, School of Medicine, Tehran University of Medical Sciences , Tehran, Iran
| | - Mohammad Heiat
- 4 Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences , Tehran, Iran
| | - Ali Mirhosseini
- 5 Applied Microbiology Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences , Tehran, Iran
| | | | - Reza Mirnejad
- 1 Molecular Biology Research Center, Systems Biology and Poisoning Institute, Baqiyatallah University of Medical Sciences , Tehran, Iran
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Allane D, Oussedik-Oumehdi H, Harrat Z, Seve M, Laraba-Djebari F. Isolation and characterization of an anti-leishmanial disintegrin fromCerastes cerastesvenom. J Biochem Mol Toxicol 2017; 32. [DOI: 10.1002/jbt.22018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Dihia Allane
- USTHB, Faculty of Biological Sciences; Laboratory of Cellular and Molecular Biology; Bab Ezzouar Algiers 16111 Algeria
| | - Habiba Oussedik-Oumehdi
- USTHB, Faculty of Biological Sciences; Laboratory of Cellular and Molecular Biology; Bab Ezzouar Algiers 16111 Algeria
| | - Zoubir Harrat
- Institut Pasteur d'Algérie; Service d'Eco-Epidémiologie Parasitaire; Dely Ibrahim Algiers 16 047 Algeria
| | - Michel Seve
- CHU Grenoble Alpes, Institut de Biologie et de Pathologie; Promethee Proteomic Platform; Grenoble France
| | - Fatima Laraba-Djebari
- USTHB, Faculty of Biological Sciences; Laboratory of Cellular and Molecular Biology; Bab Ezzouar Algiers 16111 Algeria
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Sierra JM, Fusté E, Rabanal F, Vinuesa T, Viñas M. An overview of antimicrobial peptides and the latest advances in their development. Expert Opin Biol Ther 2017; 17:663-676. [PMID: 28368216 DOI: 10.1080/14712598.2017.1315402] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The recent dramatic increase in the incidence of antimicrobial resistance has been recognized by organizations such as the United Nations and World Health Organization as well as the governments of the USA and several European countries. A relatively new weapon in the fight against severe infections caused by multi-drug resistant bacteria is antimicrobial peptides (AMPs). These include colistin, currently regarded as the last line of antimicrobial therapy against multi-drug resistant microorganisms. Areas covered: Here, the authors provide an overview of the current research on AMPs. The focus is AMPs currently being developed for the treatment of recalcitrant bacterial infections, the synergies of AMPs and antibiotics, and the activity of AMPs against biofilm. This review also includes a brief introduction into the use of AMPs in infections caused by Mycobacterium, fungi, and parasites. Expert opinion: In research into new antimicrobials, AMPs are gaining increasing attention. While many are natural and are produced by a wide variety of organisms, others are being newly designed and chemically synthesized in the laboratory to achieve novel antimicrobial agents. The same strategy to fight infections in nature is thus being effectively exploited to safeguard human and animal health.
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Affiliation(s)
- Josep M Sierra
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain
| | - Ester Fusté
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain.,b Dept. Public Health, Mental Health and Perinatal Nursing. School of nursing , University of Barcelona , Barcelona , Spain
| | - Francesc Rabanal
- c Department of Organic Chemistry, Faculty of Chemistry , University of Barcelona , Barcelona , Spain
| | - Teresa Vinuesa
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain
| | - Miguel Viñas
- a Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, School of Medicine , University of Barcelona , Barcelona , Spain.,d Departament of Biomedicine , Cooperativa de Ensino Superior Politécnico e Universitário, IINFACTS , Gandra , Portugal
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Lenz SAP, Kohout JD, Wetmore SD. Hydrolytic Glycosidic Bond Cleavage in RNA Nucleosides: Effects of the 2'-Hydroxy Group and Acid-Base Catalysis. J Phys Chem B 2016; 120:12795-12806. [PMID: 27933981 DOI: 10.1021/acs.jpcb.6b09620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Despite the inherent stability of glycosidic linkages in nucleic acids that connect the nucleobases to sugar-phosphate backbones, cleavage of these bonds is often essential for organism survival. The current study uses DFT (B3LYP) to provide a fundamental understanding of the hydrolytic deglycosylation of the natural RNA nucleosides (A, C, G, and U), offers a comparison to DNA hydrolysis, and examines the effects of acid, base, or simultaneous acid-base catalysis on RNA deglycosylation. By initially examining HCOO-···H2O mediated deglycosylation, the barriers for RNA hydrolysis were determined to be 30-38 kJ mol-1 higher than the corresponding DNA barriers, indicating that the 2'-OH group stabilizes the glycosidic bond. Although the presence of HCOO- as the base (i.e., to activate the water nucleophile) reduces the barrier for uncatalyzed RNA hydrolysis (i.e., unactivated H2O nucleophile) by ∼15-20 kJ mol-1, the extreme of base catalysis as modeled using a fully deprotonated water molecule (i.e., OH- nucleophile) decreases the uncatalyzed barriers by up to 65 kJ mol-1. Acid catalysis was subsequently examined by selectively protonating the hydrogen-bond acceptor sites of the RNA nucleobases, which results in an up to ∼80 kJ mol-1 barrier reduction relative to the corresponding uncatalyzed pathway. Interestingly, the nucleobase proton acceptor sites that result in the greatest barrier reductions match sites typically targeted in enzyme-catalyzed reactions. Nevertheless, simultaneous acid and base catalysis is the most beneficial way to enhance the reactivity of the glycosidic bonds in RNA, with the individual effects of each catalytic approach being weakened, additive, or synergistic depending on the strength of the base (i.e., degree of water nucleophile activation), the nucleobase, and the hydrogen-bonding acceptor site on the nucleobase. Together, the current contribution provides a greater understanding of the reactivity of the glycosidic bond in natural RNA nucleosides, and has fundamental implications for the function of RNA-targeting enzymes.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Johnathan D Kohout
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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