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Swangsri T, Reamtong O, Saralamba S, Rakthong P, Thaenkham U, Saralamba N. Exploring the antimicrobial potential of crude peptide extracts from Allium sativum and Allium oschaninii against antibiotic-resistant bacterial strains. PHARMACEUTICAL BIOLOGY 2024; 62:666-675. [PMID: 39205473 PMCID: PMC11363733 DOI: 10.1080/13880209.2024.2395517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 07/04/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
CONTEXT Plant peptides garner attention for their potential antimicrobial properties amid the rising concern over antibiotic-resistant bacteria. OBJECTIVE This study investigates the antibacterial potential of crude peptide extracts from 27 Thai plants collected locally. MATERIALS AND METHODS Peptide extracts from 34 plant parts, derived from 27 Thai plants, were tested for their antimicrobial efficacy against four highly resistant bacterial strains: Streptococcus aureus MRSA, Pseudomonas aeruginosa, Acinetobacter baumannii, and Escherichia coli. The stability of these peptide extracts was examined at different temperatures, and the synergistic effects of two selected plant peptide extracts were investigated. Additionally, the time-kill kinetics of the individual extracts and their combination were determined against the tested pathogens. RESULTS Peptides from Allium sativum L. and Allium oschaninii O. Fedtsch (Amaryllidaceae) were particularly potent, inhibiting bacterial growth with MICs ranging from 1.43 to 86.50 µg/mL. The consistent MICs and MBCs of these extracts across various extraction time points highlight their reliability. Stability tests reveal that these peptides maintain their antimicrobial activity at -20 °C for over a month, emphasizing their durability for future exploration and potential applications in addressing antibiotic resistance. Time-kill assays elucidate the time and concentration-dependent nature of these antimicrobial effects, underscoring their potent initial activity and sustained efficacy over time. DISCUSSION AND CONCLUSIONS This study highlights the antimicrobial potential of Allium-derived peptides, endorsing them for combating antibiotic resistance and prompting further investigation into their mechanisms.
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Affiliation(s)
- Thitiluck Swangsri
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sompob Saralamba
- Mathematical and Economic Modelling (MAEMOD), Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pakavadee Rakthong
- Faculty of Science and Technology, Rajabhat Suratthani University, Surat Thani, Thailand
| | - Urusa Thaenkham
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Naowarat Saralamba
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Ghanbarzadeh Z, Mohagheghzadeh A, Hemmati S. The Roadmap of Plant Antimicrobial Peptides Under Environmental Stress: From Farm to Bedside. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10354-9. [PMID: 39225894 DOI: 10.1007/s12602-024-10354-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Antimicrobial peptides (AMPs) are the most favorable alternatives in overcoming multidrug resistance, alone or synergistically with conventional antibiotics. Plant-derived AMPs, as cysteine-rich peptides, widely compensate the pharmacokinetic drawbacks of peptide therapeutics. Compared to the putative genes encrypted in the genome, AMPs that are produced under stress are active forms with the ability to combat resistant microbial species. Within this study, plant-derived AMPs, namely, defensins, nodule-specific cysteine-rich peptides, snakins, lipid transfer proteins, hevein-like proteins, α-hairpinins, and aracins, expressed under biotic and abiotic stresses, are classified. We could observe that while α-hairpinins and snakins display a helix-turn-helix structure, conserved motif patterns such as β1αβ2β3 and β1β2β3 exist in plant defensins and hevein-like proteins, respectively. According to the co-expression data, several plant AMPs are expressed together to trigger synergistic effects with membrane disruption mechanisms such as toroidal pore, barrel-stave, and carpet models. The application of AMPs as an eco-friendly strategy in maintaining agricultural productivity through the development of transgenes and bio-pesticides is discussed. These AMPs can be consumed in packaging material, wound-dressing products, coating catheters, implants, and allergology. AMPs with cell-penetrating properties are verified for the clearance of intracellular pathogens. Finally, the dominant pharmacological activities of bioactive peptides derived from the gastrointestinal digestion of plant AMPs, namely, inhibitors of renin and angiotensin-converting enzymes, dipeptidyl peptidase IV and α-glucosidase inhibitors, antioxidants, anti-inflammatory, immunomodulating, and hypolipidemic peptides, are analyzed. Conclusively, as phytopathogens and human pathogens can be affected by plant-derived AMPs, they provide a bright perspective in agriculture, breeding, food, cosmetics, and pharmaceutical industries, translated as farm to bedside.
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Affiliation(s)
- Zohreh Ghanbarzadeh
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolali Mohagheghzadeh
- Department of Phytopharmaceuticals, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, 56000, Kuala Lumpur, Malaysia.
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Uncu AT, Patat AS, Uncu AO. Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species. Funct Integr Genomics 2024; 24:142. [PMID: 39187716 DOI: 10.1007/s10142-024-01423-x] [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: 07/04/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
Parsley is a commonly cultivated Apiaceae species of culinary and medicinal importance. Parsley has several recognized health benefits and the species has been utilized in traditional medicine since ancient times. Although parsley is among the most commonly cultivated members of Apiaceae, no systematic genomic research has been conducted on parsley. In the present work, parsley genome was sequenced using the long-read HiFi (high fidelity) sequencing technology and a draft contig assembly of 1.57 Gb that represents 80.9% of the estimated genome size was produced. The assembly was highly repeat-rich with a repetitive DNA content of 81%. The assembly was phased into a primary and alternate assembly in order to minimize redundant contigs. Scaffolds were constructed with the primary assembly contigs, which were used for the identification of AMP (antimicrobial peptide) genes. Characteristic AMP domains and 3D structures were used to detect and verify antimicrobial peptides. As a result, 23 genes (PcAMP1-23) representing defensin, snakin, thionin, lipid transfer protein and vicilin-like AMP classes were identified. Bioinformatic analyses for the characterization of peptide physicochemical properties indicated that parsley AMPs are extracellular peptides, therefore, plausibly exert their antimicrobial effects through the most commonly described AMP action mechanism of membrane attack. AMPs are attracting increasing attention since they display their fast antimicrobial effects in small doses on both plant and animal pathogens with a significantly reduced risk of resistance development. Therefore, identification and characterization of AMPs is important for their incorporation into plant disease management protocols as well as medicinal research for the treatment of multi-drug resistant infections.
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Affiliation(s)
- Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey
| | - Aysenur Soyturk Patat
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey
| | - Ayse Ozgur Uncu
- Department of Biotechnology, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey.
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Angelini P. Plant-Derived Antimicrobials and Their Crucial Role in Combating Antimicrobial Resistance. Antibiotics (Basel) 2024; 13:746. [PMID: 39200046 PMCID: PMC11350763 DOI: 10.3390/antibiotics13080746] [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: 06/22/2024] [Revised: 07/27/2024] [Accepted: 07/31/2024] [Indexed: 09/01/2024] Open
Abstract
Antibiotic resistance emerged shortly after the discovery of the first antibiotic and has remained a critical public health issue ever since. Managing antibiotic resistance in clinical settings continues to be challenging, particularly with the rise of superbugs, or bacteria resistant to multiple antibiotics, known as multidrug-resistant (MDR) bacteria. This rapid development of resistance has compelled researchers to continuously seek new antimicrobial agents to curb resistance, despite a shrinking pipeline of new drugs. Recently, the focus of antimicrobial discovery has shifted to plants, fungi, lichens, endophytes, and various marine sources, such as seaweeds, corals, and other microorganisms, due to their promising properties. For this review, an extensive search was conducted across multiple scientific databases, including PubMed, Elsevier, ResearchGate, Scopus, and Google Scholar, encompassing publications from 1929 to 2024. This review provides a concise overview of the mechanisms employed by bacteria to develop antibiotic resistance, followed by an in-depth exploration of plant secondary metabolites as a potential solution to MDR pathogens. In recent years, the interest in plant-based medicines has surged, driven by their advantageous properties. However, additional research is essential to fully understand the mechanisms of action and verify the safety of antimicrobial phytochemicals. Future prospects for enhancing the use of plant secondary metabolites in combating antibiotic-resistant pathogens will also be discussed.
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Affiliation(s)
- Paola Angelini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06122 Perugia, Italy
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Jaiswal M, Kumar S. smAMPsTK: a toolkit to unravel the smORFome encoding AMPs of plant species. J Biomol Struct Dyn 2024; 42:6600-6612. [PMID: 37464885 DOI: 10.1080/07391102.2023.2235605] [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] [Received: 04/07/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
The pervasive repertoire of plant molecules with the potential to serve as a substitute for conventional antibiotics has led to obtaining better insights into plant-derived antimicrobial peptides (AMPs). The massive distribution of Small Open Reading Frames (smORFs) throughout eukaryotic genomes with proven extensive biological functions reflects their practicality as antimicrobials. Here, we have developed a pipeline named smAMPsTK to unveil the underlying hidden smORFs encoding AMPs for plant species. By applying this pipeline, we have elicited AMPs of various functional activity of lengths ranging from 5 to 100 aa by employing publicly available transcriptome data of five different angiosperms. Later, we studied the coding potential of AMPs-smORFs, the inclusion of diverse translation initiation start codons, and amino acid frequency. Codon usage study signifies no such codon usage biases for smORFs encoding AMPs. Majorly three start codons are prominent in generating AMPs. The evolutionary and conservational study proclaimed the widespread distribution of AMPs encoding genes throughout the plant kingdom. Domain analysis revealed that nearly all AMPs have chitin-binding ability, establishing their role as antifungal agents. The current study includes a developed methodology to characterize smORFs encoding AMPs, and their implications as antimicrobial, antibacterial, antifungal, or antiviral provided by SVM score and prediction status calculated by machine learning-based prediction models. The pipeline, complete package, and the results derived for five angiosperms are freely available at https://github.com/skbinfo/smAMPsTK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohini Jaiswal
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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6
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Cherene MB, Taveira GB, Almeida-Silva F, da Silva MS, Cavaco MC, da Silva-Ferreira AT, Perales JEA, de Oliveira Carvalho A, Venâncio TM, da Motta OV, Rodrigues R, Castanho MARB, Gomes VM. Structural and Biochemical Characterization of Three Antimicrobial Peptides from Capsicum annuum L. var. annuum Leaves for Anti-Candida Use. Probiotics Antimicrob Proteins 2024; 16:1270-1287. [PMID: 37365421 DOI: 10.1007/s12602-023-10112-3] [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] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
The emergence of resistant microorganisms has reduced the effectiveness of currently available antimicrobials, necessitating the development of new strategies. Plant antimicrobial peptides (AMPs) are promising candidates for novel drug development. In this study, we aimed to isolate, characterize, and evaluate the antimicrobial activities of AMPs isolated from Capsicum annuum. The antifungal potential was tested against Candida species. Three AMPs from C. annuum leaves were isolated and characterized: a protease inhibitor, a defensin-like protein, and a lipid transporter protein, respectively named CaCPin-II, CaCDef-like, and CaCLTP2. All three peptides had a molecular mass between 3.5 and 6.5 kDa and caused morphological and physiological changes in four different species of the genus Candida, such as pseudohyphae formation, cell swelling and agglutination, growth inhibition, reduced cell viability, oxidative stress, membrane permeabilization, and metacaspase activation. Except for CaCPin-II, the peptides showed low or no hemolytic activity at the concentrations used in the yeast assays. CaCPin-II inhibited α-amylase activity. Together, these results suggest that these peptides have the potential as antimicrobial agents against species of the genus Candida and can serve as scaffolds for the development of synthetic peptides for this purpose.
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Affiliation(s)
- Milena Bellei Cherene
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Gabriel Bonan Taveira
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Fabricio Almeida-Silva
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Marciele Souza da Silva
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Marco Calvinho Cavaco
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | | | | | - André de Oliveira Carvalho
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Thiago Motta Venâncio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Olney Vieira da Motta
- Laboratório de Sanidade Animal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Rosana Rodrigues
- Laboratório de Melhoramento e Genética Vegetal, Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | | | - Valdirene Moreira Gomes
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, 28013-602, Brazil.
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7
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Osorio J, Rosas RC, Vega MB, Reyes AL, Paolino A, Menéndez F, Vega-Teijido M, Savio E, Giglio J, Cecchetto G, Terán M. Peptide derived from plant defensins: A promising 68Ga radiolabelled agent for diagnostic of infection foci in PET. Chem Biol Drug Des 2024; 104:e14578. [PMID: 39044291 DOI: 10.1111/cbdd.14578] [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: 01/31/2024] [Revised: 06/21/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024]
Abstract
The development of new radiopharmaceuticals for the detection of hidden infection foci has great relevance for early detection and the selection of the correct treatment, particularly in immunosuppressed patients. In that sense, the labelling of antimicrobial peptides (AMPs) that are capable of binding specifically to the pathogenic microorganism which causes the infection, should provide a sufficiently specific agent, able to distinguish an infection from a sterile inflammation. Defensins are particularly interesting molecules with antimicrobial activity, the EcgDf1 defensin was identified from the genome of a Uruguayan native plant, Erythrina crista-galli, the 'Ceibo' tree. Our group has previously reported a synthetic biologically active short analogue EcgDf21 (ERFTGGHCRGFRRRCFCTKHC) successfully labelled with 99mTc. Herein we present a shorter analogue which also preserves the γ-core domain, as a pharmacophore for a potential infection detection agent. This peptide was derivatized with the bifunctional chelating agent 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA) through a lysine linker in the amino-terminal group (NOTA-KGHCRGFRRRC) and radiolabelled with 68Ga ([68Ga]Ga-NOTA-K-EcgDf1(10)). The [68Ga]Ga-NOTA-K-EcgDf1(10) labelling procedure rendered a product with high radiochemical purity and stability in the labelling milieu. The Log P value indicated that the complex has a hydrophilic behaviour, confirmed by the biodistribution profile. The [68Ga]Ga-NOTA-K-EcgDf1(10) complex demonstrated specific binding to cultures of Candida albicans and Aspergillus niger. Its biodistribution showed renal elimination and low accumulation in the rest of the body. It was possible to successfully differentiate sterile inflammation from infection by PET images in nude mice with a target/non-target ratio of 3.3 for C. albicans and 3.7 for A. niger, respectively.
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Affiliation(s)
- Jessica Osorio
- Área de Radioquímica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Roberto Castro Rosas
- Área de Microbiología, Instituto de Química Biológica, Facultad de Ciencias-Departamento de Biociencias, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Mariana Barraco Vega
- Área de Microbiología, Instituto de Química Biológica, Facultad de Ciencias-Departamento de Biociencias, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Ana Laura Reyes
- Departamento de Radiofarmacia, Centro Uruguayo de Imagenología Molecular (CUDIM), Montevideo, Uruguay
| | - Andrea Paolino
- Departamento de Radiofarmacia, Centro Uruguayo de Imagenología Molecular (CUDIM), Montevideo, Uruguay
| | - Florencia Menéndez
- Área de Radioquímica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
- Área de Microbiología, Instituto de Química Biológica, Facultad de Ciencias-Departamento de Biociencias, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
- Departamento de Radiofarmacia, Centro Uruguayo de Imagenología Molecular (CUDIM), Montevideo, Uruguay
- Computacional Chemistry and Biological Group, DETEMA, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Mauricio Vega-Teijido
- Computacional Chemistry and Biological Group, DETEMA, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Eduardo Savio
- Departamento de Radiofarmacia, Centro Uruguayo de Imagenología Molecular (CUDIM), Montevideo, Uruguay
| | - Javier Giglio
- Departamento de Radiofarmacia, Centro Uruguayo de Imagenología Molecular (CUDIM), Montevideo, Uruguay
| | - Gianna Cecchetto
- Área de Microbiología, Instituto de Química Biológica, Facultad de Ciencias-Departamento de Biociencias, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Mariella Terán
- Área de Radioquímica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
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Parisi MG, Ozón B, Vera González SM, García-Pardo J, Obregón WD. Plant Protease Inhibitors as Emerging Antimicrobial Peptide Agents: A Comprehensive Review. Pharmaceutics 2024; 16:582. [PMID: 38794245 PMCID: PMC11125377 DOI: 10.3390/pharmaceutics16050582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Antimicrobial peptides (AMPs) are important mediator molecules of the innate defense mechanisms in a wide range of living organisms, including bacteria, mammals, and plants. Among them, peptide protease inhibitors (PPIs) from plants play a central role in their defense mechanisms by directly attacking pathogens or by modulating the plant's defense response. The growing prevalence of microbial resistance to currently available antibiotics has intensified the interest concerning these molecules as novel antimicrobial agents. In this scenario, PPIs isolated from a variety of plants have shown potential in inhibiting the growth of pathogenic bacteria, protozoans, and fungal strains, either by interfering with essential biochemical or physiological processes or by altering the permeability of biological membranes of invading organisms. Moreover, these molecules are active inhibitors of a range of proteases, including aspartic, serine, and cysteine types, with some showing particular efficacy as trypsin and chymotrypsin inhibitors. In this review, we provide a comprehensive analysis of the potential of plant-derived PPIs as novel antimicrobial molecules, highlighting their broad-spectrum antimicrobial efficacy, specificity, and minimal toxicity. These natural compounds exhibit diverse mechanisms of action and often multifunctionality, positioning them as promising molecular scaffolds for developing new therapeutic antibacterial agents.
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Affiliation(s)
- Mónica G. Parisi
- Instituto de Ecología y Desarrollo Sustentable (INEDES, CONICET-UNLu) and Departamento de Ciencias Básicas, Universidad Nacional de Luján, Ruta 5 y Avenida Constitución, Luján B6700, Buenos Aires, Argentina;
| | - Brenda Ozón
- Centro de Investigación de Proteínas Vegetales (CIProVe) and Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 y 115 s/N, La Plata B1900, Buenos Aires, Argentina; (B.O.); (S.M.V.G.)
| | - Sofía M. Vera González
- Centro de Investigación de Proteínas Vegetales (CIProVe) and Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 y 115 s/N, La Plata B1900, Buenos Aires, Argentina; (B.O.); (S.M.V.G.)
| | - Javier García-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Walter David Obregón
- Centro de Investigación de Proteínas Vegetales (CIProVe) and Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 47 y 115 s/N, La Plata B1900, Buenos Aires, Argentina; (B.O.); (S.M.V.G.)
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Iwaniak A, Minkiewicz P, Darewicz M. Bioinformatics and bioactive peptides from foods: Do they work together? ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 108:35-111. [PMID: 38461003 DOI: 10.1016/bs.afnr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.
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Affiliation(s)
- Anna Iwaniak
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland.
| | - Piotr Minkiewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| | - Małgorzata Darewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
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Velayatipour F, Tarrahimofrad H, Zamani J, Fotouhi F, Aminzadeh S. In-vitro antimicrobial activity of AF-DP protein and in-silico approach of cell membrane disruption. J Biomol Struct Dyn 2024:1-18. [PMID: 38319027 DOI: 10.1080/07391102.2024.2308763] [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: 08/31/2023] [Accepted: 01/14/2024] [Indexed: 02/07/2024]
Abstract
Microbial resistance against common antibiotics has become one of the most serious threats to human health. The increasing statistics on this problem show the necessity of finding a way to deal with it. In recent years, antimicrobial peptides with unique properties and the capability of targeting a wide range of pathogens, have been considered as a potential for replacing common antibiotics. A small chitin-binding protein with anticandidal activity was isolated from Moringa oleifera seeds by Neto and colleagues in 2017, which very much resembled antimicrobial peptides. In this study, the antimicrobial protein 'AF-DP' was identified and characterized. AF-DP was heterologously expressed, purified, and characterized, and its 3D structure was predicted. Six molecular dynamic simulations were performed to investigate how the protein interacts with Gram-negative inner and outer, Gram-positive, fungal, cancerous, and normal mammalian membranes. Also, its antimicrobial and anticancer activity was assessed in vitro via minimum inhibition concentration (MIC) and MTT assays, respectively. This protein with 111 amino acids and a total net charge (of 10.5) has been predicted to be mainly composed of alpha helix and random coils. Its MIC affecting the growth of Escherichia coli, Staphylococcus aureus, and Candida albicans was 30 µg/ml, 100 µg/ml, and 100 µg/ml, respectively; AF-DP showed anticancer activity against MCF-7 breast cancer cell line. Scanning electron microscopic analysis confirmed the creation of pores and scratches on the surface of the bacterial membrane. The results of this research show that AF-DP can be a candidate for the production of new drugs as an AMP with antimicrobial activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatemeh Velayatipour
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Tarrahimofrad
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Javad Zamani
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Fatemeh Fotouhi
- Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Aminzadeh
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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11
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Ludwig-Müller J. Production of Plant Proteins and Peptides with Pharmacological Potential. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 188:51-81. [PMID: 38286902 DOI: 10.1007/10_2023_246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
The use of plant proteins or peptides in biotechnology is based on their identification as possessing bioactive potential in plants. This is usually the case for antimicrobial, fungicidal, or insecticidal components of the plant's defense system. They function in addition to a large number of specialized metabolites. Such proteins can be classified according to their sequence, length, and structure, and this has been tried to describe for a few examples here. Even though such proteins or peptides can be induced during plant-pathogen interaction, they are still present in rather small amounts that make the system not suitable for the production in large-scale systems. Therefore, a suitable type of host needs to be identified, such as cell cultures or adult plants. Bioinformatic predictions can also be used to add to the number of bioactive sequences. Some problems that can occur in production by the plant system itself will be discussed, such as choice of promoter for gene expression, posttranslational protein modifications, protein stability, secretion of proteins, or induction by elicitors. Finally, the plant needs to be set up by biotechnological or molecular methods for production, and the product needs to be enriched or purified. In some cases of small peptides, a direct chemical synthesis might be feasible. Altogether, the process needs to be considered marketable.
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Gasser M, Keller J, Fournier P, Pujic P, Normand P, Boubakri H. Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24. Sci Rep 2023; 13:16020. [PMID: 37749152 PMCID: PMC10520049 DOI: 10.1038/s41598-023-41117-1] [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: 03/16/2023] [Accepted: 08/22/2023] [Indexed: 09/27/2023] Open
Abstract
Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leading to root nodule formation. nsLTPs are involved in processes active in early step of symbiosis and functional nodule in both models. In legumes, nsLTPs have been shown to regulate symbiont entry, promote root cortex infection, membrane biosynthesis, and improve symbiosis efficiency. More recently, a nsLTP, AgLTP24 has been described in the context of actinorhizal symbiosis between Alnus glutinosa and Frankia alni ACN14a. AgLTP24 is secreted at an early step of symbiosis on the deformed root hairs and targets the symbiont in the nitrogen-fixing vesicles in functional nodules. nsLTPs are involved in RNF, but their functions and evolutionary history are still largely unknown. Numerous putative nsLTPs were found up-regulated in functional nodules compared to non-infected roots in different lineages within the RNF clade. Here, results highlight that nodulating plants that are co-evolving with their nitrogen-fixing symbionts appear to have independently specialized nsLTPs for this interaction, suggesting a possible convergence of function, which opens perspectives to investigate nsLTPs functions in RNF.
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Affiliation(s)
- Mélanie Gasser
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Jean Keller
- LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Castanet-Tolosan, France
| | - Pascale Fournier
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Petar Pujic
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Philippe Normand
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France
| | - Hasna Boubakri
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622, Villeurbanne, France.
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Aldakhil T, Alshammari SO, Siraj B, El-Aarag B, Zarina S, Salehi D, Ahmed A. The structural characterization and bioactivity assessment of nonspecific lipid transfer protein 1 (nsLTP1) from caraway (Carum carvi) seeds. BMC Complement Med Ther 2023; 23:254. [PMID: 37474939 PMCID: PMC10357877 DOI: 10.1186/s12906-023-04083-9] [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: 02/08/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Carum carvi (caraway) of the Apiaceae family has been used in many cultures as a cooking spice and part of the folk medicine. Previous reports primarily focus on the medicinal properties of caraway seed essential oil and the whole seeds extract. However, no effort has been made to study caraway proteins and their potential pharmacological properties, including nonspecific lipid transfer protein (nsLTP), necessitating further research. The current study aimed to characterize nonspecific lipid transfer protein 1 (nsLTP1) from caraway seed, determine its three-dimensional structure, and analyze protein-ligand complex interactions through docking studies. We also evaluated nsLTP1 in vitro cytotoxic effect and antioxidant capacity. Additionally, nsLTP1 thermal- and pH- stability were investigated. METHODS Caraway nsLTP1 was purified using two-dimensional chromatography. The complete amino acid sequence of nsLTP1 was achieved by intact protein sequence for the first 20 residues and the overlapping digested peptides. The three-dimensional structure was predicted using MODELLER. Autodock Vina software was employed for docking fatty acids against caraway nsLTP1. Assessment of nsLTP1 cytotoxic activity was achieved by MTS assay, and the Trolox equivalent antioxidant capacity (TAC) was determined. Thermal and pH stability of the nsLTP1 was examined by circular dichroism (CD) spectroscopy. RESULTS Caraway nsLTP1 is composed of 91 residues and weighs 9652 Da. The three-dimensional structure of caraway nsLTP1 sequence was constructed based on searching known structures in the PDB. We chose nsLTP of Solanum melongena (PDB ID: 5TVI) as the modeling template with the highest identity among all other homologous proteins. Docking linolenic acid with caraway protein showed a maximum binding score of -3.6 kcal/mol. A preliminary screening of caraway nsLTP1 suppressed the proliferation of human breast cancer cell lines MDA-MB-231 and MCF-7 in a dose‑dependent manner with an IC50 value of 52.93 and 44.76 μM, respectively. Also, nsLTP1 (41.4 μM) showed TAC up to 750.4 μM Trolox equivalent. Assessment of nsLTP1 demonstrated high thermal/pH stability. CONCLUSION To the best of our knowledge, this is the first study carried out on nsLTP1 from caraway seeds. We hereby report the sequence of nsLTP1 from caraway seeds and its possible interaction with respective fatty acids using in silico approach. Our data indicated that the protein had anticancer and antioxidant activities and was thermally stable.
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Affiliation(s)
- Taibah Aldakhil
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 16278, Saudi Arabia
| | - Saud O Alshammari
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
- Department of Plant Chemistry and Natural Products, Faculty of Pharmacy, Northern Border University, Arar, 91431, Saudi Arabia
| | - Bushra Siraj
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi, Pakistan
| | - Bishoy El-Aarag
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
- Biochemistry Division, Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Koom, 32512, Egypt
| | - Shamshad Zarina
- Dr. Zafar H. Zaidi Center for Proteomics, University of Karachi, Karachi, Pakistan
| | - David Salehi
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Aftab Ahmed
- Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 92618, USA.
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Santos-Silva CAD, Ferreira-Neto JRC, Amador VC, Bezerra-Neto JP, Vilela LMB, Binneck E, Rêgo MDS, da Silva MD, Mangueira de Melo ALT, da Silva RH, Benko-Iseppon AM. From Gene to Transcript and Peptide: A Deep Overview on Non-Specific Lipid Transfer Proteins (nsLTPs). Antibiotics (Basel) 2023; 12:antibiotics12050939. [PMID: 37237842 DOI: 10.3390/antibiotics12050939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Non-specific lipid transfer proteins (nsLTPs) stand out among plant-specific peptide superfamilies due to their multifaceted roles in plant molecular physiology and development, including their protective functions against pathogens. These antimicrobial agents have demonstrated remarkable efficacy against bacterial and fungal pathogens. The discovery of plant-originated, cysteine-rich antimicrobial peptides such as nsLTPs has paved the way for exploring the mentioned organisms as potential biofactories for synthesizing antimicrobial compounds. Recently, nsLTPs have been the focus of a plethora of research and reviews, providing a functional overview of their potential activity. The present work compiles relevant information on nsLTP omics and evolution, and it adds meta-analysis of nsLTPs, including: (1) genome-wide mining in 12 plant genomes not studied before; (2) latest common ancestor analysis (LCA) and expansion mechanisms; (3) structural proteomics, scrutinizing nsLTPs' three-dimensional structure/physicochemical characteristics in the context of nsLTP classification; and (4) broad nsLTP spatiotemporal transcriptional analysis using soybean as a study case. Combining a critical review with original results, we aim to integrate high-quality information in a single source to clarify unexplored aspects of this important gene/peptide family.
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Affiliation(s)
| | | | - Vinícius Costa Amador
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | | | - Lívia Maria Batista Vilela
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | - Eliseu Binneck
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Soja, Londrina 86085-981, Brazil
| | - Mireli de Santana Rêgo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | - Manassés Daniel da Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | | | - Rahisa Helena da Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife 50670-901, Brazil
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15
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Terán M, Osorio J, Cardoso E, Tejería E, Paolino A, Reyes AL, Cecchetto G. [ 99m Tc]Tc-HYNIC-EcgDf21: A defensin short analogue with potential application in infection foci imaging. Chem Biol Drug Des 2023; 101:593-604. [PMID: 36138520 DOI: 10.1111/cbdd.14149] [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: 02/24/2022] [Revised: 08/24/2022] [Accepted: 09/19/2022] [Indexed: 11/30/2022]
Abstract
Opportunistic infections are a problem of great relevance in public health and the precise detection and localization of infection in the early stages of the disease is of great importance for patient management as well as cost containment. Our proposal seeks to contribute to developing a new agent that meets the needs of diagnosis and follow-up of fungal and bacterial infections, focused on the design of a radiotracer with the potential for recognition of hidden infection foci. Defensins are plant antimicrobial peptides that not only show activity against plant pathogens but also against human ones. A short analogue of EcgDf1 defensin, EcgDf21d (NH2 -ERFTGGHCRGFRRRCFCTKHC-COOH), was labelled through the formation of a 99m Tc-HYNIC complex which was assessed for physicochemical and biological behaviour both in vitro and in vivo. The [99m Tc]Tc-HYNIC-EcgDf21 labelling procedure rendered a single product with remarkably high RCP and stability in the labelling milieu. The Log p value indicated that [99m Tc]Tc-HYNIC-EcgDf21 has a hydrophilic behaviour, confirmed by the biodistribution profiles. The optimal uptake value was obtained for Candida albicans infection model reaching a lesion/muscle ratio of 3, this correlates with in vitro binding studies, and the lesion can be definitely observed in the scintigraphic images.
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Affiliation(s)
- Mariella Terán
- Área de Radioquímica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Jessica Osorio
- Área de Radioquímica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Elena Cardoso
- Área de Radioquímica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Emilia Tejería
- Área de Radioquímica, Departamento Estrella Campos, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
| | - Andrea Paolino
- Centro Uruguayo de Imagenología Molecular (CUDIM), Montevideo, Uruguay
| | - Ana Laura Reyes
- Centro Uruguayo de Imagenología Molecular (CUDIM), Montevideo, Uruguay
| | - Gianna Cecchetto
- Área de Microbiología, Instituto de Química Biológica, Facultad de Ciencias-Departamento de Biociencias, Facultad de Química, Universidad de la República (Udelar), Montevideo, Uruguay
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16
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Roy S, Agarwal T, Das A, Halder T, Upadhyaya G, Chaubey B, Ray S. The C-terminal stretch of glycine-rich proline-rich protein (SbGPRP1) from Sorghum bicolor serves as an antimicrobial peptide by targeting the bacterial outer membrane protein. PLANT MOLECULAR BIOLOGY 2023; 111:131-151. [PMID: 36271987 DOI: 10.1007/s11103-022-01317-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The C-terminal stretch in SbGPRP1 (Sorghum glycine-rich proline-rich protein) acts as an antimicrobial peptide in the host innate defense mechanism. Cationic antimicrobial proteins or peptides can either bind to the bacterial membrane or target a specific protein on the bacterial membrane thus leading to membrane perturbation. The 197 amino acid polypeptide of SbGPRP1 showed disordered structure at the N-terminal end and ordered conformation at the C-terminal end. In the present study, the expression of N-SbGPRP1, C-SbGPRP1, and ∆SbGPRP1 followed by antimicrobial assays showed potential antimicrobial property of the C-terminal peptide against gram-positive bacteria Bacillus subtilis and phytopathogen Rhodococcus fascians. The SbGPRP1 protein loses its antimicrobial property when the 23 amino acid sequence (GHGGHGVFGGGYGHGGYGHGYGG) from position 136 to 158 is deleted from the protein. Thus, it can be concluded that the 23 amino acid sequence is vital for the said antimicrobial property. NPN assay, SEM analysis, and electrolyte leakage assays showed potent antimicrobial activity for C-SbGPRP1. Overexpression of the C-SbGPRP1 mutant protein in tobacco followed by infection with Rhodococcus fascians inhibited bacterial growth as shown by SEM analysis. To determine if C-SbGPRP1 might target any protein on the bacterial membrane we isolated the bacterial membrane protein from both Bacillus subtilis and Rhodococcus fascians. Bacterial membrane protein that interacted with the column-bound C-SbGPRP1 was eluted and subjected to LC-MS/MS. LC-MS/MS data analysis showed peptide hit with membrane protein YszA from Bacillus subtilis and a membrane protein from Rhodococcus fascians. Isolated bacterial membrane protein from Bacillus subtilis or Rhodococcus fascians was able to reduce the antimicrobial activity of C-SbGPRP1. Furthermore, BiFC experiments showed interactions between C-SbGPRP1 and YszA protein from Bacillus subtilis leading to the conclusion that bacterial membrane protein was targeted in such membrane perturbation leading to antimicrobial activity.
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Affiliation(s)
- Shuddhanjali Roy
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Tanushree Agarwal
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Arup Das
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Tanmoy Halder
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Gouranga Upadhyaya
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Binay Chaubey
- Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Sudipta Ray
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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17
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In Silico and In Vitro Analyses Reveal Promising Antimicrobial Peptides from Myxobacteria. Probiotics Antimicrob Proteins 2023; 15:202-214. [PMID: 36586039 PMCID: PMC9839799 DOI: 10.1007/s12602-022-10036-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2022] [Indexed: 01/01/2023]
Abstract
Antimicrobial resistance (AMR) is a global concern, and as soon as new antibiotics are introduced, resistance to those agents emerges. Therefore, there is an increased appetite for alternative antimicrobial agents to traditional antibiotics. Here, we used in silico methods to investigate potential antimicrobial peptides (AMPs) from predatory myxobacteria. Six hundred seventy-two potential AMP sequences were extracted from eight complete myxobacterial genomes. Most putative AMPs were predicted to be active against Klebsiella pneumoniae with least activity being predicted against Staphylococcus aureus. One hundred seventeen AMPs (defined here as 'potent putative AMPs') were predicted to have very good activity against more than two bacterial pathogens, and these were characterized further in silico. All potent putative AMPs were predicted to have anti-inflammatory and antifungal properties, but none was predicted to be active against viruses. Twenty six (22%) of them were predicted to be hemolytic to human erythrocytes, five were predicted to have anticancer properties, and 56 (47%) were predicted to be biofilm active. In vitro assays using four synthesized AMPs showed high MIC values (e.g. So_ce_56_913 250 µg/ml and Coral_AMP411 125 µg/ml against E. coli). However, antibiofilm assays showed a substantial reduction in numbers (e.g. Coral_AMP411 and Myxo_mac104 showed a 69% and 73% reduction, respectively, at the lowest concentration against E. coli) compared to traditional antibiotics. Fourteen putative AMPs had high sequence similarity to proteins which were functionally associated with proteins of known function. The myxobacterial genomes also possessed a variety of biosynthetic gene clusters (BGCs) that can encode antimicrobial secondary metabolites, but their numbers did not correlate with those of the AMPs. We suggest that AMPs from myxobacteria are a promising source of novel antimicrobial agents with a plethora of biological properties.
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18
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Jaiswal M, Singh A, Kumar S. PTPAMP: prediction tool for plant-derived antimicrobial peptides. Amino Acids 2023; 55:1-17. [PMID: 35864258 DOI: 10.1007/s00726-022-03190-0] [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: 05/21/2022] [Accepted: 07/12/2022] [Indexed: 01/28/2023]
Abstract
The emergence of antimicrobial peptides (AMPs) as a potential alternative to conventional antibiotics has led to the development of efficient computational methods for predicting AMPs. Among all organisms, the presence of multiple genes encoding AMPs in plants demands the development of a plant-based prediction tool. To this end, we developed models based on multiple peptide features like amino acid composition, dipeptide composition, and physicochemical attributes for predicting plant-derived AMPs. The selected compositional models are integrated into a web server termed PTPAMP. The designed web server is capable of classifying a query peptide sequence into four functional activities, i.e., antimicrobial (AMP), antibacterial (ABP), antifungal (AFP), and antiviral (AVP). Our models achieved an average area under the curve of 0.95, 0.91, 0.85, and 0.88 for AMP, ABP, AFP, and AVP, respectively, on benchmark datasets, which were ~ 6.75% higher than the state-of-the-art methods. Moreover, our analysis indicates the abundance of cysteine residues in plant-derived AMPs and the distribution of other residues like G, S, K, and R, which differ as per the peptide structural family. Finally, we have developed a user-friendly web server, available at the URL: http://www.nipgr.ac.in/PTPAMP/ . We expect the substantial input of this predictor for high-throughput identification of plant-derived AMPs followed by additional insights into their functions.
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Affiliation(s)
- Mohini Jaiswal
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ajeet Singh
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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19
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Dini I, De Biasi MG, Mancusi A. An Overview of the Potentialities of Antimicrobial Peptides Derived from Natural Sources. Antibiotics (Basel) 2022; 11:1483. [PMID: 36358138 PMCID: PMC9686932 DOI: 10.3390/antibiotics11111483] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 07/21/2023] Open
Abstract
Antimicrobial peptides (AMPs) are constituents of the innate immune system in every kind of living organism. They can act by disrupting the microbial membrane or without affecting membrane stability. Interest in these small peptides stems from the fear of antibiotics and the emergence of microorganisms resistant to antibiotics. Through membrane or metabolic disruption, they defend an organism against invading bacteria, viruses, protozoa, and fungi. High efficacy and specificity, low drug interaction and toxicity, thermostability, solubility in water, and biological diversity suggest their applications in food, medicine, agriculture, animal husbandry, and aquaculture. Nanocarriers can be used to protect, deliver, and improve their bioavailability effectiveness. High cost of production could limit their use. This review summarizes the natural sources, structures, modes of action, and applications of microbial peptides in the food and pharmaceutical industries. Any restrictions on AMPs' large-scale production are also taken into consideration.
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Affiliation(s)
- Irene Dini
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Napoli, Italy
| | | | - Andrea Mancusi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici, Italy
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20
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Synthetic Peptides against Plant Pathogenic Bacteria. Microorganisms 2022; 10:microorganisms10091784. [PMID: 36144386 PMCID: PMC9504393 DOI: 10.3390/microorganisms10091784] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
The control of plant diseases caused by bacteria that seriously compromise crop productivity around the world is still one of the most important challenges in food security. Integrated approaches for disease control generally lack plant protection products with high efficacy and low environmental and health adverse effects. Functional peptides, either from natural sources or synthetic, are considered as novel candidates to develop biopesticides. Synthetic peptides can be obtained based on the structure of natural compounds or de novo designed, considering the features of antimicrobial peptides. The advantage of this approach is that analogues can be conveniently prepared, enabling the identification of sequences with improved biological properties. Several peptide libraries have been designed and synthetized, and the best sequences showed strong bactericidal activity against important plant pathogenic bacteria, with a good profile of biodegradability and low toxicity. Among these sequences, there are bacteriolytic or antibiofilm peptides that work against the target bacteria, plant defense elicitor peptides, and multifunctional peptides that display several of these properties. Here, we report the research performed by our groups during the last twenty years, as well as our ongoing work. We also highlight those peptides that can be used as candidates to develop novel biopesticides, and the main challenges and prospects.
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21
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Zupin L, dos Santos-Silva CA, Al Mughrbi ARH, Vilela LMB, Benko-Iseppon AM, Crovella S. Bioactive Antimicrobial Peptides: A New Weapon to Counteract Zoonosis. Microorganisms 2022; 10:1591. [PMID: 36014009 PMCID: PMC9414035 DOI: 10.3390/microorganisms10081591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Zoonoses have recently become the center of attention of the general population and scientific community. Notably, more than 30 new human pathogens have been identified in the last 30 years, 75% of which can be classified as zoonosis. The complete eradication of such types of infections is far out of reach, considering the limited understanding of animal determinants in zoonoses and their causes of emergence. Therefore, efforts must be doubled in examining the spread, persistence, and pathogenicity of zoonosis and studying possible clinical interventions and antimicrobial drug development. The search for antimicrobial bioactive compounds has assumed great emphasis, considering the emergence of multi-drug-resistant microorganisms. Among the biomolecules of emerging scientific interest are antimicrobial peptides (AMPs), potent biomolecules that can potentially act as important weapons against infectious diseases. Moreover, synthetic AMPs are easily tailored (bioinformatically) to target specific features of the pathogens to hijack, inducing no or very low resistance. Although very promising, previous studies on SAMPs' efficacy are still at their early stages. Indeed, further studies and better characterization on their mechanism of action with in vitro and in vivo assays are needed so as to proceed to their clinical application on human beings.
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Affiliation(s)
- Luisa Zupin
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy
| | | | | | - Livia Maria Batista Vilela
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Ana Maria Benko-Iseppon
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
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Gbala ID, Macharia RW, Bargul JL, Magoma G. Membrane Permeabilization and Antimicrobial Activity of Recombinant Defensin-d2 and Actifensin against Multidrug-Resistant Pseudomonas aeruginosa and Candida albicans. Molecules 2022; 27:molecules27144325. [PMID: 35889198 PMCID: PMC9317813 DOI: 10.3390/molecules27144325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/10/2022] Open
Abstract
Antimicrobial resistance requires urgent efforts towards the discovery of active antimicrobials, and the development of strategies to sustainably produce them. Defensin and defensin-like antimicrobial peptides (AMPs) are increasingly gaining pharmacological interest because of their potency against pathogens. In this study, we expressed two AMPs: defensin-d2 derived from spinach, and defensin-like actifensin from Actinomyces ruminicola. Recombinant pTXB1 plasmids carrying the target genes encoding defensin-d2 and actifensin were generated by the MEGAWHOP cloning strategy. Each AMP was first expressed as a fusion protein in Escherichia coli, purified by affinity chromatography, and was thereafter assayed for antimicrobial activity against multidrug-resistant (MDR) pathogens. Approximately 985 µg/mL and 2895 µg/mL of recombinant defensin-d2 and actifensin, respectively, were recovered with high purity. An analysis by MALDI-TOF MS showed distinct peaks corresponding to molecular weights of approximately 4.1 kDa for actifensin and 5.8 kDa for defensin-d2. An in vitro antimicrobial assay showed that MDR Pseudomonas aeruginosa and Candida albicans were inhibited at minimum concentrations of 7.5 µg/mL and 23 µg/mL for recombinant defensin-d2 and actifensin, respectively. The inhibitory kinetics of the peptides revealed cidal activity within 4 h of the contact time. Furthermore, both peptides exhibited an antagonistic interaction, which could be attributed to their affinities for similar ligands, as deduced by peptide–ligand profiling. Moreover, both peptides inhibited biofilm formation, and they exhibited no resistance potential and low hemolytic activity. The peptides also possess the ability to permeate and disrupt the cell membranes of MDR P. aeruginosa and C. albicans. Therefore, recombinant actifensin and defensin-d2 exhibit broad-spectrum antimicrobial activity and have the potential to be used as therapy against MDR pathogens.
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Affiliation(s)
- Ifeoluwa D. Gbala
- Molecular Biology and Biotechnology, Institute for Basic Sciences, Technology and Innovation, Pan African University, Nairobi P.O. Box 62000-00200, Kenya;
- Correspondence:
| | - Rosaline W. Macharia
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi P.O. Box 30197-00100, Kenya;
| | - Joel L. Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya;
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Gabriel Magoma
- Molecular Biology and Biotechnology, Institute for Basic Sciences, Technology and Innovation, Pan African University, Nairobi P.O. Box 62000-00200, Kenya;
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya;
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Bakare OO, Gokul A, Fadaka AO, Wu R, Niekerk LA, Barker AM, Keyster M, Klein A. Plant Antimicrobial Peptides (PAMPs): Features, Applications, Production, Expression, and Challenges. Molecules 2022; 27:3703. [PMID: 35744828 PMCID: PMC9229691 DOI: 10.3390/molecules27123703] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023] Open
Abstract
The quest for an extraordinary array of defense strategies is imperative to reduce the challenges of microbial attacks on plants and animals. Plant antimicrobial peptides (PAMPs) are a subset of antimicrobial peptides (AMPs). PAMPs elicit defense against microbial attacks and prevent drug resistance of pathogens given their wide spectrum activity, excellent structural stability, and diverse mechanism of action. This review aimed to identify the applications, features, production, expression, and challenges of PAMPs using its structure-activity relationship. The discovery techniques used to identify these peptides were also explored to provide insight into their significance in genomics, transcriptomics, proteomics, and their expression against disease-causing pathogens. This review creates awareness for PAMPs as potential therapeutic agents in the medical and pharmaceutical fields, such as the sensitive treatment of bacterial and fungal diseases and others and their utilization in preserving crops using available transgenic methods in the agronomical field. PAMPs are also safe to handle and are easy to recycle with the use of proteases to convert them into more potent antimicrobial agents for sustainable development.
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Affiliation(s)
- Olalekan Olanrewaju Bakare
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (R.W.); (L.-A.N.); (A.M.B.); (M.K.)
- Department of Biochemistry, Faculty of Basic Medical Sciences, Olabisi Onabanjo University, Sagamu 121001, Ogun State, Nigeria
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of the Free State, Phuthadithjaba 9866, South Africa;
| | - Adewale Oluwaseun Fadaka
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Bio labels Node, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville 7535, South Africa;
| | - Ruomou Wu
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (R.W.); (L.-A.N.); (A.M.B.); (M.K.)
| | - Lee-Ann Niekerk
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (R.W.); (L.-A.N.); (A.M.B.); (M.K.)
| | - Adele Mariska Barker
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (R.W.); (L.-A.N.); (A.M.B.); (M.K.)
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (R.W.); (L.-A.N.); (A.M.B.); (M.K.)
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
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24
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León Madrazo A, Segura Campos MR. In silico prediction of peptide variants from chia (S. hispanica L.) with antimicrobial, antibiofilm, and antioxidant potential. Comput Biol Chem 2022; 98:107695. [DOI: 10.1016/j.compbiolchem.2022.107695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 11/03/2022]
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25
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Abstract
Antibiotic resistance constitutes a global threat and could lead to a future pandemic. One strategy is to develop a new generation of antimicrobials. Naturally occurring antimicrobial peptides (AMPs) are recognized templates and some are already in clinical use. To accelerate the discovery of new antibiotics, it is useful to predict novel AMPs from the sequenced genomes of various organisms. The antimicrobial peptide database (APD) provided the first empirical peptide prediction program. It also facilitated the testing of the first machine-learning algorithms. This chapter provides an overview of machine-learning predictions of AMPs. Most of the predictors, such as AntiBP, CAMP, and iAMPpred, involve a single-label prediction of antimicrobial activity. This type of prediction has been expanded to antifungal, antiviral, antibiofilm, anti-TB, hemolytic, and anti-inflammatory peptides. The multiple functional roles of AMPs annotated in the APD also enabled multi-label predictions (iAMP-2L, MLAMP, and AMAP), which include antibacterial, antiviral, antifungal, antiparasitic, antibiofilm, anticancer, anti-HIV, antimalarial, insecticidal, antioxidant, chemotactic, spermicidal activities, and protease inhibiting activities. Also considered in predictions are peptide posttranslational modification, 3D structure, and microbial species-specific information. We compare important amino acids of AMPs implied from machine learning with the frequently occurring residues of the major classes of natural peptides. Finally, we discuss advances, limitations, and future directions of machine-learning predictions of antimicrobial peptides. Ultimately, we may assemble a pipeline of such predictions beyond antimicrobial activity to accelerate the discovery of novel AMP-based antimicrobials.
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Affiliation(s)
- Guangshun Wang
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, 985900 Nebraska Medical Center, Omaha, NE 68198-5900, USA;,Corresponding to: Dr. Monique van Hoek: ; Dr. Iosif Vaisman: ; Dr. Guangshun Wang:
| | - Iosif I. Vaisman
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA.,Corresponding to: Dr. Monique van Hoek: ; Dr. Iosif Vaisman: ; Dr. Guangshun Wang:
| | - Monique L. van Hoek
- School of Systems Biology, George Mason University, 10920 George Mason Circle, Manassas, VA, 20110, USA.,Corresponding to: Dr. Monique van Hoek: ; Dr. Iosif Vaisman: ; Dr. Guangshun Wang:
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26
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Quintans ILADCR, de Araújo JVA, Rocha LNM, de Andrade AEB, do Rêgo TG, Deyholos MK. An overview of databases and bioinformatics tools for plant antimicrobial peptides. Curr Protein Pept Sci 2021; 23:6-19. [PMID: 34951361 DOI: 10.2174/1389203723666211222170342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 11/22/2022]
Abstract
Antimicrobial peptides (AMPs) are small, ribosomally synthesized proteins found in nearly all forms of life. In plants, AMPs play a central role in plant defense due to their distinct physicochemical properties. Due to their broad-spectrum antimicrobial activity and rapid killing action, plant AMPs have become important candidates for the development of new drugs to control plant and animal pathogens that are resistant to multiple drugs. Further research is required to explore the potential uses of these natural compounds. Computational strategies have been increasingly used to understand key aspects of antimicrobial peptides. These strategies will help to minimize the time and cost of "wet-lab" experimentation. Researchers have developed various tools and databases to provide updated information on AMPs. However, despite the increased availability of antimicrobial peptide resources in biological databases, finding AMPs from plants can still be a difficult task. The number of plant AMP sequences in current databases is still small and yet often redundant. To facilitate further characterization of plant AMPs, we have summarized information on the location, distribution, and annotations of plant AMPs available in the most relevant databases for AMPs research. We also mapped and categorized the bioinformatics tools available in these databases. We expect that this will allow researchers to advance in the discovery and development of new plant AMPs with potent biological properties. We hope to provide insights to further expand the application of AMPs in the fields of biotechnology, pharmacy, and agriculture.
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Affiliation(s)
| | | | | | | | | | - Michael K Deyholos
- IK Barber School of Arts and Sciences, University of British Columbia, Kelowna, BC. Canada
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dos Santos-Silva CA, Tricarico PM, Vilela LMB, Roldan-Filho RS, Amador VC, d’Adamo AP, Rêgo MDS, Benko-Iseppon AM, Crovella S. Plant Antimicrobial Peptides as Potential Tool for Topic Treatment of Hidradenitis Suppurativa. Front Microbiol 2021; 12:795217. [PMID: 34966375 PMCID: PMC8710806 DOI: 10.3389/fmicb.2021.795217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
Among chronic skin autoinflammatory diseases, Hidradenitis Suppurativa (HS) stands out for its chronicity, highly variable condition, and profound impact on the patients' quality of life. HS is characterized by suppurative skin lesions in diverse body areas, including deep-seated painful nodules, abscesses, draining sinus, and bridged scars, among others, with typical topography. To date, HS is considered a refractory disease and medical treatments aim to reduce the incidence, the infection, and the pain of the lesions. For this purpose, different classes of drugs, including anti-inflammatory molecules, antibiotics and biological drugs are being used. Antimicrobial peptides (AMPs), also called defense peptides, emerge as a new class of therapeutic compounds, with broad-spectrum antimicrobial action, in addition to reports on their anti-inflammatory, healing, and immunomodulating activity. Such peptides are present in prokaryotes and eukaryotes, as part of the innate eukaryotic immune system. It has been proposed that a deregulation in the expression of AMPs in human epithelial tissues of HS patients may be associated with the etiology of this skin disease. In this scenario, plant AMPs stand out for their richness, diversity of types, and broad antimicrobial effects, with potential application for topical systemic use in patients affected by HS.
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Affiliation(s)
| | | | | | | | - Vinícius Costa Amador
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Adamo Pio d’Adamo
- Institute for Maternal and Child Health – IRCCS Burlo Garofolo, Trieste, Italy
- Department of Medical Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Mireli de Santana Rêgo
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
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28
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Péter B, Boldizsár I, Kovács GM, Erdei A, Bajtay Z, Vörös A, Ramsden JJ, Szabó I, Bősze S, Horvath R. Natural Compounds as Target Biomolecules in Cellular Adhesion and Migration: From Biomolecular Stimulation to Label-Free Discovery and Bioactivity-Based Isolation. Biomedicines 2021; 9:1781. [PMID: 34944597 PMCID: PMC8698624 DOI: 10.3390/biomedicines9121781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 01/07/2023] Open
Abstract
Plants and fungi can be used for medical applications because of their accumulation of special bioactive metabolites. These substances might be beneficial to human health, exerting also anti-inflammatory and anticancer (antiproliferative) effects. We propose that they are mediated by influencing cellular adhesion and migration via various signaling pathways and by directly inactivating key cell adhesion surface receptor sites. The evidence for this proposition is reviewed (by summarizing the natural metabolites and their effects influencing cellular adhesion and migration), along with the classical measuring techniques used to gain such evidence. We systematize existing knowledge concerning the mechanisms of how natural metabolites affect adhesion and movement, and their role in gene expression as well. We conclude by highlighting the possibilities to screen natural compounds faster and more easily by applying new label-free methods, which also enable a far greater degree of quantification than the conventional methods used hitherto. We have systematically classified recent studies regarding the effects of natural compounds on cellular adhesion and movement, characterizing the active substances according to their organismal origin (plants, animals or fungi). Finally, we also summarize the results of recent studies and experiments on SARS-CoV-2 treatments by natural extracts affecting mainly the adhesion and entry of the virus.
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Affiliation(s)
- Beatrix Péter
- Nanobiosensorics Group, Research Centre for Energy Research, Institute for Technical Physics and Materials Science, Konkoly-Thege u 29-33, 1120 Budapest, Hungary; (A.V.); (R.H.)
| | - Imre Boldizsár
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (I.B.); (G.M.K.)
- Department of Pharmacognosy, Semmelweis University, Üllői út 26, 1085 Budapest, Hungary
| | - Gábor M. Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (I.B.); (G.M.K.)
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, 1022 Budapest, Hungary
| | - Anna Erdei
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.E.); (Z.B.)
- MTA-ELTE Immunology Research Group, Eötvös Loránd Research Network (ELKH), Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zsuzsa Bajtay
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.E.); (Z.B.)
- MTA-ELTE Immunology Research Group, Eötvös Loránd Research Network (ELKH), Eötvös Loránd University, 1117 Budapest, Hungary
| | - Alexandra Vörös
- Nanobiosensorics Group, Research Centre for Energy Research, Institute for Technical Physics and Materials Science, Konkoly-Thege u 29-33, 1120 Budapest, Hungary; (A.V.); (R.H.)
| | - Jeremy J. Ramsden
- Clore Laboratory, University of Buckingham, Buckingham MK18 1EG, UK;
| | - Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (I.S.); (S.B.)
- National Public Health Center, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - Szilvia Bősze
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (I.S.); (S.B.)
- National Public Health Center, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - Robert Horvath
- Nanobiosensorics Group, Research Centre for Energy Research, Institute for Technical Physics and Materials Science, Konkoly-Thege u 29-33, 1120 Budapest, Hungary; (A.V.); (R.H.)
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29
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Amador VC, dos Santos-Silva CA, Vilela LMB, Oliveira-Lima M, de Santana Rêgo M, Roldan-Filho RS, de Oliveira-Silva RL, Lemos AB, de Oliveira WD, Ferreira-Neto JRC, Crovella S, Benko-Iseppon AM. Lipid Transfer Proteins (LTPs)-Structure, Diversity and Roles beyond Antimicrobial Activity. Antibiotics (Basel) 2021; 10:1281. [PMID: 34827219 PMCID: PMC8615156 DOI: 10.3390/antibiotics10111281] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 01/21/2023] Open
Abstract
Lipid transfer proteins (LTPs) are among the most promising plant-exclusive antimicrobial peptides (AMPs). They figure among the most challenging AMPs from the point of view of their structural diversity, functions and biotechnological applications. This review presents a current picture of the LTP research, addressing not only their structural, evolutionary and further predicted functional aspects. Traditionally, LTPs have been identified by their direct isolation by biochemical techniques, whereas omics data and bioinformatics deserve special attention for their potential to bring new insights. In this context, new possible functions have been identified revealing that LTPs are actually multipurpose, with many additional predicted roles. Despite some challenges due to the toxicity and allergenicity of LTPs, a systematic review and search in patent databases, indicate promising perspectives for the biotechnological use of LTPs in human health and also plant defense.
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Affiliation(s)
- Vinícius Costa Amador
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Carlos André dos Santos-Silva
- Department of Advanced Diagnostics, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, 34100 Trieste, Italy;
| | - Lívia Maria Batista Vilela
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Marx Oliveira-Lima
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Mireli de Santana Rêgo
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Ricardo Salas Roldan-Filho
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Roberta Lane de Oliveira-Silva
- General Microbiology Laboratory, Agricultural Science Campus, Universidade Federal do Vale do São Francisco, Petrolina 56300-990, Brazil;
| | - Ayug Bezerra Lemos
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Wilson Dias de Oliveira
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - José Ribamar Costa Ferreira-Neto
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
| | - Sérgio Crovella
- Department of Biological and Environmental Sciences, College of Arts and Science, Qatar University, Doha 1883, Qatar;
| | - Ana Maria Benko-Iseppon
- Bioscience Centre, Genetics Department, Universidade Federal de Pernambuco, Recife 50670-420, Brazil; (V.C.A.); (L.M.B.V.); (M.O.-L.); (M.d.S.R.); (R.S.R.-F.); (A.B.L.); (W.D.d.O.); (J.R.C.F.-N.)
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30
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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Capecchi A, Reymond JL. Classifying natural products from plants, fungi or bacteria using the COCONUT database and machine learning. J Cheminform 2021; 13:82. [PMID: 34663470 PMCID: PMC8524952 DOI: 10.1186/s13321-021-00559-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/02/2021] [Indexed: 01/13/2023] Open
Abstract
Natural products (NPs) represent one of the most important resources for discovering new drugs. Here we asked whether NP origin can be assigned from their molecular structure in a subset of 60,171 NPs in the recently reported Collection of Open Natural Products (COCONUT) database assigned to plants, fungi, or bacteria. Visualizing this subset in an interactive tree-map (TMAP) calculated using MAP4 (MinHashed atom pair fingerprint) clustered NPs according to their assigned origin ( https://tm.gdb.tools/map4/coconut_tmap/ ), and a support vector machine (SVM) trained with MAP4 correctly assigned the origin for 94% of plant, 89% of fungal, and 89% of bacterial NPs in this subset. An online tool based on an SVM trained with the entire subset correctly assigned the origin of further NPs with similar performance ( https://np-svm-map4.gdb.tools/ ). Origin information might be useful when searching for biosynthetic genes of NPs isolated from plants but produced by endophytic microorganisms.
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Affiliation(s)
- Alice Capecchi
- 1 Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- 1 Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
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32
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Hernández-Aristizábal I, Ocampo-Ibáñez ID. Antimicrobial Peptides with Antibacterial Activity against Vancomycin-Resistant Staphylococcus aureus Strains: Classification, Structures, and Mechanisms of Action. Int J Mol Sci 2021; 22:7927. [PMID: 34360692 PMCID: PMC8347216 DOI: 10.3390/ijms22157927] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
The emergence of bacteria resistant to conventional antibiotics is of great concern in modern medicine because it renders ineffectiveness of the current empirical antibiotic therapies. Infections caused by vancomycin-resistant Staphylococcus aureus (VRSA) and vancomycin-intermediate S. aureus (VISA) strains represent a serious threat to global health due to their considerable morbidity and mortality rates. Therefore, there is an urgent need of research and development of new antimicrobial alternatives against these bacteria. In this context, the use of antimicrobial peptides (AMPs) is considered a promising alternative therapeutic strategy to control resistant strains. Therefore, a wide number of natural, artificial, and synthetic AMPs have been evaluated against VRSA and VISA strains, with great potential for clinical application. In this regard, we aimed to present a comprehensive and systematic review of research findings on AMPs that have shown antibacterial activity against vancomycin-resistant and vancomycin-intermediate resistant strains and clinical isolates of S. aureus, discussing their classification and origin, physicochemical and structural characteristics, and possible action mechanisms. This is the first review that includes all peptides that have shown antibacterial activity against VRSA and VISA strains exclusively.
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Affiliation(s)
| | - Iván Darío Ocampo-Ibáñez
- Research Group of Microbiology, Industry and Environment, Faculty of Basic Sciences, Universidad Santiago de Cali, Cali 760035, Colombia;
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Santos-Silva CAD, Vilela LMB, Oliveira-Silva RLD, Silva JBD, Machado AR, Bezerra-Neto JP, Crovella S, Benko-Iseppon AM. Cassava (Manihot esculenta) defensins: Prospection, structural analysis and tissue-specific expression under biotic/abiotic stresses. Biochimie 2021; 186:1-12. [PMID: 33789147 DOI: 10.1016/j.biochi.2021.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 11/26/2022]
Abstract
Defensins are a prominent family of antimicrobial peptides. They play sophisticated roles in the defense against pathogens in all living organisms, but few works address their expression under different conditions and plant tissues. The present work prospected defensins of Manihot esculenta Crantz, popularly known as cassava. Five defensin candidates (MeDefs) were retrieved from the genome sequences and characterized. Considering chromosome distribution, only MeDef1 and 2 occupy adjacent positions in the same chromosome arm. All 3D structures had antiparallel ß-sheets, an α-helix, and amphipathic residues distributed throughout the peptides with a predominance of cationic surface charge. MeDefs expression was validated by RT-qPCR, including two stress types (biotic: fungus Macrophomina pseudophaseolina, and abiotic: mechanical injury) and a combination of both stresses (fungus+injury) in three different tissues (root, stem, and leaf). For this purpose, ten reference genes (RGs) were tested, and three were chosen to characterize MeDef expression. MeDef3 was up-regulated at roots in all stress situations tested. MeDef1 and MeDef5 were induced in leaves under biotic and abiotic stresses, but not in both stress types simultaneously. Only MeDef2 was down-regulated in the stem tissue also with biotic/abiotic combined stresses. These results indicate that although defensins are known to be responsive to pathogen infection, they may act as preformed defense or, still, have tissue or stress specificities. Aspects of their structure, stability and evolution are also discussed.
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Affiliation(s)
- Carlos André Dos Santos-Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Lívia Maria Batista Vilela
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Roberta Lane de Oliveira-Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Jéssica Barboza da Silva
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Alexandre Reis Machado
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - João Pacífico Bezerra-Neto
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Sergio Crovella
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil
| | - Ana Maria Benko-Iseppon
- Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, 1235, CEP 50.670-423, Recife, PE, Brazil.
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Moyer TB, Allen JL, Shaw LN, Hicks LM. Multiple Classes of Antimicrobial Peptides in Amaranthus tricolor Revealed by Prediction, Proteomics, and Mass Spectrometric Characterization. JOURNAL OF NATURAL PRODUCTS 2021; 84:444-452. [PMID: 33576231 PMCID: PMC8601116 DOI: 10.1021/acs.jnatprod.0c01203] [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: 05/05/2023]
Abstract
Traditional medicinal plants are rich reservoirs of antimicrobial agents, including antimicrobial peptides (AMPs). Advances in genomic sequencing, in silico AMP predictions, and mass spectrometry-based peptidomics facilitate increasingly high-throughput bioactive peptide discovery. Herein, Amaranthus tricolor aerial tissue was profiled via MS-based proteomics/peptidomics, identifying AMPs predicted in silico. Bottom-up proteomics identified seven novel peptides spanning three AMP classes including lipid transfer proteins, snakins, and a defensin. Characterization via top-down peptidomic analysis of Atr-SN1, Atr-DEF1, and Atr-LTP1 revealed unexpected proteolytic processing and enumerated disulfide bonds. Bioactivity screening of isolated Atr-LTP1 showed activity against the high-risk ESKAPE bacterial pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Enterobacter cloacae). These results highlight the potential for integrating AMP prediction algorithms with complementary -omics approaches to accelerate characterization of biologically relevant AMP peptidoforms.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jessie L Allen
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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Kurpe SR, Grishin SY, Surin AK, Panfilov AV, Slizen MV, Chowdhury SD, Galzitskaya OV. Antimicrobial and Amyloidogenic Activity of Peptides. Can Antimicrobial Peptides Be Used against SARS-CoV-2? Int J Mol Sci 2020; 21:E9552. [PMID: 33333996 PMCID: PMC7765370 DOI: 10.3390/ijms21249552] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023] Open
Abstract
At present, much attention is paid to the use of antimicrobial peptides (AMPs) of natural and artificial origin to combat pathogens. AMPs have several points that determine their biological activity. We analyzed the structural properties of AMPs, as well as described their mechanism of action and impact on pathogenic bacteria and viruses. Recently published data on the development of new AMP drugs based on a combination of molecular design and genetic engineering approaches are presented. In this article, we have focused on information on the amyloidogenic properties of AMP. This review examines AMP development strategies from the perspective of the current high prevalence of antibiotic-resistant bacteria, and the potential prospects and challenges of using AMPs against infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Stanislav R. Kurpe
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Sergei Yu. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Alexander V. Panfilov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Mikhail V. Slizen
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Saikat D. Chowdhury
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India;
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
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Rodríguez-Decuadro S, da Rosa G, Radío S, Barraco-Vega M, Benko-Iseppon AM, Dans PD, Smircich P, Cecchetto G. Antimicrobial peptides in the seedling transcriptome of the tree legume Peltophorum dubium. Biochimie 2020; 180:229-242. [PMID: 33197551 DOI: 10.1016/j.biochi.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/14/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Antimicrobial peptides (AMPs) play an essential role in plant defense against invading pathogens. Due to their biological properties, these molecules have been considered useful for drug development, as novel agents in disease therapeutics, applicable to both agriculture and medicine. New technologies of massive sequencing open opportunities to discover novel AMP encoding genes in wild plant species. This work aimed to identify cysteine-rich AMPs from Peltophorum dubium, a legume tree from South America. We performed whole-transcriptome sequencing of P. dubium seedlings followed by de novo transcriptome assembly, uncovering 78 AMP transcripts classified into five families: hevein-like, lipid-transfer proteins (LTPs), alpha hairpinins, defensins, and snakin/GASA (Giberellic Acid Stimulated in Arabidopsis) peptides. No transcripts with similarity to cyclotide or thionin genes were identified. Genomic DNA analysis by PCR confirmed the presence of 18 genes encoding six putative defensins and 12 snakin/GASA peptides and allowed the characterization of their exon-intron structure. The present work demonstrates that AMP prediction from a wild species is possible using RNA sequencing and de novo transcriptome assembly, regarding a starting point for studies focused on AMP gene evolution and expression. Moreover, this study allowed the detection of strong AMP candidates for drug development and novel biotechnological products.
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Affiliation(s)
- Susana Rodríguez-Decuadro
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Garzón 780, Montevideo 12900, Uruguay.
| | - Gabriela da Rosa
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11800, Uruguay.
| | - Santiago Radío
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable. MEC - Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
| | - Mariana Barraco-Vega
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11800, Uruguay.
| | - Ana Maria Benko-Iseppon
- Universidade Federal de Pernambuco, Centro de Biociências, Av. Prof. Moraes Rego, 1235. CEP 50.670-420, Recife, PE, Brazil.
| | - Pablo D Dans
- Departamento de Ciencias Biológicas, CENUR Litoral Norte, Universidad de la República. General Fructuoso Rivera 1350, Laboratorio Genética Funcional, Institut Pasteur de Montevideo. Mataojo 2020, Salto 50000, Montevideo, 11400, Uruguay.
| | - Pablo Smircich
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable. MEC - Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
| | - Gianna Cecchetto
- Departamento de Biociencias, Facultad de Química, Universidad de la República, General Flores 2124, Montevideo 11800, Uruguay; Instituto de Química Biológica, Facultad de Ciencias - Facultad de Química, Universidad de la República, General Flores 2124, Montevideo, 11800, Uruguay.
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Albakri AH, Al-Shuhaib MBS, Alwan SL, AbdulAzeez S, Borgio JF. Deleterious missense variants in the aflatoxin biosynthesis genes explain the low toxicity of Aspergillus flavus from infected rice. Microb Pathog 2020; 152:104605. [PMID: 33166617 DOI: 10.1016/j.micpath.2020.104605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/23/2020] [Accepted: 11/02/2020] [Indexed: 01/10/2023]
Abstract
Aspergillus flavus is one of the most natural contaminants of the improperly stored rice grains. It produces several secondary metabolites, like aflatoxins, which are well known hepatotoxic, hepatocarcinogenic and mutagenic agents. This study describes the in silico consequences of the missense mutations identified in several genes of aflatoxins biosynthesis in rice-contaminating A. flavus isolates. In the in vitro portion of the study, aflatoxins production profile was measured, and PCR-single strand-conformation polymorphism (SSCP)-sequencing method was used to genotype the studied genetic loci: aflP, aflM, aflR, PEP, and cob. Results showed aflatoxigenic potential in 79 out of 109 A. flavus isolates. Twenty-two missense and fifty-five synonymous mutations were found to be distributed variably on the studied loci. In the in silico portion of this study, several computations were utilized to predict the effect of each observed missense mutation on proteins structure, function, and stability. Seven mutations (O-methyl transferase: p.G256C; ver-1 dehydrogenase: p.K179 N and p.V183L; aspergillopepsin-1: p.P137L, p.S138F, p.G154C, and p.S158C) were found to be highly deleterious among the missense variants with damaging effects on their proteins' structure and function. In contrast to these detected variations in the aflatoxigenic loci, all missense mutations in the control non-aflatoxigenic cob gene were found to be neutral. These findings indicated that the observed mutations may reduce the concomitant biohazard of their biosynthesized aflatoxins. The current findings suggest that the naturally available variants may reduce or eliminates the dangerous consequences of aflatoxins upon ingesting the rice infected with A. flavus. To the best of our knowledge, this study is the first comprehensive report to analyze the missense mutations on the aflatoxin biosynthesis genes using in vitro and the state-of-art bio-computational tools.
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Affiliation(s)
- Ali H Albakri
- Department of Plant Protection, College of Agriculture, University of Kufa, Al-Kufa, Najaf, 54001, Iraq.
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, 51001, Iraq.
| | - Sabah L Alwan
- Department of Plant Protection, College of Agriculture, University of Kufa, Al-Kufa, Najaf, 54001, Iraq.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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