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Tučs A, Berenger F, Yumoto A, Tamura R, Uzawa T, Tsuda K. Quantum Annealing Designs Nonhemolytic Antimicrobial Peptides in a Discrete Latent Space. ACS Med Chem Lett 2023; 14:577-582. [PMID: 37197452 PMCID: PMC10184305 DOI: 10.1021/acsmedchemlett.2c00487] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Increasing the variety of antimicrobial peptides is crucial in meeting the global challenge of multi-drug-resistant bacterial pathogens. While several deep-learning-based peptide design pipelines are reported, they may not be optimal in data efficiency. High efficiency requires a well-compressed latent space, where optimization is likely to fail due to numerous local minima. We present a multi-objective peptide design pipeline based on a discrete latent space and D-Wave quantum annealer with the aim of solving the local minima problem. To achieve multi-objective optimization, multiple peptide properties are encoded into a score using non-dominated sorting. Our pipeline is applied to design therapeutic peptides that are antimicrobial and non-hemolytic at the same time. From 200 000 peptides designed by our pipeline, four peptides proceeded to wet-lab validation. Three of them showed high anti-microbial activity, and two are non-hemolytic. Our results demonstrate how quantum-based optimizers can be taken advantage of in real-world medical studies.
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Affiliation(s)
- Andrejs Tučs
- Graduate
School of Frontier Sciences, The University
of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
| | - Francois Berenger
- Graduate
School of Frontier Sciences, The University
of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
| | - Akiko Yumoto
- Emergent
Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ryo Tamura
- Graduate
School of Frontier Sciences, The University
of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
- International
Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), Tsukuba 305−0044, Japan
- Research
and Services Division of Materials Data and Integrated System, National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
- RIKEN
Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Takanori Uzawa
- Emergent
Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Nano Medical
Engineering Laboratory, RIKEN Cluster for
Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- E-mail:
| | - Koji Tsuda
- Graduate
School of Frontier Sciences, The University
of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan
- Research
and Services Division of Materials Data and Integrated System, National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
- RIKEN
Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
- E-mail:
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2
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Gawde U, Chakraborty S, Waghu FH, Barai RS, Khanderkar A, Indraguru R, Shirsat T, Idicula-Thomas S. CAMPR4: a database of natural and synthetic antimicrobial peptides. Nucleic Acids Res 2022; 51:D377-D383. [PMID: 36370097 PMCID: PMC9825550 DOI: 10.1093/nar/gkac933] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/25/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
There has been an exponential increase in the design of synthetic antimicrobial peptides (AMPs) for its use as novel antibiotics. Synthetic AMPs are substantially enriched in residues with physicochemical properties known to be critical for antimicrobial activity; such as positive charge, hydrophobicity, and higher alpha helical propensity. The current prediction algorithms for AMPs have been developed using AMP sequences from natural sources and hence do not perform well for synthetic peptides. In this version of CAMP database, along with updating sequence information of AMPs, we have created separate prediction algorithms for natural and synthetic AMPs. CAMPR4 holds 24243 AMP sequences, 933 structures, 2143 patents and 263 AMP family signatures. In addition to the data on sequences, source organisms, target organisms, minimum inhibitory and hemolytic concentrations, CAMPR4 provides information on N and C terminal modifications and presence of unusual amino acids, as applicable. The database is integrated with tools for AMP prediction and rational design (natural and synthetic AMPs), sequence (BLAST and clustal omega), structure (VAST) and family analysis (PRATT, ScanProsite, CAMPSign). The data along with the algorithms of CAMPR4 will aid to enhance AMP research. CAMPR4 is accessible at http://camp.bicnirrh.res.in/.
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Affiliation(s)
| | | | | | - Ram Shankar Barai
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai 400012, Maharashtra, India
| | - Ashlesha Khanderkar
- Department of Bioinformatics, Guru Nanak Khalsa College, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Rishikesh Indraguru
- Department of Bioinformatics, Guru Nanak Khalsa College, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India
| | - Tanmay Shirsat
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai 400012, Maharashtra, India
| | - Susan Idicula-Thomas
- To whom correspondence should be addressed. Tel: +91 22 24192107; Fax: +91 22 24139412;
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3
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Culver KD, Allen JL, Shaw LN, Hicks LM. Too Hot to Handle: Antibacterial Peptides Identified in Ghost Pepper. JOURNAL OF NATURAL PRODUCTS 2021; 84:2200-2208. [PMID: 34445876 PMCID: PMC8600445 DOI: 10.1021/acs.jnatprod.1c00281] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Capsicum spp. (hot peppers) demonstrate a range of interesting bioactive properties spanning anti-inflammatory, antioxidant, and antimicrobial activities. While several species within the genus are known to produce antimicrobial peptides (AMPs), AMP sequence mining of genomic data indicates this space remains largely unexplored. Herein, in silico AMP predictions were paired with peptidomics to identify novel AMPs from the interspecific hybrid ghost pepper (Capsicum chinense × frutescens). AMP prediction algorithms revealed 115 putative AMPs within the Capsicum chinense genome, of which 14 were identified in the aerial tissue peptidome. PepSAVI-MS, de novo sequencing, and complementary approaches were used to fully molecularly characterize two novel AMPs, CC-AMP1 and CC-AMP2, including elucidation of a pyroglutamic acid post-translational modification of CC-AMP1 and disulfide bond connectivity of both. Both CC-AMP1 and CC-AMP2 have little homology with known AMPs and exhibited low μM antimicrobial activity against Gram-negative bacteria, including Escherichia coli. These findings demonstrate the complementary nature of peptidomics, bioactivity-guided discovery, and bioinformatics-based investigations to characterize plant AMP profiles.
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Affiliation(s)
- Kevin D. Culver
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jessie L. Allen
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Téllez Ramirez GA, Osorio-Méndez JF, Henao Arias DC, Toro S. LJ, Franco Castrillón J, Rojas-Montoya M, Castaño Osorio JC. New Insect Host Defense Peptides (HDP) From Dung Beetle (Coleoptera: Scarabaeidae) Transcriptomes. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:12. [PMID: 34374763 PMCID: PMC8353981 DOI: 10.1093/jisesa/ieab054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Indexed: 06/13/2023]
Abstract
The Coleoptera Scarabaeidae family is one of the most diverse groups of insects on the planet, which live in complex microbiological environments. Their immune systems have evolved diverse families of Host Defense Peptides (HDP) with strong antimicrobial and immunomodulatory activities. However, there are several peptide sequences that await discovery in this group of organisms. This would pave the way to identify molecules with promising therapeutic potential. This work retrieved two sources of information: 1) De-novo transcriptomic data from two species of neotropical Scarabaeidae (Dichotomius satanas and Ontophagus curvicornis); 2) Sequence data deposited in available databases. A Blast-based search was conducted against the transcriptomes with a subset of sequences representative of the HDP. This work reports 155 novel HDP sequences identified in nine transcriptomes from seven species of Coleoptera: D. satanas (n = 76; 49.03%), O. curvicornis (n = 23; 14.83%), (Trypoxylus dichotomus) (n = 18; 11.61%), (Onthophagus nigriventris) (n = 10; 6.45%), (Heterochelus sp) (n = 6; 3.87%), (Oxysternon conspicillatum) (n = 18; 11.61%), and (Popillia japonica) (n = 4; 2.58%). These sequences were identified based on similarity to known HDP insect families. New members of defensins (n = 58; 37.42%), cecropins (n = 18; 11.61%), attancins (n = 41; 26.45%), and coleoptericins (n = 38; 24.52%) were described based on their physicochemical and structural characteristics, as well as their sequence relationship to other insect HDPs. Therefore, the Scarabaeidae family is a complex and rich group of insects with a great diversity of antimicrobial peptides with potential antimicrobial activity.
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Affiliation(s)
- Germán Alberto Téllez Ramirez
- Center of Biomedical Research, Group of Molecular Immunology, Universidad del Quindío, Carrera 15 and Calle 12 Norte, Armenia, Quindío, Colombia
| | - Juan Felipe Osorio-Méndez
- Center of Biomedical Research, Group of Molecular Immunology, Universidad del Quindío, Carrera 15 and Calle 12 Norte, Armenia, Quindío, Colombia
| | - Diana Carolina Henao Arias
- Center of Biomedical Research, Group of Molecular Immunology, Universidad del Quindío, Carrera 15 and Calle 12 Norte, Armenia, Quindío, Colombia
| | - Lily Johanna Toro S.
- Center of Biomedical Research, Group of Molecular Immunology, Universidad del Quindío, Carrera 15 and Calle 12 Norte, Armenia, Quindío, Colombia
| | - Juliana Franco Castrillón
- Center of Biomedical Research, Group of Molecular Immunology, Universidad del Quindío, Carrera 15 and Calle 12 Norte, Armenia, Quindío, Colombia
| | - Maribel Rojas-Montoya
- Center of Biomedical Research, Group of Molecular Immunology, Universidad del Quindío, Carrera 15 and Calle 12 Norte, Armenia, Quindío, Colombia
| | - Jhon Carlos Castaño Osorio
- Center of Biomedical Research, Group of Molecular Immunology, Universidad del Quindío, Carrera 15 and Calle 12 Norte, Armenia, Quindío, Colombia
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Jin Y, Wang Z, Dong AY, Huang YQ, Hao GF, Song BA. Web repositories of natural agents promote pests and pathogenic microbes management. Brief Bioinform 2021; 22:6294160. [PMID: 34098581 DOI: 10.1093/bib/bbab205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
The grand challenge to meet the increasing demands for food by a rapidly growing global population requires protecting crops from pests. Natural active substances play a significant role in the sustainable pests and pathogenic microbes management. In recent years, natural products- (NPs), antimicrobial peptides- (AMPs), medicinal plant- and plant essential oils (EOs)-related online resources have greatly facilitated the development of pests and pathogenic microbes control agents in an efficient and economical manner. However, a comprehensive comparison, analysis and summary of these existing web resources are still lacking. Here, we surveyed these databases of NPs, AMPs, medicinal plants and plant EOs with insecticidal, antibacterial, antiviral and antifungal activity, and we compared their functionality, data volume, data sources and applicability. We comprehensively discussed the limitation of these web resources. This study provides a toolbox for bench scientists working in the pesticide, botany, biomedical and pharmaceutical engineering fields. The aim of the review is to hope that these web resources will facilitate the discovery and development of potential active ingredients of pests and pathogenic microbes control agents.
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Affiliation(s)
- Yin Jin
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Zheng Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - An-Yu Dong
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Yuan-Qin Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Bao-An Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
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Abstract
Anaerobic gut fungi are important members of the gut microbiome of herbivores, yet they exist in small numbers relative to bacteria. Here, we show that these early-branching fungi produce a wealth of secondary metabolites (natural products) that may act to regulate the gut microbiome. We use an integrated 'omics'-based approach to classify the biosynthetic genes predicted from fungal genomes, determine transcriptionally active genes, and verify the presence of their enzymatic products. Our analysis reveals that anaerobic gut fungi are an untapped reservoir of bioactive compounds that could be harnessed for biotechnology. Anaerobic fungi (class Neocallimastigomycetes) thrive as low-abundance members of the herbivore digestive tract. The genomes of anaerobic gut fungi are poorly characterized and have not been extensively mined for the biosynthetic enzymes of natural products such as antibiotics. Here, we investigate the potential of anaerobic gut fungi to synthesize natural products that could regulate membership within the gut microbiome. Complementary 'omics' approaches were combined to catalog the natural products of anaerobic gut fungi from four different representative species: Anaeromyces robustus (A. robustus), Caecomyces churrovis (C. churrovis), Neocallimastix californiae (N. californiae), and Piromyces finnis (P. finnis). In total, 146 genes were identified that encode biosynthetic enzymes for diverse types of natural products, including nonribosomal peptide synthetases and polyketide synthases. In addition, N. californiae and C. churrovis genomes encoded seven putative bacteriocins, a class of antimicrobial peptides typically produced by bacteria. During standard laboratory growth on plant biomass or soluble substrates, 26% of total core biosynthetic genes in all four strains were transcribed. Across all four fungal strains, 30% of total biosynthetic gene products were detected via proteomics when grown on cellobiose. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of fungal supernatants detected 72 likely natural products from A. robustus alone. A compound produced by all four strains of anaerobic fungi was putatively identified as the polyketide-related styrylpyrone baumin. Molecular networking quantified similarities between tandem mass spectrometry (MS/MS) spectra among these fungi, enabling three groups of natural products to be identified that are unique to anaerobic fungi. Overall, these results support the finding that anaerobic gut fungi synthesize natural products, which could be harnessed as a source of antimicrobials, therapeutics, and other bioactive compounds.
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Waghu FH, Gawde U, Gomatam A, Coutinho E, Idicula‐Thomas S. A QSAR modeling approach for predicting myeloid antimicrobial peptides with high sequence similarity. Chem Biol Drug Des 2020; 96:1408-1417. [DOI: 10.1111/cbdd.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/20/2020] [Accepted: 06/14/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Faiza Hanif Waghu
- Biomedical Informatics Centre Indian Council of Medical Research‐National Institute for Research in Reproductive Health MumbaiIndia
| | - Ulka Gawde
- Biomedical Informatics Centre Indian Council of Medical Research‐National Institute for Research in Reproductive Health MumbaiIndia
| | - Anish Gomatam
- Molecular Simulations Group, Department of Pharmaceutical Chemistry Bombay College of Pharmacy MumbaiIndia
| | - Evans Coutinho
- Molecular Simulations Group, Department of Pharmaceutical Chemistry Bombay College of Pharmacy MumbaiIndia
| | - Susan Idicula‐Thomas
- Biomedical Informatics Centre Indian Council of Medical Research‐National Institute for Research in Reproductive Health MumbaiIndia
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8
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Shelomi M, Jacobs C, Vilcinskas A, Vogel H. The unique antimicrobial peptide repertoire of stick insects. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 103:103471. [PMID: 31634521 DOI: 10.1016/j.dci.2019.103471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 06/10/2023]
Abstract
The comparative analysis of innate immunity across different insect taxa has revealed unanticipated evolutionary plasticity, providing intriguing examples of immunity-related effector gene expansion and loss. Phasmatodea, the stick and leaf insects, is an order of hemimetabolous insects that can provide insight into ancestral innate immunity genes lost by later insect clades. We injected the stick insect Peruphasma schultei with a mixture of microbial elicitors to activate a strong immune response, followed by RNA-Seq analysis to screen for induced immunity-related effector genes. This revealed a highly diverse spectrum of antimicrobial peptides (AMPs) belonging to the attacin, coleoptericin, defensin, thaumatin, and tachystatin families. In addition, we identified a large group of short, cysteine-rich putative AMPs, some of which were strongly elicited. The immunity-related effector gene repertoire also included c-type and i-type lysozymes and several pattern-recognition proteins, such as proteins that recognize Gram-negative bacteria and peptidoglycans. Finally, we identified 45 hemolymph lipopolysaccharide-binding protein sequences, an unusually large number for insects. Taken together, our results indicate that at least some phasmids synthesize a broad spectrum of diverse AMPs that deserve further in-depth analysis.
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Affiliation(s)
- Matan Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan.
| | - Chris Jacobs
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Giessen, Germany
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Jena, Germany
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9
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Hansen IKØ, Isaksson J, Poth AG, Hansen KØ, Andersen AJC, Richard CSM, Blencke HM, Stensvåg K, Craik DJ, Haug T. Isolation and Characterization of Antimicrobial Peptides with Unusual Disulfide Connectivity from the Colonial Ascidian Synoicum turgens. Mar Drugs 2020; 18:md18010051. [PMID: 31940927 PMCID: PMC7024374 DOI: 10.3390/md18010051] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/16/2022] Open
Abstract
This study reports the isolation of two novel cysteine-rich antibacterial peptides, turgencin A and turgencin B, along with their oxidized derivatives, from the Arctic marine colonial ascidian Synoicum turgens. The peptides are post-translationally modified, containing six cysteines with an unusual disulfide connectivity of Cys1-Cys6, Cys2-Cys5, and Cys3-Cys4 and an amidated C-terminus. Furthermore, the peptides contain methionine residues resulting in the isolation of peptides with different degrees of oxidation. The most potent peptide, turgencin AMox1 with one oxidized methionine, displayed antimicrobial activity against both Gram-negative and Gram-positive bacteria with a minimum inhibitory concentration (MIC) as low as 0.4 µM against selected bacterial strains. In addition, the peptide inhibited the growth of the melanoma cancer cell line A2058 (IC50 = 1.4 µM) and the human fibroblast cell line MRC-5 (IC50 = 4.8 µM). The results from this study show that natural peptides isolated from marine tunicates have the potential to be promising drug leads.
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Affiliation(s)
- Ida K. Ø. Hansen
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (C.S.M.R.); (H.-M.B.); (K.S.)
- Correspondence: (I.K.Ø.H.); (T.H.); Tel.: +47-77-64-92-66 (I.K.Ø.H.); +47-77-64-60-71 (T.H.)
| | - Johan Isaksson
- Department of Chemistry, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway;
| | - Aaron G. Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia; (A.G.P.); (D.J.C.)
| | - Kine Ø. Hansen
- Marbio, UiT The Arctic University of Norway, Breivika, N-9037, Tromsø, Norway;
| | - Aaron J. C. Andersen
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (C.S.M.R.); (H.-M.B.); (K.S.)
| | - Céline S. M. Richard
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (C.S.M.R.); (H.-M.B.); (K.S.)
| | - Hans-Matti Blencke
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (C.S.M.R.); (H.-M.B.); (K.S.)
| | - Klara Stensvåg
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (C.S.M.R.); (H.-M.B.); (K.S.)
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia; (A.G.P.); (D.J.C.)
| | - Tor Haug
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway (C.S.M.R.); (H.-M.B.); (K.S.)
- Correspondence: (I.K.Ø.H.); (T.H.); Tel.: +47-77-64-92-66 (I.K.Ø.H.); +47-77-64-60-71 (T.H.)
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10
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Waghu FH, Idicula-Thomas S. Collection of antimicrobial peptides database and its derivatives: Applications and beyond. Protein Sci 2019; 29:36-42. [PMID: 31441165 DOI: 10.1002/pro.3714] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 01/07/2023]
Abstract
Collection of antimicrobial peptides (CAMP), CAMPSign, and ClassAMP are open-access resources that have been developed to enhance research on antimicrobial peptides (AMPs). Comprehensive information on AMPs and machine learning-based predictive models are made available for users through these resources. As of date, CAMPR3 has 10,247 sequences, 757 structures, and 114 family-specific signatures of AMPs along with associated tools for AMP sequence and structure analysis. CAMPSign uses family-specific sequence conservation, in the form of patterns and hidden Markov models for identification of AMPs. ClassAMP can be used to classify AMPs as antibacterial, antifungal, or antiviral based on sequence information. Here we describe CAMP and its derivatives and illustrate, with a few examples, the contribution of these online resources to the advancement of our current understanding of AMPs.
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Affiliation(s)
- Faiza Hanif Waghu
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Centre, ICMR-National Institute for Research in Reproductive Health, Mumbai, India
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11
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DRAMP 2.0, an updated data repository of antimicrobial peptides. Sci Data 2019; 6:148. [PMID: 31409791 PMCID: PMC6692298 DOI: 10.1038/s41597-019-0154-y] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/17/2019] [Indexed: 12/20/2022] Open
Abstract
Data Repository of Antimicrobial Peptides (DRAMP, http://dramp.cpu-bioinfor.org/) is an open-access comprehensive database containing general, patent and clinical antimicrobial peptides (AMPs). Currently DRAMP has been updated to version 2.0, it contains a total of 19,899 entries (newly added 2,550 entries), including 5,084 general entries, 14,739 patent entries, and 76 clinical entries. The update covers new entries, structures, annotations, classifications and downloads. Compared with APD and CAMP, DRAMP contains 14,040 (70.56% in DRAMP) non-overlapping sequences. In order to facilitate users to trace original references, PubMed_ID of references have been contained in activity information. The data of DRAMP can be downloaded by dataset and activity, and the website source code is also available on dedicatedly designed download webpage. Although thousands of AMPs have been reported, only a few parts have entered clinical stage. In the paper, we described several AMPs in clinical trials, including their properties, indications and clinicaltrials.gov identifiers. Finally, we provide the applications of DRAMP in the development of AMPs.
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12
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Xu J, Wang X, Xu P, Liu S, Teng F, Liu X, Zhu Q, Hua X, Gong Z, Jia X. Mass spectrometry-based peptidome profiling of human serous ovarian cancer tissues. Int J Biochem Cell Biol 2018; 107:53-61. [PMID: 30543932 DOI: 10.1016/j.biocel.2018.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/23/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Bioactive peptides existing in vivo have been considered as an important class of natural medicines for the treatment of diseases. Peptidome analysis of tissues and biofluids had provided important information about the differentially expressed bioactive peptides in vivo. METHODS Here, we analyzed the peptidome of serous ovarian cancer tissue samples and normal ovarian epithelial tissue samples by mass spectrometry and further investigated the possible bioactive peptides that were differentially expressed. RESULTS We identified 634 differentially expressed peptides, 508 of these peptides were highly abundant in serous ovarian cancer tissues, a result consistent with higher protease activity in ovarian cancer patients. The difference in preferred cleavage sites between the serous ovarian cancer tissues and normal ovarian epithelium indicated the characteristic peptidome of ovarian cancer and the nature of cancer-associated protease activity. Interestingly, KEGG pathway analysis of the peptide precursors indicated that the differentially regulated pathways in ovarian cancer are highly consistent with the pathways discovered in other cancers. Besides, we found that a proportion of the differentially expressed peptides are similar to the known immune-regulatory peptides and anti-bacterial peptides. Then we further investigated the function of the two down-regulated peptides in ovarian cancer cells and found that peptide P1DS significantly inhibited the invasion and migration of OVCAR3 and SKOV3 ovarian cancer cells. CONCLUSIONS Our results are the first to identify the differentially expressed peptides between the serous ovarian cancer tissue and the normal ovarian epithelium. Our results indicate that bioactive peptides involved in tumorigenesis are existed in vivo.
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Affiliation(s)
- Juan Xu
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Xusu Wang
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Pengfei Xu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Siyu Liu
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Fang Teng
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Xiaoguang Liu
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Qiaoying Zhu
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Xiangdong Hua
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Zhen Gong
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China
| | - Xuemei Jia
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, 210004, China.
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13
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Panya A, Yongpitakwattana P, Budchart P, Sawasdee N, Krobthong S, Paemanee A, Roytrakul S, Rattanabunyong S, Choowongkomon K, Yenchitsomanus PT. Novel bioactive peptides demonstrating anti-dengue virus activity isolated from the Asian medicinal plant Acacia Catechu. Chem Biol Drug Des 2018; 93:100-109. [PMID: 30225997 DOI: 10.1111/cbdd.13400] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 01/03/2023]
Abstract
The therapeutic activities of food-derived bioactive proteins and peptides are attracting increased attention within the research community. Medicinal plants used in traditional medicines are an excellent source of bioactive proteins and peptides, especially those traditionally prepared by water extraction for use as tea or food supplement. In this study, novel bioactive peptides were isolated from enzymatic digests of 33 Thai medicinal plants. The inhibitory activity of each against dengue virus (DENV) infection was investigated. Of 33 plants, peptides from Acacia catechu extract demonstrated the most pronounced anti-DENV activity. Half maximal inhibitory concentration of 0.18 μg/ml effectively inhibited DENV foci formation. Treatment with 1.25 μg/ml crude peptide extract could reduce virus production less than 100-fold with no observable cell toxicity. Peptide sequences were determined by high-performance liquid chromatography and liquid chromatography-tandem mass spectrometry. Two bioactive peptides isolated from Acacia catechu inhibited DENV foci formation >90% at the concentration of 50 μM; therefore, they are recommended for further investigation as antiviral peptides against DENV infection.
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Affiliation(s)
- Aussara Panya
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Petlada Yongpitakwattana
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prapaphan Budchart
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nunghathai Sawasdee
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sucheewin Krobthong
- Proteomics Research Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Atchara Paemanee
- Proteomics Research Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | | | | | - Pa-Thai Yenchitsomanus
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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