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Zancolli G, von Reumont BM, Anderluh G, Caliskan F, Chiusano ML, Fröhlich J, Hapeshi E, Hempel BF, Ikonomopoulou MP, Jungo F, Marchot P, de Farias TM, Modica MV, Moran Y, Nalbantsoy A, Procházka J, Tarallo A, Tonello F, Vitorino R, Zammit ML, Antunes A. Web of venom: exploration of big data resources in animal toxin research. Gigascience 2024; 13:giae054. [PMID: 39250076 PMCID: PMC11382406 DOI: 10.1093/gigascience/giae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/01/2024] [Accepted: 07/13/2024] [Indexed: 09/10/2024] Open
Abstract
Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.
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Affiliation(s)
- Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Goethe University Frankfurt, Faculty of Biological Sciences, 60438 Frankfurt, Germany
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Figen Caliskan
- Department of Biology, Faculty of Science, Eskisehir Osmangazi University, 26040 Eskişehir, Turkey
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University Federico II of Naples, 80055 Portici, Naples, Italy
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Jacob Fröhlich
- Veterinary Center for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Evroula Hapeshi
- Department of Health Sciences, School of Life and Health Sciences, University of Nicosia, 1700 Nicosia, Cyprus
| | - Benjamin-Florian Hempel
- Veterinary Center for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Maria P Ikonomopoulou
- Madrid Institute of Advanced Studies in Food, Precision Nutrition & Aging Program, 28049 Madrid, Spain
| | - Florence Jungo
- SIB Swiss Institute of Bioinformatics, Swiss-Prot Group, 1211 Geneva, Switzerland
| | - Pascale Marchot
- Laboratory Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille University, Centre National de la Recherche Scientifique, Faculté des Sciences, Campus Luminy, 13288 Marseille, France
| | - Tarcisio Mendes de Farias
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 00198 Rome, Italy
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Ayse Nalbantsoy
- Engineering Faculty, Bioengineering Department, Ege University, 35100 Bornova-Izmir, Turkey
| | - Jan Procházka
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, 252 50 Vestec, Czech Republic
| | - Andrea Tarallo
- Institute of Research on Terrestrial Ecosystems (IRET), National Research Council (CNR), 73100 Lecce, Italy
| | - Fiorella Tonello
- Neuroscience Institute, National Research Council (CNR), 35131 Padua, Italy
| | - Rui Vitorino
- Department of Medical Sciences, iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Mark Lawrence Zammit
- Department of Clinical Pharmacology & Therapeutics, Faculty of Medicine & Surgery, University of Malta, 2090 Msida, Malta
- Malta National Poisons Centre, Malta Life Sciences Park, 3000 San Ġwann, Malta
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
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Salinas-Restrepo C, Naranjo-Duran AM, Quintana J, Bueno J, Guzman F, Hoyos Palacio LM, Segura C. Short Antimicrobial Peptide Derived from the Venom Gland Transcriptome of Pamphobeteus verdolaga Increases Gentamicin Susceptibility of Multidrug-Resistant Klebsiella pneumoniae. Antibiotics (Basel) 2023; 13:6. [PMID: 38275316 PMCID: PMC10812672 DOI: 10.3390/antibiotics13010006] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 01/27/2024] Open
Abstract
Infectious diseases account for nine percent of annual human deaths, and the widespread emergence of antimicrobial resistances threatens to significantly increase this number in the coming decades. The prospect of antimicrobial peptides (AMPs) derived from venomous animals presents an interesting alternative for developing novel active pharmaceutical ingredients (APIs). Small, cationic and amphiphilic peptides were predicted from the venom gland transcriptome of Pamphobeteus verdolaga using a custom database of the arthropod's AMPs. Ninety-four candidates were chemically synthesized and screened against ATCC® strains of Escherichia coli and Staphylococcus aureus. Among them, one AMP, named PvAMP66, showed broad-spectrum antimicrobial properties with selectivity towards Gram-negative bacteria. It also exhibited activity against Pseudomonas aeruginosa, as well as both an ATCC® and a clinically isolated multidrug-resistant (MDR) strain of K. pneumoniae. The scanning electron microscopy analysis revealed that PvAMP66 induced morphological changes of the MDR K. pneumoniae strain suggesting a potential "carpet model" mechanism of action. The isobologram analysis showed an additive interaction between PvAMP66 and gentamicin in inhibiting the growth of MDR K. pneumoniae, leading to a ten-fold reduction in gentamicin's effective concentration. A cytotoxicity against erythrocytes or peripheral blood mononuclear cells was observed at concentrations three to thirteen-fold higher than those exhibited against the evaluated bacterial strains. This evidence suggests that PvAMP66 can serve as a template for the development of AMPs with enhanced activity and deserves further pre-clinical studies as an API in combination therapy.
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Affiliation(s)
- Cristian Salinas-Restrepo
- Grupo Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 050012, Colombia; (C.S.-R.); (A.M.N.-D.)
| | - Ana María Naranjo-Duran
- Grupo Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 050012, Colombia; (C.S.-R.); (A.M.N.-D.)
| | - Juan Quintana
- Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050012, Colombia;
| | - Julio Bueno
- Grupo Reproducción, Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia;
| | - Fanny Guzman
- Núcleo Biotecnología Curauma (NBC), Pontificia Universidad Católica de Valparaíso, Valparaíso 3100000, Chile;
| | - Lina M. Hoyos Palacio
- Escuela de Ciencias de la Salud, Grupo de Investigación Biología de Sistemas, Universidad Pontificia Bolivariana, Medellín 050031, Colombia;
| | - Cesar Segura
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
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