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Screening for Potential Antiviral Compounds from Cyanobacterial Secondary Metabolites Using Machine Learning.
Mar Drugs
November 2024
Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China.
The secondary metabolites of seawater and freshwater blue-green algae are a rich natural product pool containing diverse compounds with various functions, including antiviral compounds; however, high-efficiency methods to screen such compounds are lacking. Advanced virtual screening techniques can significantly reduce the time and cost of novel antiviral drug identification. In this study, we used a cyanobacterial secondary metabolite library as an example and trained three models to identify compounds with potential antiviral activity using a machine learning method based on message-passing neural networks.
View Article and Find Full Text PDFNetwork for knowledge Organization (NEKO): An AI knowledge mining workflow for synthetic biology research.
Metab Eng
January 2025
Department of Energy, Environment, and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, United States. Electronic address:
Large language models (LLMs) can complete general scientific question-and-answer, yet they are constrained by their pretraining cut-off dates and lack the ability to provide specific, cited scientific knowledge. Here, we introduce Network for Knowledge Organization (NEKO), a workflow that uses LLM Qwen to extract knowledge through scientific literature text mining. When user inputs a keyword of interest, NEKO can generate knowledge graphs to link bioinformation entities and produce comprehensive summaries from PubMed search.
View Article and Find Full Text PDFCyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria.
ISME J
January 2024
Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan.
Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored.
View Article and Find Full Text PDFTransdisciplinary approaches for the study of cyanobacteria and cyanotoxins.
Curr Res Microb Sci
October 2024
Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P.85000, Col. Centro, Ciudad Obregón, Sonora, Mexico.
Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring.
View Article and Find Full Text PDFRibosomal peptides with polycyclic isoprenoid moieties.
Chem
October 2024
Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog Weg 4, 8093 Zürich, Switzerland.
Isoprenoid modifications of proteins and peptides serve fundamental biological functions and are of therapeutic interest. While C (farnesyl) and C (geranylgeranyl) moieties are prevalent among proteins, known ribosomal peptide prenylations involve shorter-chain units not exceeding farnesyl in size. To our knowledge, cyclized terpene moieties have not been reported from either biomolecule class.
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