Artificial intelligence for natural product drug discovery

MW Mullowney, KR Duncan, SS Elsayed… - Nature Reviews Drug …, 2023 - nature.com
Developments in computational omics technologies have provided new means to access
the hidden diversity of natural products, unearthing new potential for drug discovery. In …

The critical role that spectral libraries play in capturing the metabolomics community knowledge

W Bittremieux, M Wang, PC Dorrestein - Metabolomics, 2022 - Springer
Background Spectral library searching is currently the most common approach for
compound annotation in untargeted metabolomics. Spectral libraries applicable to liquid …

Advanced analytical and informatic strategies for metabolite annotation in untargeted metabolomics

Y Cai, Z Zhou, ZJ Zhu - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
Liquid chromatography–mass spectrometry (LC–MS)-based untargeted metabolomics is
constantly challenged by large-scale and unambiguous metabolite annotation in complex …

Annotating metabolite mass spectra with domain-inspired chemical formula transformers

S Goldman, J Wohlwend, M Stražar… - Nature Machine …, 2023 - nature.com
Metabolomics studies have identified small molecules that mediate cell signaling,
competition and disease pathology, in part due to large-scale community efforts to measure …

Artificial intelligence in microbial natural product drug discovery: current and emerging role

VJ Sahayasheela, MB Lankadasari, VM Dan… - Natural product …, 2022 - pubs.rsc.org
Covering: up to the end of 2022 Microorganisms are exceptional sources of a wide array of
unique natural products and play a significant role in drug discovery. During the golden era …

Recent advances in mass spectrometry-based computational metabolomics

TMD Ebbels, JJJ van der Hooft, H Chatelaine… - Current opinion in …, 2023 - Elsevier
The computational metabolomics field brings together computer scientists, bioinformaticians,
chemists, clinicians, and biologists to maximize the impact of metabolomics across a wide …

Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools

NF de Jonge, K Mildau, D Meijer, JJR Louwen… - Metabolomics, 2022 - Springer
Background Untargeted metabolomics approaches based on mass spectrometry obtain
comprehensive profiles of complex biological samples. However, on average only 10% of …

MS2Query: reliable and scalable MS2 mass spectra-based analogue search

NF de Jonge, JJR Louwen, E Chekmeneva… - Nature …, 2023 - nature.com
Metabolomics-driven discoveries of biological samples remain hampered by the grand
challenge of metabolite annotation and identification. Only few metabolites have an …

Machine learning-assisted structure annotation of natural products based on MS and NMR data

G Hu, M Qiu - Natural Product Reports, 2023 - pubs.rsc.org
Covering: up to March 2023Machine learning (ML) has emerged as a popular tool for
analyzing the structures of natural products (NPs). This review presents a summary of the …

AI/ML-driven advances in untargeted metabolomics and exposomics for biomedical applications

LM Petrick, N Shomron - Cell Reports Physical Science, 2022 - cell.com
Metabolomics describes a high-throughput approach for measuring a repertoire of
metabolites and small molecules in biological samples. One utility of untargeted …