ArticleMolecular cell2019
Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies.
Article in Molecular cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
41 citing papers in PubMed.
- Article
- Model-based inference of enzyme inhibitions from perturbation-induced metabolic dynamics.bioRxiv : the preprint server for biology · 2026Article
- Small is big: growing impact of small molecule mass spectrometry in infectious disease drug development.mSphere · 2026Review
- Off-label and repurposed use of disulfiram beyond alcohol dependence: A systematic review of clinical and preclinical evidence.iScience · 2026Article
- A comprehensive review of cluster methods for drug-drug interaction network.Quantitative biology (Beijing, China) · 2026Review
- Metabolomics-driven prediction of antibiotic resistance: a perspective on pre-genetic intervention.npj antimicrobials and resistance · 2025Review
- Unlocking drug modes of action with multi-dimensional high-throughput metabolic profiling.Nature biotechnology · 2025Article
- A human metabolic map of pharmacological perturbations reveals drug modes of action.Nature biotechnology · 2025Article
- Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Bacteria carrying mobile colistin resistance genes and their control measures, an updated review.Archives of microbiology · 2024Review
- Review
- Arcopilins: A New Family ofJournal of medicinal chemistry · 2024Article
- Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products.Natural product reports · 2024Review
- Metabolomics in drug research and development: The recent advances in technologies and applications.Acta pharmaceutica Sinica. B · 2023Review
- Small molecule metabolites: discovery of biomarkers and therapeutic targets.Signal transduction and targeted therapy · 2023Review
- Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli.mSystems · 2023Article
- Enhancers of Host Immune Tolerance to Bacterial Infection Discovered Using Linked Computational and Experimental Approaches.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Exogenous metabolite feeding on altering antibiotic susceptibility in Gram-negative bacteria through metabolic modulation: a review.Metabolomics : Official journal of the Metabolomic Society · 2022Review
- Expanding the search for small-molecule antibacterials by multidimensional profiling.Nature chemical biology · 2022Review
- Metabolomics-based phenotypic screens for evaluation of drug synergy via direct-infusion mass spectrometry.iScience · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative to the conventional search for single-target, single-compound treatments, combination therapies can open entirely new opportunities to fight antibiotic resistance. However, combinatorial complexity prohibits experimental testing of drug combinations on a large scale, and methods to rationally design combination therapies are lagging behind. Here, we developed a combined experimental-computational approach to predict drug-drug interactions using high-throughput metabolomics. The approach was tested on 1,279 pharmacologically diverse drugs applied to the gram-negative bacterium Escherichia coli. Combining our metabolic profiling of drug response with previously generated metabolic and chemogenomic profiles of 3,807 single-gene deletion strains revealed an unexpectedly large space of inhibited gene functions and enabled rational design of drug combinations. This approach is applicable to other therapeutic areas and can unveil unprecedented insights into drug tolerance, side effects, and repurposing. The compendium of drug-associated metabolome profiles is available at https://zampierigroup.shinyapps.io/EcoPrestMet, providing a valuable resource for the microbiological and pharmacological communities.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.