{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:58:56Z","timestamp":1787029136978,"version":"build-2736575974"},"reference-count":33,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2024,12,28]],"date-time":"2024-12-28T00:00:00Z","timestamp":1735344000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institutes of Health (NIAID)","award":["U19AI142720"],"award-info":[{"award-number":["U19AI142720"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>Recently expanded reports of multidrug-resistant fungal infections underscore the need to develop new and more efficient methods for antifungal drug discovery. A ubiquitous problem in natural product drug discovery campaigns is the rediscovery of known compounds or their relatives; accordingly, we have integrated Liquid Chromatography\u2013Tandem Mass Spectrometry (LC-MS\/MS) for structural dereplication and Yeast Chemical Genomics for bioprocess evaluation into a screening platform to identify such compounds early in the screening process. We identified 450 fractions inhibiting Candida albicans and the resistant strains of C. auris and C. glabrata among more than 40,000 natural product fractions. LC-MS\/MS and chemical genomics were then used to identify those with known chemistry and mechanisms of action. The parallel deployment of these orthogonal methods improved the detection of unwanted compound classes over the methods applied individually.<\/jats:p>","DOI":"10.3390\/molecules30010077","type":"journal-article","created":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T14:35:42Z","timestamp":1735742142000},"page":"77","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Dereplication of Natural Product Antifungals via Liquid Chromatography\u2013Tandem Mass Spectrometry and Chemical Genomics"],"prefix":"10.3390","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-4309-7735","authenticated-orcid":false,"given":"Nathaniel J.","family":"Brittin","sequence":"first","affiliation":[{"name":"Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA"},{"name":"Lachman Institute for Pharmaceutical Development, University of Wisconsin-Madison, Madison, WI 53705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3627-6274","authenticated-orcid":false,"given":"David J.","family":"Aceti","sequence":"additional","affiliation":[{"name":"Small Molecule Screening Facility, UW Carbone Cancer Center, Madison, WI 53792, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doug R.","family":"Braun","sequence":"additional","affiliation":[{"name":"Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josephine M.","family":"Anderson","sequence":"additional","affiliation":[{"name":"Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4907-1160","authenticated-orcid":false,"given":"Spencer S.","family":"Ericksen","sequence":"additional","affiliation":[{"name":"Small Molecule Screening Facility, UW Carbone Cancer Center, Madison, WI 53792, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0238-8411","authenticated-orcid":false,"given":"Scott R.","family":"Rajski","sequence":"additional","affiliation":[{"name":"Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cameron R.","family":"Currie","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON L8S 4L8, Canada"},{"name":"Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Andes","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA"},{"name":"Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA"},{"name":"William S. Middleton Memorial VA Hospital, Madison, WI 53705, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4502-3084","authenticated-orcid":false,"given":"Tim S.","family":"Bugni","sequence":"additional","affiliation":[{"name":"Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA"},{"name":"Lachman Institute for Pharmaceutical Development, University of Wisconsin-Madison, Madison, WI 53705, USA"},{"name":"Small Molecule Screening Facility, UW Carbone Cancer Center, Madison, WI 53792, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,12,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1038\/s41579-022-00720-1","article-title":"Tackling the Emerging Threat of Antifungal Resistance to Human Health","volume":"20","author":"Fisher","year":"2022","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"165rv13","DOI":"10.1126\/scitranslmed.3004404","article-title":"Hidden Killers: Human Fungal Infections","volume":"4","author":"Brown","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3390","DOI":"10.1021\/acs.chemrev.0c00199","article-title":"Antifungal Drug Resistance: Molecular Mechanisms in Candida albicans and Beyond","volume":"121","author":"Lee","year":"2021","journal-title":"Chem. Rev."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1111\/jam.15032","article-title":"A Global View on Fungal Infections in Humans and Animals: Opportunistic Infections and Microsporidioses","volume":"131","author":"Gnat","year":"2021","journal-title":"J. Appl. Microbiol."},{"key":"ref_5","unstructured":"WHO (2022). WHO Fungal Priority Pathogens List to Guide Research, Development and Public Health, World Health Organization."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1021\/acsbiomedchemau.2c00055","article-title":"Antifungal Development and the Urgency of Minimizing the Impact of Fungal Diseases on Public Health","volume":"3","author":"Bezerra","year":"2023","journal-title":"ACS Bio Med Chem Au"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"i4","DOI":"10.1093\/jac\/dkx444","article-title":"Changes in the Epidemiological Landscape of Invasive Candidiasis","volume":"73","author":"Lamoth","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Rabaan, A.A., Sulaiman, T., Al-Ahmed, S.H., Buhaliqah, Z.A., Buhaliqah, A.A., AlYuosof, B., Alfaresi, M., Al Fares, M.A., Alwarthan, S., and Alkathlan, M.S. (2023). Potential Strategies to Control the Risk of Antifungal Resistance in Humans: A Comprehensive Review. Antibiotics, 12.","DOI":"10.3390\/antibiotics12030608"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"4277","DOI":"10.1021\/ac202623g","article-title":"Microbial Strain Prioritization Using Metabolomics Tools for the Discovery of Natural Products","volume":"84","author":"Hou","year":"2012","journal-title":"Anal. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Chanana, S., Thomas, C.S., Zhang, F., Rajski, S.R., and Bugni, T.S. (2020). HCAPCA: Automated Hierarchical Clustering and Principal Component Analysis of Large Metabolomic Datasets in R. Metabolites, 10.","DOI":"10.3390\/metabo10070297"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/s41467-019-08438-0","article-title":"The Antimicrobial Potential of Streptomyces from Insect Microbiomes","volume":"10","author":"Chevrette","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2338","DOI":"10.1021\/np200254t","article-title":"Dereplication of Microbial Natural Products by LC-DAD-TOFMS","volume":"74","author":"Nielsen","year":"2011","journal-title":"J. Nat. Prod."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2636","DOI":"10.1021\/acs.jchemed.1c01212","article-title":"Incorporating LC-MS\/MS Analysis and the Dereplication of Natural Product Samples into an Upper-Division Undergraduate Laboratory Course","volume":"99","author":"Jouaneh","year":"2022","journal-title":"J. Chem. Ed."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1080\/1040841X.2021.1907302","article-title":"Microbial Symbionts of Insects as a Source of New Antimicrobials: A Review","volume":"47","author":"Cos","year":"2021","journal-title":"Crit. Rev. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1126\/science.abd6919","article-title":"A Marine Microbiome Antifungal Targets Urgent-Threat 1 Drug-Resistant Fungi","volume":"370","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1954","DOI":"10.1038\/s41596-020-0317-5","article-title":"Reproducible Molecular Networking of Untargeted Mass Spectrometry Data Using GNPS","volume":"15","author":"Aron","year":"2020","journal-title":"Nat. Protoc."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1186\/s13321-016-0174-y","article-title":"ClassyFire: Automated Chemical Classification with a Comprehensive, Computable Taxonomy","volume":"8","author":"Eisner","year":"2016","journal-title":"J. Cheminform."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1038\/s41587-020-0740-8","article-title":"Systematic Classification of Unknown Metabolites Using High-Resolution Fragmentation Mass Spectra","volume":"39","author":"Nothias","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/s41587-021-01045-9","article-title":"High-Confidence Structural Annotation of Metabolites Absent from Spectral Libraries","volume":"40","author":"Hoffmann","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/s41592-019-0344-8","article-title":"SIRIUS 4: A Rapid Tool for Turning Tandem Mass Spectra into Metabolite Structure Information","volume":"16","author":"Fleischauer","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/nature00935","article-title":"Functional Profiling of the Saccharomyces cerevisiae Genome","volume":"418","author":"Giaever","year":"2002","journal-title":"Nature"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1016\/j.cell.2006.06.040","article-title":"Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast","volume":"126","author":"Parsons","year":"2006","journal-title":"Cell"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1038\/nchembio.2436","article-title":"Functional Annotation of Chemical Libraries across Diverse Biologic Processes","volume":"13","author":"Piotrowski","year":"2017","journal-title":"Nat. Chem. Biol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/s41596-018-0099-1","article-title":"Using BEAN-Counter to Quantify Genetic Interactions from Multiplexed Barcode Sequencing Experiments","volume":"14","author":"Simpkins","year":"2019","journal-title":"Nat. Protoc."},{"key":"ref_25","first-page":"5281","article-title":"Treeview 3.0 (beta 1)\u2014Visualization and analysis of large data matrices","volume":"10","author":"Keil","year":"2016","journal-title":"Zenodo"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Simpkins, S.W., Nelson, J., Deshpande, R., Li, S.C., Piotrowski, J.S., Wilson, E.H., Gebre, A.A., Safizadeh, H., Okamoto, R., and Yoshimura, M. (2018). Predicting Bioprocess Targets of Chemical Compounds through Integration of Chemical-Genetic and Genetic Interactions. PLoS Comput. Biol., 14.","DOI":"10.1371\/journal.pcbi.1006532"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1534\/g3.117.040220","article-title":"TheCellMap.Org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network","volume":"7","author":"Usaj","year":"2017","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/nchembio.1496","article-title":"Amphotericin Forms an Extramembranous and Fungicidal Sterol Sponge","volume":"10","author":"Anderson","year":"2014","journal-title":"Nat. Chem. Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1021\/acscentsci.1c00148","article-title":"Sterol Sponge Mechanism Is Conserved for Glycosylated Polyene Macrolides","volume":"7","author":"Guo","year":"2021","journal-title":"ACS Cent. Sci."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Szomek, M., Reinholdt, P., Petersen, D., Caci, A., Kongsted, J., and W\u00fcstner, D. (2021). Direct Observation of Nystatin Binding to the Plasma Membrane of Living Cells. Biochim. Biophys. Acta Biomembr., 1863.","DOI":"10.1016\/j.bbamem.2020.183528"},{"key":"ref_31","first-page":"000988","article-title":"Evolutionary Investigations of the Biosynthetic Diversity in the Skin Microbiome Using IsaBGC","volume":"9","author":"Salamzade","year":"2023","journal-title":"Microb. Genom."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1021\/np300034c","article-title":"Universal Quantification of Structurally Diverse Natural Products Using an Evaporative Light Scattering Detector","volume":"75","author":"Adnani","year":"2012","journal-title":"J. Nat. Prod."},{"key":"ref_33","unstructured":"Hempel, J.E., Williams, C.H., and Hong, C.C. (2015). Chemical Genomic Profiling via Barcode Sequencing to Predict Compound Mode of Action. Chemical Biology: Methods and Protocols, Humana Press."}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/30\/1\/77\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T16:55:28Z","timestamp":1760115328000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/30\/1\/77"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,28]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,1]]}},"alternative-id":["molecules30010077"],"URL":"https:\/\/doi.org\/10.3390\/molecules30010077","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,28]]}}}