{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T03:24:45Z","timestamp":1788319485291,"version":"build-2803163510"},"reference-count":74,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2020,10,29]],"date-time":"2020-10-29T00:00:00Z","timestamp":1603929600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["IG-15267"],"award-info":[{"award-number":["IG-15267"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["19050"],"award-info":[{"award-number":["19050"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003407","name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","doi-asserted-by":"publisher","award":["PRIN 2017SBFHLH"],"award-info":[{"award-number":["PRIN 2017SBFHLH"]}],"id":[{"id":"10.13039\/501100003407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>NF-Y is a transcription factor (TF) comprising three subunits (NF-YA, NF-YB, NF-YC) that binds with high specificity to the CCAAT sequence, a widespread regulatory element in gene promoters of prosurvival, cell-cycle-promoting, and metabolic genes. Tumor cells undergo \u201cmetabolic rewiring\u201d through overexpression of genes involved in such pathways, many of which are under NF-Y control. In addition, NF-YA appears to be overexpressed in many tumor types. Thus, limiting NF-Y activity may represent a desirable anti-cancer strategy, which is an ongoing field of research. With virtual-screening docking simulations on a library of pharmacologically active compounds, we identified suramin as a potential NF-Y inhibitor. We focused on suramin given its high water-solubility that is an important factor for in vitro testing, since NF-Y is sensitive to DMSO. By electrophoretic mobility shift assays (EMSA), isothermal titration calorimetry (ITC), STD NMR, X-ray crystallography, and molecular dynamics (MD) simulations, we showed that suramin binds to the histone fold domains (HFDs) of NF-Y, preventing DNA-binding. Our analyses, provide atomic-level detail on the interaction between suramin and NF-Y and reveal a region of the protein, nearby the suramin-binding site and poorly conserved in other HFD-containing TFs, that may represent a promising starting point for rational design of more specific and potent inhibitors with potential therapeutic applications.<\/jats:p>","DOI":"10.3390\/cells9112370","type":"journal-article","created":{"date-parts":[[2020,10,29]],"date-time":"2020-10-29T21:21:00Z","timestamp":1604006460000},"page":"2370","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Structural Basis of Inhibition of the Pioneer Transcription Factor NF-Y by Suramin"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3729-0200","authenticated-orcid":false,"given":"Valentina","family":"Nardone","sequence":"first","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3287-9024","authenticated-orcid":false,"given":"Antonio","family":"Chaves-Sanjuan","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7613-2275","authenticated-orcid":false,"given":"Michela","family":"Lapi","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3670-6262","authenticated-orcid":false,"given":"Cristina","family":"Airoldi","sequence":"additional","affiliation":[{"name":"Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5035-5174","authenticated-orcid":false,"given":"Andrea","family":"Saponaro","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9038-7768","authenticated-orcid":false,"given":"Sebastiano","family":"Pasqualato","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5346-6096","authenticated-orcid":false,"given":"Diletta","family":"Dolfini","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9923-8590","authenticated-orcid":false,"given":"Carlo","family":"Camilloni","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5082-5295","authenticated-orcid":false,"given":"Andrea","family":"Bernardini","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2465-8881","authenticated-orcid":false,"given":"Nerina","family":"Gnesutta","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberto","family":"Mantovani","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3718-2165","authenticated-orcid":false,"given":"Marco","family":"Nardini","sequence":"additional","affiliation":[{"name":"Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,10,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/S0378-1119(99)00368-6","article-title":"The molecular biology of the CCAAT-binding factor 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