{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T15:39:39Z","timestamp":1787499579959,"version":"build-2736575974"},"reference-count":53,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T00:00:00Z","timestamp":1748908800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Center for Gene Therapy and Drugs Based on RNA Technology\u2014MUR","award":["CN_00000041"],"award-info":[{"award-number":["CN_00000041"]}]},{"name":"NextGeneration EU program","award":["CN_00000041"],"award-info":[{"award-number":["CN_00000041"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Autophagy plays a central role in cellular degradation and recycling pathways involving the formation of autophagosomes from cellular components. The Atg8 protein family, particularly LC3, is essential to this process, and dysregulation has been implicated in many diseases (including cancer). Furthermore, therapeutic strategies targeting Atg8 proteins like LC3 can be advanced by exploiting the expanding knowledge of the \u201cLC3 interacting region\u201d (LIR) domain to develop inhibitory ligands. Here, we report a computational approach to design novel peptides that inhibit LC3B. The LIR domain of a known LC3B binder (the FYCO1 peptide) was used as a starting point to design new peptides with unnatural amino acids and conformational restraints. Accomplishing molecular dynamics simulations and binding free energy calculations on the complex of peptide\u2013LC3B, new promising FYCO1 analogs were selected. These peptides were synthesized and investigated by biophysical and biological experiments. Their ability to affect cellular viability was determined in different cancer cell lines (prostate cancer, breast cancer, lung cancer, and melanoma). In addition, the ability to inhibit autophagy and enhance the apoptotic activity of Docetaxel was evaluated in PC-3 prostate cancer cells. In conclusion, this research presents a rational approach to designing and developing LC3B inhibitors based on the FYCO1-LIR domain. The designed peptides hold promise as potential therapeutic agents for cancer and as tools for further elucidating the role of LC3B in autophagy.<\/jats:p>","DOI":"10.3390\/ijms26115365","type":"journal-article","created":{"date-parts":[[2025,6,3]],"date-time":"2025-06-03T11:55:52Z","timestamp":1748951752000},"page":"5365","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["FYCO1 Peptide Analogs: Design and Characterization of Autophagy Inhibitors as Co-Adjuvants in Taxane Chemotherapy of Prostate Cancer"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6282-4273","authenticated-orcid":false,"given":"Enrico Mario Alessandro","family":"Fassi","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences, Universit\u00e0 degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6456-5869","authenticated-orcid":false,"given":"Roberta Manuela","family":"Moretti","sequence":"additional","affiliation":[{"name":"Department of Pharmacological and Biomolecular Sciences, Universit\u00e0 degli Studi di Milano, Via G. Balzaretti 9, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3739-6278","authenticated-orcid":false,"given":"Marina","family":"Montagnani Marelli","sequence":"additional","affiliation":[{"name":"Department of Pharmacological and Biomolecular Sciences, Universit\u00e0 degli Studi di Milano, Via G. Balzaretti 9, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariangela","family":"Garofalo","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical and Pharmacological Sciences, Universit\u00e0 di Padova, Via F. Marzolo 5, 35131 Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1640-7238","authenticated-orcid":false,"given":"Alessandro","family":"Gori","sequence":"additional","affiliation":[{"name":"National Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche (SCITEC-CNR), Via M. Bianco 9, 20131 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7789-2877","authenticated-orcid":false,"given":"Cristiano","family":"Pesce","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical and Pharmacological Sciences, Universit\u00e0 di Padova, Via F. Marzolo 5, 35131 Padova, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-0093-0945","authenticated-orcid":false,"given":"Marco","family":"Albani","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, Universit\u00e0 degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erica Ginevra","family":"Milano","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, Universit\u00e0 degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8633-1032","authenticated-orcid":false,"given":"Jacopo","family":"Sgrignani","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine (IRB), Via Chiesa 5, 6500 Bellinzona, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Cavalli","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine (IRB), Via Chiesa 5, 6500 Bellinzona, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3261-9356","authenticated-orcid":false,"given":"Giovanni","family":"Grazioso","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, Universit\u00e0 degli Studi di Milano, Via L. Mangiagalli 25, 20133 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature09204","article-title":"Network Organization of the Human Autophagy System","volume":"466","author":"Behrends","year":"2010","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1038\/ncb1007-1102","article-title":"Autophagosome Formation: Core Machinery and Adaptations","volume":"9","author":"Xie","year":"2007","journal-title":"Nat. Cell Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrmicro3160","article-title":"Bacteria-Autophagy Interplay: A Battle for Survival","volume":"12","author":"Huang","year":"2014","journal-title":"Nat. Rev. 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