{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T03:27:09Z","timestamp":1777087629733,"version":"3.51.4"},"reference-count":53,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T00:00:00Z","timestamp":1768435200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>HDAC8 is a histone deacetylase enzyme that plays a key role in the development of various diseases in humans, including cancers, neurodegenerative diseases, and alcohol use disorder. Although HDAC8 is classified as a Zn2+-dependent metalloenzyme, available data regarding the affinity of other biologically relevant ions, such as Fe2+, Ni2+, Co2+, and Mg2+, for the HDAC8 enzyme active site remain unclear and contradictory. The mechanism by which these ions compete with Zn2+ for the HDAC8 active site is not well understood. In this study, we performed density functional theory (DFT) calculations at the B3LYP\/6-31+G(d) level of theory, combined with polarizable continuum model computations (PCM) in water (\u03b5 = 78) and methanol (\u03b5 = 32). The results show that Zn2+ remains the thermodynamically preferred cofactor across all modeled reactions. Although Fe2+ and Co2+ gain partial stabilization upon increasing coordination number, the associated entropic and desolvation penalties prevent them from outcompeting Zn2+ under physiologically relevant conditions. Only a limited number of substitution reactions for Fe2+ and Co2+ yield \u2206G values near thermodynamic neutrality, and only in specific coordination states. In contrast, all modeled Ni2+ substitution reactions are unfavorable, and Mg2+ is strongly excluded from the HDAC8 active site in all reactions. The resulting metal preference hierarchy\u2014Zn2+ &gt; Co2+ \u2248 Fe2+ &gt; Ni2+ &gt; Mg2+\u2014supports experimental observations and clarifies the intrinsic selectivity of the HDAC8 enzyme towards Zn2+. These insights provide a molecular basis for understanding HDAC8 metallo-regulation and may guide the rational design of novel, isoform-specific HDACi with improved binding properties.<\/jats:p>","DOI":"10.3390\/molecules31020306","type":"journal-article","created":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T11:13:21Z","timestamp":1768475601000},"page":"306","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Metal Preference Hierarchy in the HDAC8 Active Site: A DFT Study"],"prefix":"10.3390","volume":"31","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3637-6897","authenticated-orcid":false,"given":"Nikolay","family":"Toshev","sequence":"first","affiliation":[{"name":"Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vassil Aprilov Blvd, 4002 Plovdiv, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9344-9282","authenticated-orcid":false,"given":"Diana","family":"Cheshmedzhieva","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry and Pharmacy, Sofia University \u201cSt. Kliment Ohridski\u201d, 1 James Bourchier Blvd, 1164 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6423-5998","authenticated-orcid":false,"given":"Yordanka","family":"Uzunova","sequence":"additional","affiliation":[{"name":"Department of Bioorganic Chemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vassil Aprilov Blvd, 4002 Plovdiv, Bulgaria"},{"name":"Research Institute, Medical University of Plovdiv, 15A Vassil Aprilov Blvd, 4002 Plovdiv, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-9527-9854","authenticated-orcid":false,"given":"Kristiyan","family":"Velichkov","sequence":"additional","affiliation":[{"name":"Medical Faculty, Medical University of Plovdiv, 15A Vassil Aprilov Blvd, 4002 Plovdiv, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Todor","family":"Dudev","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical and Applied Organic Chemistry, Faculty of Chemistry and Pharmacy, Sofia University \u201cSt. Kliment Ohridski\u201d, 1 James Bourchier Blvd, 1164 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.cell.2007.02.005","article-title":"Chromatin modifications and their function","volume":"128","author":"Kouzarides","year":"2007","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.molonc.2012.07.003","article-title":"Histone deacetylases and cancer","volume":"6","author":"Parra","year":"2012","journal-title":"Mol. 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