{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T01:31:02Z","timestamp":1786325462542,"version":"build-2736575974"},"reference-count":37,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,8]],"date-time":"2026-08-08T00:00:00Z","timestamp":1786147200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pharmaceuticals"],"abstract":"<jats:p>Background\/Objectives: Boronic acid-based proteasome inhibitors (BABPIs) including Bortezomib, Ixazomib, and Delanzomib are clinically relevant anticancer agents whose mechanism of action depends on direct interaction between the boronic acid warhead and the threonine residue at the first position (Thr1), leading to the formation of covalent tetrahedral complex. Although the formation of this complex is well studied, the subsequent behavior of the boronic acid warhead, particularly the possible formation of monoanionic boronate species through deprotonation of one of the two boronic hydroxyl groups, remains unexplored. Therefore, the present study addresses whether the formation of Thr1-OH and a monoanionic boronate species is thermodynamically favorable and which of the two hydroxyl groups is more favorable for deprotonation. Methods: Density Functional Theory (DFT) calculations at the B3LYP\/6-311+G(d,p) level, combined with the Polarizable Continuum Model (PCM), were used to study two competing deprotonation pathways for the inhibitors and for a simplified warhead model. To mimic the proteasome environment, reactions were modeled in different polar media\u2014diethyl ether (\u03b5 = 4), methanol (\u03b5 = 33), and water (\u03b5 = 78). Results: Our DFT calculations confirmed that the covalent tetrahedral complex could convert into Thr1-OH and a monoanionic boronate species, representing the deprotonation of one of the boronic hydroxyl groups. Deprotonation via pathway 1 is more favorable than deprotonation via pathway 2 for all inhibitors, especially in polar solvents. Bortezomib demonstrated a strong preference for -OH1 deprotonation with \u2206\u2206G \u2248 \u22127 kcal\u00b7mol\u22121. In contrast, Ixazomib, Delanzomib, and the simplified warhead model showed smaller \u2206\u2206G values (\u2248\u22122 kcal\u00b7mol\u22121), within the method\u2019s uncertainty (\u00b12 kcal\u00b7mol\u22121), suggesting both deprotonation modes under physiological conditions. Conclusions: These results provide comparative thermodynamic insight into the deprotonation behavior of BABPIs, suggesting that the two hydroxyl groups are not equivalent during deprotonation. This finding offers a physicochemical framework that may support the rational design of next-generation BABPIs.<\/jats:p>","DOI":"10.3390\/ph19081251","type":"journal-article","created":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T01:20:03Z","timestamp":1786324803000},"page":"1251","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Thermodynamic Preference Between Deprotonation Pathways in Boronic Acid-Based Proteasome Inhibitors: Insights from a DFT Study"],"prefix":"10.3390","volume":"19","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":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8988-0072","authenticated-orcid":false,"given":"Iliyan","family":"Dimitrov","sequence":"additional","affiliation":[{"name":"Department of Medical Biochemistry, Faculty of Pharmacy, Medical University of Plovdiv, 15A Vassil Aprilov Blvd., 4002 Plovdiv, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ovanes","family":"Muradyan","sequence":"additional","affiliation":[{"name":"Medical Faculty, Medical University of Plovdiv, 15A Vassil Aprilov Blvd., 4002 Plovdiv, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8305-413X","authenticated-orcid":false,"given":"Vassil","family":"Delchev","sequence":"additional","affiliation":[{"name":"Department of Physical Chemistry, Faculty of Chemistry, Plovdiv University \u201cPaisii Hilendarski\u201d, 24 Tsar Asen Str., 4000 Plovdiv, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1146\/annurev.biophys.28.1.295","article-title":"The proteasome","volume":"28","author":"Bochtler","year":"1999","journal-title":"Annu. 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