{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T20:35:36Z","timestamp":1789850136156,"version":"4.0.1"},"reference-count":85,"publisher":"American Chemical Society (ACS)","issue":"48","license":[{"start":{"date-parts":[[2015,11,19]],"date-time":"2015-11-19T00:00:00Z","timestamp":1447891200000},"content-version":"vor","delay-in-days":365,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["CA113746"],"award-info":[{"award-number":["CA113746"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000078","name":"Division of Materials Research","doi-asserted-by":"publisher","award":["DMR 1306154"],"award-info":[{"award-number":["DMR 1306154"]}],"id":[{"id":"10.13039\/100000078","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000097","name":"National Center for Research Resources","doi-asserted-by":"publisher","award":["NCRR-P20-RR15566"],"award-info":[{"award-number":["NCRR-P20-RR15566"]}],"id":[{"id":"10.13039\/100000097","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Among the different histone deacetylase (HDAC) isozymes, HDAC8 is the most highly malleable enzyme, and it exhibits the potential to accommodate structurally diverse ligands (albeit with moderate binding affinities) in its active site pocket. To probe the molecular basis of this feature, we performed detailed thermodynamic studies of the binding of structurally similar ligands, which differed with respect to the \u201ccap\u201d, \u201clinker\u201d, and \u201cmetal-binding\u201d regions of the suberoylanilide hydroxamic acid (SAHA) pharmacophore, to HDAC8. The experimental data revealed that although the enthalpic (\u0394H\u00b0) and entropic (\u0394S\u00b0) changes for the binding of individual SAHA analogues to HDAC8 were substantially different, their binding free energies (\u0394G\u00b0) were markedly similar, conforming to a strong enthalpy\u2013entropy compensation effect. This effect was further observed in the temperature-dependent thermodynamics of binding of all SAHA analogues to the enzyme. Notably, in contrast to other metalloenzymes, our isothermal titration calorimetry experiments (performed in different buffers of varying ionization enthalpies) suggest that depending on the ligand, its zinc-binding group may or may not be deprotonated upon the binding to HDAC8. Furthermore, the heat capacity changes (\u0394Cp\u00b0) associated with the ligand binding to HDAC8 markedly differed from one SAHA analogue to the other, and such features could primarily be rationalized in light of the dynamic flexibility in the enzyme structure in conjunction with the reorganization of the active site resident water molecules. Arguments are presented that although the binding thermodynamic features described above would facilitate identification of weak to moderately tight-binding HDAC8 inhibitors (by a high-throughput and\/or virtual screening of libraries of small molecules), they would pose major challenges for the structure-based rational design of highly potent and isozyme-selective inhibitors of human HDAC8.<\/jats:p>","DOI":"10.1021\/bi500711x","type":"journal-article","created":{"date-parts":[[2014,11,19]],"date-time":"2014-11-19T10:22:18Z","timestamp":1416392538000},"page":"7445-7458","source":"Crossref","is-referenced-by-count":15,"title":["Thermodynamics of Binding of Structurally Similar\nLigands to Histone Deacetylase 8 Sheds Light on Challenges in the\nRational Design of Potent and Isozyme-Selective Inhibitors of the\nEnzyme"],"prefix":"10.1021","volume":"53","author":[{"given":"Raushan K.","family":"Singh","sequence":"first","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takayoshi","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Kyoto Prefectural University of Medicine , , ,","place":["Kyoto, Japan, 603-8334"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanmay","family":"Mandal","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Narayanaganesh","family":"Balsubramanian","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manas","family":"Haldar","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dustin J.","family":"Mueller","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerrod A.","family":"Strode","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gregory","family":"Cook","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanku","family":"Mallik","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D. K.","family":"Srivastava","sequence":"additional","affiliation":[{"name":"North Dakota State University , , , ,","place":["Fargo, North Dakota, United States, 58102"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2014,11,19]]},"reference":[{"key":"2026090213165852700_cit1","volume-title":"Structure\nand Mechanism in Protein Science: A Guide to Enzyme Catalysis and\nProtein Folding","author":"Fersht","year":"1998","edition":"1"},{"key":"2026090213165852700_cit2","volume-title":"Novel\nTherapeutic Proteins: Selected Case Studies","author":"Dembowsky","year":"2001","edition":"1"},{"key":"2026090213165852700_cit3","volume-title":"Structure-Based Drug Design: Thermodynamics, Modeling, and Strategy\n(Biotechnology Intelligence Unit)","author":"Ladbury","year":"1997","edition":"1"},{"key":"2026090213165852700_cit4","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1038\/nrd1129","article-title":"Implications\nof protein flexibility for drug discovery","volume":"2","author":"Teague","year":"2003","journal-title":"Nat.\nRev. 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