User:Asif Hossain/Sandbox 1: Difference between revisions

There are four major classes of HDAC proteins (I,II, III, and IV). Other than the Class III “[https://en.wikipedia.org/wiki/Sirtuin sirtuins]” that utilize a [https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/2016/bichaw.2016.55.issue-11/acs.biochem.5b01210/20160316/images/medium/bi-2015-01210h_0006.gif NAD⁺ cofactor-dependent mechanism], all other HDAC classes use Zn²⁺-assisted catalysis through mechanisms (Figure 3) reminiscent of a typical [https://en.wikipedia.org/wiki/Serine_protease serine protease].<ref name="DesJarlais, R., & Tummino, P. J.">DesJarlais, R., & Tummino, P. J. (2016). Role of histone-modifying enzymes and their complexes in regulation of chromatin biology. Biochemistry, 55(11), 1584-1599. https://doi.org/10.1021/acs.biochem.5b01210 </ref> While Classes I, II, and IV do have some major distinctions such as size of the protein, in general, they share homology at the catalytic site. HDAC 8 is classified as a Class I HDAC alongside HDACs 1-3. In fact, within Class I HDACs,  there are many invariant residues involved in the catalytic site (such as His-Asp dyads), Zn-binding, and ligand binding pocket (such as Asp101) (Figure 1). <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref>  

The crystal structure of human HDAC8 was determined using x-ray crystallography at a 2.0Å resolution. <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref> The structure includes two structural K⁺ ion and one catalytic Zn²⁺ ion. HDAC8 is bound to a [https://en.wikipedia.org/wiki/P53 p-53] <scene name='81/811084/Ligand/9'>derived diacetylated peptide substrate</scene> as opposed to the natural histone substrate. This peptide includes a <scene name='81/811084/Coumarin/2'>fluorescent coumarin ring</scene> likely used in past kinetic assays. The HDAC8 is made up of a <scene name='81/811084/Beta_sheets/6'>β-sheet</scene> with eight parallel β-strands located between 13 <scene name='81/811084/Alpha_helicesv2/4'>α-helices</scene>. The HDAC8 consists of 377 amino acids.  <ref name="Somoza"> Somoza J, Skene R. Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure, 12(7), 1325-1334.2004. https://doi.org/10.1016/j.str.2004.04.012 </ref>

The pentacoordinated Zn²⁺ ion involved in the metalloenzyme catalysis is tethered to the protein through interactions with <scene name='81/811085/Zinc_binding/2'>Asp178, His180, and Asp267</scene> . This positions the metal ion to favorably interact with the catalytic water and acetylated lysine substrate. <ref name="Vannini, A., Volpari, C., Gallinari, P.">Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., ... & Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8–substrate complex. EMBO reports, 8(9), 879-884. https://doi.org/10.1038/sj.embor.7401047 </ref> The Zn²⁺ ion lowers the pKa of a water molecule that activates it as a nucleophile. By binding to both the nucleophile and the substrate simultaneously, the Zn²⁺ ion also assists the deacetylation process by lowering the entropy of the reaction. This polarizes the carbonyl of the acetyl-lysine and stabilizes the transition state.<ref name="Somoza">Somoza J, Skene R. Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure, 12(7), 1325-1334.2004. https://doi.org/10.1016/j.str.2004.04.012 </ref>

Besides controlling gene regulation through deacetylation of histones, HDAC8 also regulates other non-histone proteins such as chaperones, hormone receptors and signaling molecules. <ref name="Eckschlager">Eckschlager T, Plch, J, Stiborova M, Hrabeta J.Histone deacetylase inhibitors as anticancer drugs. International journal of molecular sciences, 18(7), 1414. 2017. https://dx.doi.org/10.3390%2Fijms18071414</ref> Thus, it has influences on protein stability and interactions between other proteins and DNA. HDAC8 can therefore affect the regulation of cell proliferation and cell death. These processes are typically being altered in cancer cells and that makes HDAC enzymes an interesting potential target for cancer drugs. HDAC inhibitors have been shown to be promising cancer drug agent as the HDAC inhibitors (HDACi) cease tumor growth in cancer cells by either making them differentiate, undergo apoptosis or upregulate cell cycle arrest proteins. <ref name="Eckschlager">Eckschlager T, Plch, J, Stiborova M, Hrabeta J.Histone deacetylase inhibitors as anticancer drugs. International journal of molecular sciences, 18(7), 1414. 2017. https://dx.doi.org/10.3390%2Fijms18071414</ref> One way the HDAC inhibitors cease tumor growth is by the reactivation of the transcription factor, [https://en.wikipedia.org/wiki/RUNX3 RUNX3], a known tumor suppressor. HDACi increases the acetylation of the protein and as the stability of RUNX3 is dependent on the acetylation status of the protein, the increased acetylation or HDAC inhibition will enhance the protein stability. A number of HDAC inhibitors have been purified from natural sources or synthesized and at least four structurally different inhibitor classes have been characterized: hydroxamates, cyclic peptides, aliphatic acids and benzamides. The Vorinostat (within the hydroxamate class) has been FDA-approved for treatment of cancer. A HDAC class 1 hydroxamic acid, compound 1 (Figure 3), <scene name='81/811087/Inhibitor_and_zinc_binding/13'>binds to the zinc ion</scene> in a bidendate fashion while making hydrogen bonds to important residues as His142, His143 and Tyr306 at the active site of HDAC8. Thus, the HDAC inhibitors can be used as antagonists to prevent the functioning of HDAC8 in cancer treatment. <ref name="Vannini, A., Volpari, C., Filocamo, G.">Vannini, A., Volpari, C., Filocamo, G., Casavola, E. C., Brunetti, M., Renzoni, D., ... & Steinkühler, C. (2004). Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor. Proceedings of the National Academy of Sciences, 101(42), 15064-15069. https://dx.doi.org/10.1073%2Fpnas.0404603101</ref>

Asif Hossain

Sean O'Brien

Josephine Thestrup