title: Variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to HDAC8.
abstract: The macrocyclic depsipeptide Largazole is a potent inhibitor of metal-dependent histone deacetylases (HDACs), some of which are drug targets for cancer chemotherapy. Indeed, Largazole partially resembles Romidepsin (FK228), a macrocyclic depsipeptide already approved for clinical use. Each inhibitor contains a pendant side chain thiol that coordinates to the active site Zn(2+) ion, as observed in the X-ray crystal structure of the HDAC8-Largazole complex [Cole, K. E., Dowling, D. P., Boone, M. A., Phillips, A. J., and Christianson, D. W. (2011) J. Am. Chem. Soc. 133, 12474]. Here, we report the X-ray crystal structures of HDAC8 complexed with three synthetic analogues of Largazole in which the depsipeptide ester is replaced with a rigid amide linkage. In two of these analogues, a six-membered pyridine ring is also substituted (with two different orientations) for the five-membered thiazole ring in the macrocycle skeleton. The side chain thiol group of each analogue coordinates to the active site Zn(2+) ion with nearly ideal geometry, thereby preserving the hallmark structural feature of inhibition by Largazole. Surprisingly, in comparison with the binding of Largazole, these analogues trigger alternative conformational changes in loops L1 and L2 flanking the active site. However, despite these structural differences, inhibitory potency is generally comparable to, or just moderately less than, the inhibitory potency of Largazole. Thus, this study reveals important new structure-affinity relationships for the binding of macrocyclic inhibitors to HDAC8.
authors: †Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States.
authors: Christophe
authors: C
authors: Decroos
authors: ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States.
authors: Dane J
authors: DJ
authors: Clausen
authors: §Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.
authors: Brandon E
authors: BE
authors: Haines
authors: §Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.|∥Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
authors: Olaf
authors: O
authors: Wiest
authors: ‡Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States.|⊥University of Colorado Cancer Center, Aurora, Colorado 80045, United States.
authors: Robert M
authors: RM
authors: Williams
authors: †Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States.
authors: David W
authors: DW
authors: Christianson
mesh_terms: D020134:Catalytic Domain / Q000235:genetics; D018360:Crystallography, X-Ray; D047630:Depsipeptides / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology; D056572:Histone Deacetylase Inhibitors / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology; D006655:Histone Deacetylases / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000235:genetics; D013844:Thiazoles / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology
chemical_list: D047630:Depsipeptides; D056572:Histone Deacetylase Inhibitors; D011994:Recombinant Proteins; D012097:Repressor Proteins; D013844:Thiazoles; C527895:largazole; C409470:HDAC8 protein, human; D006655:Histone Deacetylases