Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking.
J Biomol Struct Dyn
; 37(3): 584-610, 2019 Feb.
Article
em En
| MEDLINE
| ID: mdl-29447615
Histone deacetylases (HDACs) are a family of proteins whose main function is the removal of acetyl groups from lysine residues located on histone and non-histone substrates, which regulates gene transcription and other activities in cells. HDAC1 dysfunction has been implicated in cancer development and progression; thus, its inhibition has emerged as a new therapeutic strategy. Two additional metal binding sites (Site 1 and Site 2) in HDACs have been described that are primarily occupied by potassium ions, suggesting a possible structural role that affects HDAC activity. In this work, we explored the structural role of potassium ions in Site 1 and Site 2 and how they affect the interactions of compounds with high affinities for HDAC1 (AC1OCG0B, Chlamydocin, Dacinostat and Quisinostat) and SAHA (a pan-inhibitor) using molecular docking and molecular dynamics (MD) simulations in concert with a Molecular-Mechanics-Generalized-Born-Surface-Area (MMGBSA) approach. Four models were generated: one with a potassium ion (K+) in both sites (HDAC1k), a second with K+ only at site 1 (HDAC1ks1), a third with K+ only at site 2 (HDAC1ks2) and a fourth with no K+ (HDAC1wk). We found that the presence or absence of K+ not only impacted the structural flexibility of HDAC1, but also its molecular recognition, consistent with experimental findings. These results could therefore be useful for further structure-based drug design studies addressing new HDAC1 inhibitors.
Palavras-chave
3D three-dimensional; GAFF Generalized Amber Force Field; HATs Histone acetyltransferases; HDAC1; HDACi Histone deacetylase inhibitor; HDACs Histone deacetylases; HIF hypoxia-inducible factor; Hsp-90 heat-shock protein; MD Molecular dynamic; MM molecular mechanics; MMGBSA Molecular-Mechanics-Generalized-Born-Surface-Area; NAD Nicotinamide adenine dinucleotide; PDB protein data bank; RMSD root mean square deviation; RMSF root mean square fluctuation; Rg radius of gyration; SAHA suberanilohydroxamic acid; ZBG zinc-binding group; docking; molecular dynamics; molecular mechanics-generalized-Born surface area
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Histona Desacetilase 1
/
Simulação de Dinâmica Molecular
/
Simulação de Acoplamento Molecular
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
J Biomol Struct Dyn
Ano de publicação:
2019
Tipo de documento:
Article
País de afiliação:
México
País de publicação:
Reino Unido