TY - JOUR
T1 - Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking
AU - Sixto-López, Yudibeth
AU - Bello, Martiniano
AU - Correa-Basurto, José
N1 - Publisher Copyright:
© 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.
PY - 2019/2/11
Y1 - 2019/2/11
N2 - 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 (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). 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.
AB - 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 (HDAC1 k ), a second with K + only at site 1 (HDAC1 ks1 ), a third with K + only at site 2 (HDAC1 ks2 ) and a fourth with no K + (HDAC1 wk ). 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.
KW - 3D–three-dimensional
KW - GAFF–Generalized Amber Force Field
KW - HATs–Histone acetyltransferases
KW - HDAC1
KW - HDACi–Histone deacetylase inhibitor
KW - HDACs–Histone deacetylases
KW - HIF–hypoxia-inducible factor
KW - Hsp-90–heat-shock protein
KW - MD–Molecular dynamic
KW - MMGBSA–Molecular-Mechanics-Generalized-Born-Surface-Area
KW - MM–molecular mechanics
KW - NAD–Nicotinamide adenine dinucleotide
KW - PDB–protein data bank
KW - RMSD–root mean square deviation
KW - RMSF–root mean square fluctuation
KW - Rg–radius of gyration
KW - SAHA–suberanilohydroxamic acid
KW - ZBG–zinc-binding group
KW - docking
KW - molecular dynamics
KW - molecular mechanics-generalized-Born surface area
UR - http://www.scopus.com/inward/record.url?scp=85042919318&partnerID=8YFLogxK
U2 - 10.1080/07391102.2018.1441072
DO - 10.1080/07391102.2018.1441072
M3 - Artículo
C2 - 29447615
SN - 0739-1102
VL - 37
SP - 584
EP - 610
JO - Journal of Biomolecular Structure and Dynamics
JF - Journal of Biomolecular Structure and Dynamics
IS - 3
ER -