Molecular dynamics and quantum chemistry-based approaches to identify isoform selective HDAC2 inhibitor – a novel target to prevent Alzheimer’s disease

Abstract

Histone deacetylase 2 (HDAC2) is an emerging target of Alzheimer’s disease. Four featured pharmacophore model (ADRR) with one H-bond acceptor (A), one H-bond donor (D), and two aromatic rings (R) was generated using experimentally reported compounds, ((E-5[3-benzenesulfonamido) phenyl]-N-hydroxypent-2-en-4-ynamide)) and (N’-hydroxy-N-phenyloctanediamide) with IC₅₀ values of 0.16 ± 0.11 nM and 62 ± 0.15 nM, respectively. Quantum Polarized Ligand Docking and Binding Free Energy calculation was performed for the top three identified leads RH01652, JFD02573, and HTS00800 from HitFinder database. RH01652 (methyl 2-[({5-[(benzoylamino) methyl]-2-thienyl} sulfonyl) amino]-3-(1H-indol-3-yl) propanoate) with docking score (−12.62 kcal/mol) and binding free energy (−75.27 kcal/mol), shows good binding affinity. RH01652 interacts with Gly154, His183, Glu208, and Phe210 with four H-bonds and stabilized by π–π interactions with His146, Tyr209, and Phe210. DFT studies at B3LYP level with 6-31G* basis set for the lead RH01652 reveals low band gap/ΔE (E_HOMO–E_LUMO) of −0.16 eV, which illustrates good reactivity of the lead. MD simulation studies (40 ns) was performed to confirm the stability of lead binding. Comparative molecular docking studies of the lead RH01652 with class I HDACs (HDAC1, HDAC2, HDAC3, and HDAC8) shows higher binding affinity towards HDAC2. Thus, lead RH01652 could serve as template to design novel and potent inhibitor of HDAC2.

Keywords:

• E-pharmacophore
• docking
• binding free energy
• density functional theory
• MD simulation

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

JJ acknowledges DBT [No. BT/PR5985/BID/7/410/2012], DST [F. no. EMR/2016/000498], UGC Research Award [RA-2016–18-OB-TAM-7124], and ICMR [No. BIC/12(07)/2015] for providing financial assistance. Authors thankfully acknowledge the DST-FIST [grant number SR/FST/LSI-667/2016], and DST-PURSE [No. SR/PURSE Phase 2/38 (G)], New Delhi for providing infrastructure facilities.