Combinatorial In Silico Strategy towards Identifying Potential Hotspots during Inhibition of Structurally Identical HDAC1 and HDAC2 Enzymes for Effective Chemotherapy against Neurological Disorders

Abstract

Histone deacetylases (HDACs) regulate epigenetic gene expression programs by modulating chromatin architecture and are required for neuronal development. Dysregulation of HDACs and aberrant chromatin acetylation homeostasis have been implicated in various diseases ranging from cancer to neurodegenerative disorders. Histone deacetylase inhibitors (HDACi), the small molecules interfering HDACs have shown enhanced acetylation of the genome and are gaining great attention as potent drugs for treating cancer and neurodegeneration. HDAC2 overexpression has implications in decreasing dendrite spine density, synaptic plasticity and in triggering neurodegenerative signaling. Pharmacological intervention against HDAC2 though promising also targets neuroprotective HDAC1 due to high sequence identity (94%) with former in catalytic domain, culminating in debilitating off-target effects and creating hindrance in the defined intervention. This emphasizes the need of designing HDAC2-selective inhibitors to overcome these vicious effects and for escalating the therapeutic efficacy. Here we report a top-down combinatorial in silico approach for identifying the structural variants that are substantial for interactions against HDAC1 and HDAC2 enzymes. We used extra-precision (XP)-molecular docking, Molecular Mechanics Generalized Born Surface Area (MMGBSA) for predicting affinity of inhibitors against the HDAC1 and HDAC2 enzymes. Importantly, we employed a novel in silico strategy of coupling the state-of-the-art molecular dynamics simulation (MDS) to energetically-optimized structure based pharmacophores (e-Pharmacophores) method via MDS trajectory clustering for hypothesizing the e-Pharmacophore models. Further, we performed e-Pharmacophores based virtual screening against phase database containing millions of compounds. We validated the data by performing the molecular docking and MM-GBSA studies for the selected hits among the retrieved ones. Our studies attributed inhibitor potency to the ability of forming multiple interactions and infirm potency to least interactions. Moreover, our studies delineated that a single HDAC inhibitor portrays differential features against HDAC1 and HDAC2 enzymes. The high affinity and selective HDAC2 inhibitors retrieved through e-Pharmacophores based virtual screening will play a critical role in ameliorating neurodegenerative signaling without hampering the neuroprotective isoform (HDAC1).

HDAC2 Inhibitor Valproic Acid Increases Radiation Sensitivity of Drug-Resistant Melanoma Cells

“…Arg39 is a crucial binding residue for HDAC2 and forms hydrogen bond interactions with several other inhibitors of HDAC2 [44]. The stable interaction of VPA with HDAC2 may interfere with its activity of deacetylation [45]. Therefore, the inhibition of HDAC2 by VPA reverses the sensitivity of cancer cells to chemo and radiation therapy.…”

Delineating binding potential, stability of Sulforaphane‐N‐acetyl‐cysteine in the active site of histone deacetylase 2 and testing its cytotoxicity against distinct cancer lines through stringent molecular dynamics, DFT and cell‐based assays

“…As it is tangible that correct 3D models are required for molecular docking and the majority of compounds prevailing in compound databases are available as 2D structures. Thus before molecular docking transformation of 2D structures to 3D one is obligatory (Ganai et al., 2017). The coordinates of two ligands Sulforaphane N ‐acetyl‐cysteine and entinostat were fetched from PubChem with PubChem CID: 71752290 and 4261, respectively.…”

“…Prime MM‐GBSA performs variety of energy estimations including optimized free Ligand (Ligand), optimized free receptor (Receptor), Optimized complex (complex), ligand from optimized complex, and receptor from the defined complex. The binding free energy was finally calculated by using the equation described in previous literature (Ganai, 2021; Ganai et al., 2017); The more negative value of Δ G (Bind) qualitatively indicates stronger binding and for affirmation needs kinetic assays.…”

Histone deacetylases as targets for the treatment of neurodegenerative disorders: Challenges and future opportunities

“…is related to the change in the overall polarity of this compound. 151 Still worth mentioning is that some interesting in silico focused works for the identification of HDACis are coming out, [152][153][154] even regarding blood-brain-barrier permeation prediction, the so-called BBB score, 155 which can support future projects for the synthesis and pharmacological evaluation of new BBB-permeable HDACis.…”