Synthesis, molecular structure, DFT studies, in silico docking and molecular dynamics simulations of 2,6 dimethoxychalcone derivatives as BRD4 inhibitors

Abstract

Methoxyphenyl chalcone derivatives (MAHB1 and MAHB3) have been synthesized and characterised by NMR (1H&13C) spectra and single crystal X-ray diffraction techniques. The crystal structures revealed the crystallization of the both compounds in the monoclinic systems and P2(1)/c space groups. Supramolecular architecture unveiled the stability of compounds and build of crystal packings upon short contacts and weak interactions. Density functional theory (DFT) with B3LYP functional under 6–311++G(d,p) basis set have been adopted to calculate the geometry and investigate intramolecular charge transfer (ICT) using natural bond orbital analysis (NBO) as well as the frontier molecular orbitals (FMOs), hardness, softness, energy gap and other chemical reactivity parameters. Hirshfeld surface and energy frameworks were adopted to evaluate the different intermolecular interaction and energies based on the anisotropy of the topology. The inhibitory activity of the compounds against the first bromodomain of human BRD4 protein have been assessed by using in silico molecular docking and molecular dynamics simulations against 5H21 protein (homo sapiens), which revealed prominent interactions of both the ligands at the active site of BRD4 protein showing with a reasonable conformity as similar with the co-crystal ligand interactions. Furthermore, apo and holo states in the molecular dynamic simulations confirmed the stability and structural constancy of the protein-ligand complexes with minimal deviation based on RMSD and RMSF plots. Both the simulation results confirmed the hydrogen bonds of the compounds with the vital amino acid ASN140 which is necessary for the inhibition of BRD4 as well as exhibiting similar hydrophobic residues interactions. Furthermore, the newly synthesized compounds were screened against human leukemia MV4–11 cells based on MTT and apoptosis assays system. These compounds exhibited anti-proliferation activity and induced the apoptotic effect. This study indicated that the MAHB1 is a promising compound against leukaemia with IC50 value of 79.10 μM and exhibited better apoptogenic effect. Furthermore, the expression of BRD4 in MV4–11 cell line was measured by western blotting, while the protein thermal shift assay was conducted to determine the impact of MAHB1 compound against the thermal stability of BRD4.