Conformational stability, spectroscopic and computational studies, HOMO-LUMO, NBO, ESP analysis, thermodynamic parameters of natural bioactive compound with anticancer potential of 2-(hydroxymethyl)anthraquinone

New flavone-based arylamides as potential V600E-BRAF inhibitors: Molecular docking, DFT, and pharmacokinetic properties

Objectives

The V600E-BRAF protein kinase is an attractive and essential therapeutic target in melanoma and other tumors. However, because of its resistance to the known inhibitors and side effects of some identified inhibitors, new potent inhibitors need to be identified.

Methods

In the present work, in silico strategies such as the molecular docking simulation, DFT (Density-Functional-Theory) computations, and pharmacokinetic evaluation were used to determine potential V600E-BRAF inhibitors from a set of 31 synthesized novel flavone-based arylamides.

Results

The docking result demonstrated that four compounds (10, 11, 28, and 31) had acceptable docking scores (MolDock score of -167.523 kcal mol^-1, -158.168 kcal mol^-1, -160.581 kcal mol^-1,-162.302 kcal mol^-1, and a Rerank score of -124.365, -129.365, -135.878 and -117.081, respectively) appeared as most active and potent V600E-BRAF inhibitors that topped vemurafenib (-158.139 and -118.607 kcal mol^-1). The appearance of H-bonds and hydrophobic interactions with essential residues for V600E-BRAF proved the high stability of these complexes. The energy for the frontier molecular orbitals such as HOMO, LUMO, energy gap, and other reactivity parameters was computed using DFT. The frontier molecular-orbital surfaces and electrostatic potentials (EPs) were investigated to demonstrate the charge-density distributions that might be linked to anticancer activity. Similarly, the chosen compounds revealed superior pharmacological properties according to the drug-likeness rules (bioavailability) and pharmacokinetic properties.

Conclusion

The chosen compounds were recognized as potent V600E-BRAF inhibitors with superior pharmacokinetic properties and could be promising cancer drug candidates.

Acetophenone-Based 3,4-Dihydropyrimidine-2(1H)-Thione as Potential Inhibitor of Tyrosinase and Ribonucleotide Reductase: Facile Synthesis, Crystal Structure, In-Vitro and In-Silico Investigations

The acetophenone-based 3,4-dihydropyrimidine-2(1H)-thione was synthesized by the reaction of 4-methylpent-3-en-2-one (1), 4-acetyl aniline (2) and potassium thiocyanate. The spectroscopic analysis including: FTIR, 1H-NMR, and single crystal analysis proved the structure of synthesized compound (4), with the six-membered nonplanar ring in envelope conformation. In crystal structure, the intermolecular N-H ⋯ S and C-H ⋯ O hydrogen bonds link the molecule in a two-dimensional manner which is parallel to (010) the plane enclosing R22 (8) and R22 (10) ring motifs. After that, the Hirshfeld surfaces and their related two-dimensional fingerprint plots were used for thorough investigation of intermolecular interactions. According to Hirshfeld surface analysis, the most substantial contributions to the crystal packing are from H ⋯ H (59.5%), H ⋯ S/S ⋯ H (16.1%), and H ⋯ C/C ⋯ H (13.1%) interactions. The electronic properties and stability of the compound were investigated through density functional theory (DFT) studies using B3LYP functional and 6-31G* as a basis set. The compound 4 displayed the high chemical reactivity with chemical softness of 2.48. In comparison to the already reported known tyrosinase inhibitor, the newly synthesized derivatives exhibited almost seven-fold better inhibition of tyrosinase (IC50 = 1.97 μM), which was further supported by molecular docking studies. The compound 4 inside the active pocket of ribonucleotide reductase (RNR) exhibited a binding energy of -19.68 kJ/mol, and with mammalian deoxy ribonucleic acid (DNA) it acts as an effective DNA groove binder with a binding energy of -21.32 kJ/mol. The results suggested further exploration of this compound at molecular level to synthesize more potential leads for the treatment of cancer.

Synthesis of Novel Tritopic Hydrazone Ligands: Spectroscopy, Biological Activity, DFT, and Molecular Docking Studies

Polytopic organic ligands with hydrazone moiety are at the forefront of new drug research among many others due to their unique and versatile functionality and ease of strategic ligand design. Quantum chemical calculations of these polyfunctional ligands can be carried out in silico to determine the thermodynamic parameters. In this study two new tritopic dihydrazide ligands, N’2, N’6-bis[(1E)-1-(thiophen-2-yl) ethylidene] pyridine-2,6-dicarbohydrazide (L1) and N’2, N’6-bis[(1E)-1-(1H-pyrrol-2-yl) ethylidene] pyridine-2,6-dicarbohydrazide (L2) were successfully prepared by the condensation reaction of pyridine-2,6-dicarboxylic hydrazide with 2-acetylthiophene and 2-acetylpyrrole. The FT-IR, 1H, and 13C NMR, as well as mass spectra of both L1 and L2, were recorded and analyzed. Quantum chemical calculations were performed at the DFT/B3LYP/cc-pvdz/6-311G+(d,p) level of theory to study the molecular geometry, vibrational frequencies, and thermodynamic properties including changes of ∆H, ∆S, and ∆G for both the ligands. The optimized vibrational frequency and (1H and 13C) NMR obtained by B3LYP/cc-pvdz/6-311G+(d,p) showed good agreement with experimental FT-IR and NMR data. Frontier molecular orbital (FMO) calculations were also conducted to find the HOMO, LUMO, and HOMO−LUMO gaps of the two synthesized compounds. To investigate the biological activities of the ligands, L1 and L2 were tested using in vitro bioassays against some Gram-negative and Gram-positive bacteria and fungus strains. In addition, molecular docking was used to study the molecular behavior of L1 and L2 against tyrosinase from Bacillus megaterium. The outcomes revealed that both L1 and L2 can suppress microbial growth of bacteria and fungi with variable potency. The antibacterial activity results demonstrated the compound L2 to be potentially effective against Bacillus megaterium with inhibition zones of 12 mm while the molecular docking study showed the binding energies for L1 and L2 to be −7.7 and −8.8 kcal mol−1, respectively, with tyrosinase from Bacillus megaterium.

Ligand Exchange Strategy to Achieve Chiral Perovskite Nanocrystals with a High Photoluminescence Quantum Yield and Regulation of the Chiroptical Property

Chiral nanomaterials have drawn extensive attention on account of numerous application prospects in optoelectronics, asymmetric catalysis, chiral recognition, and three-dimensional (3D) display. Thereinto, chiral perovskite has been a hotspot due to brilliant optoelectronic properties, but some problems limit the development, including low quantum yield, low chiral intensity, and the lack of facile regulation. To overcome these issues, an effective ligand exchange strategy, i.e. the interface modification has been proposed for chiral perovskite nanocrystals (PNCs). With the surface modification of CsPbBr₃ PNCs with chiral organic ammonium in methyl acetate in the typical purification process, excellent circular dichroism (CD) signals were obtained and defects were eliminated, leading to an increase in the photoluminescence quantum yield (PLQY) from 50% to nearly 100%. The CD signal can be regulated through a ligand exchange strategy in the longitudinal dimension, the chiral intensity, and the transverse dimension, the wavelength range. Here, the proper addition of R-α-PEAI into the R-α-PEABr-capped CsPbBr₃ PNCs can produce a superstrong CD signal with the highest anisotropy factor (g-factor) of 0.0026 in the visible region among reported chiral colloidal PNCs. Simultaneously, the luminescence emission can be tuned from the green to red region with boosted PLQY through the approach. The density functional theory (DFT) calculation result supports that chirality comes from the hybridization between the energy level of a perovskite structure and that of chiral organic molecules. These properties can be used in the structural engineering of high-performance chiral optical materials, spin-polarized light-emitting devices, and polarized optoelectronic devices.

The structural, spectral, frontier molecular orbital and thermodynamic analysis of 2-hydroxy 2-methyl propiophenone by MP2 and B3LYP methods

In the present work, we have studied the 2-hydroxy 2-methyl propiophenone (2H2MPP) theoretically as well as experimentally. The optimized molecular structure has been obtained by the density functional theory (DFT), second-order Moller–Plesset perturbation theory (MP2) and Hartree Fock (HF) in the gas phase as well as in different media like ethanol, DMSO and heptane. FT-IR and FT-Raman spectra were computed as well as recorded and fundamental vibrational wavenumbers were assigned. The electronic absorption spectra were calculated by employing the time-dependent density functional theory (TD-DFT) to get the information about excitation energies, oscillator strength and excited state geometries in gas phase and in different solvent media. Chemical activity and chemical stability obtained by HOMO-LUMO studies using a HF/6-31[Formula: see text]G and MP2/6-311[Formula: see text]G calculations. The chemical interpretation of hyperconjugation interactions obtained by the Natural Bond Orbital (NBO) analysis. Moreover, electrostatic potential (ESP) calculations performed to get the visual representation of relative polarity of molecule. Thermodynamic parameters like enthalpy, entropy, heat capacity, and Gibbs free energy computed with varying temperature from 10[Formula: see text]K to 500[Formula: see text]K. The aim of the current investigation is to find out the quantum chemical properties of the title compound which show an active role in the pharmaceutical and printing industries.

Layer-by-layer films containing emodin or emodin encapsulated in liposomes for transdermal applications

Dermal drug release systems are an important area of research because they can be applied to the skin in a non-invasive procedure using a lower concentration of drugs. In this study, we have developed two types of Layer-by-Layer (LbL) films for releasing emodin (EM). In one system, EM was intercalated with poly(ethylenimine) PEI and poly(vinyl sufonate) (PVS) polyelectrolytes, forming (PEI/PVS)₂(PEI/EM)₇; in another, EM was incorporated in liposomes obtained by mixing dipalmitoyl phosphatidyl glycerol (DPPG) and palmitoyl oleoyl phosphatidyl glycerol (POPG) lipids, forming (PEI/PVS)₂(PEI/DPPG-POPG-EM)₇. UV-vis and FTIR spectroscopies were used to characterize the LbL films. These showed that the depositions of material by LbL were efficient, with increases in the absorbance of each bilayer evidencing the presence of EM in the film. The (PEI/PVS)₂(PEI/EM)₇ and (PEI/PVS)₂(PEI/DPPG-POPG-EM)₇ films released EM in three and five days, respectively. The cyclic voltammetry (CV) assay of the (PEI/PVS)₂(PEI/EM)₇ results are in agreement with UV-vis measurements, which suggest that EM was protonated in acid environments, while the CV of (PEI/PVS)₂(PEI/DPPG-POPG-EM)₇ demonstrated distinct protonation behaviour for EM within the inner liposome structure, even in acid solutions. Therefore, this study presents two systems based on LbL films and provides additional details about the release of EM from these films to create a viable alternative for transdermal applications.

Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives

Apigenin is an important flavonoids due to its antidiabetic bioactivity. It was reported experimentally that the 7-substituent derivative of apigenin has higher biological activity than 4'- and 5-substituted derivatives while introducing sole carboxyalkyl group -(CH₂)₇COOH into the parent structure. Molecular docking studies indicated that the other two derivatives have lower binding affinities than the 7-substituent derivative (-7.52 kcal mol^-1), which is considered to be a better inhibitor than the parent molecule. Almost all of the carbon atoms and oxygen atoms are coplaner for all three molecules in solution phase, however, all carboxyalkyl groups bend inside into the parent molecules in the active site, and the jagged geometries of the carbon chains are destroyed correspondingly. In addition, most of the electron densities of the chemical bonds for all molecules are decreased, especially the 7-substituent derivative. In contrast, most of the Laplacian values for three molecules are increased in the active site, which suggests that the charge densities at the bond critical point (bcp) are much more depleted than the solution phase. Dipole moments of derivatives are all increased in the active site, suggesting strong intermolecular interactions. After interacting with the S. cerevisiae α-glucosidase, only the 7-substituent derivative has the lowest energy gap ΔE _HOMO-LUMO, which indicates the lowest stability and the highest inhibition activity. Graphical abstract Probing the influence of carboxyalkyl groups on the molecular flexibility and the charge density of apigenin derivatives.