Synthesis, crystal structure, hirshfeld surface analysis, DFT calculations, anti-diabetic activity and molecular docking studies of (E)-N’-(5-bromo-2-hydroxybenzylidene) isonicotinohydrazide

Novel isoniazid-hydrazone derivatives induce cell growth inhibition, cell cycle arrest and apoptosis via mitochondria-dependent caspase activation and PI3K/AKT inhibition

In this study, seven isoniazid-hydrazone derivatives (3a-g) were synthesized and their structures elucidated by chromatographic techniques, and then the antiproliferative effects of these compounds on various cancer cells were tested. The advanced anticancer mechanism of the most potent compound was then investigated. Antiproliferative activities of the synthesized compounds were evaluated on human breast cancer MCF-7, lung cancer A-549, colon cancer HT-29, and non-cancerous mouse fibroblast 3T3-L1 cell lines by XTT assay. Flow cytometry analysis were carried out to determine cell cycle distribution, apoptosis, mitochondrial membrane potential, multi-caspase activity, and expression of PI3K/AKT signaling pathway. The XTT results showed that all the title molecules displayed cytotoxic activity at varying strengths in different dose ranges, and among them, the strongest cytotoxic effect and high selectivity were exerted by 3d against MCF-7 cells with the IC50 value of 11.35 µM and selectivity index of 8.65. Flow cytometry results revealed that compound 3d induced apoptosis through mitochondrial membrane disruption and multi-caspase activation in MCF-7 cells. It also inhibited the cell proliferation via inhibition of expression of PI3K/AKT and arrested the cell cycle at G0/G1 phase. In conclusion, all these data disclosed that among the synthesized compounds, 3d is notable for in vivo anticancer studies.

Biological, toxicological and molecular docking evaluations of isoxazoline-thiazolidine-2,4-dione analogues as new class of anti-hyperglycemic agents

In this work, three isoxazoline-thiazolidine-2,4-dione derivatives were synthesized and characterized by FT-IR, ¹H-NMR, ¹³C-NMR and ESI-MS spectrometry. All compounds have been investigated for their α-amylase and α-glucosidase inhibitory activities. In vitro enzymatic evaluation revealed that all compounds were inhibitory potent against α-glucosidase with IC₅₀ values varied from 40.67 ± 1.81 to 92.54 ± 0.43 µM, and α-amylase with IC₅₀ in the range of 07.01 ± 0.02 to 75.10 ± 1.06 µM. One of the tested compounds were found to be more potent inhibitor compared to other compounds and standard drug Acarbose (IC_{50 glucosidase}= 97.12 ± 0.35 µM and IC_{50 amylase}= 2.97 ± 0.01 μM). All compounds were then evaluated for their acute toxicity in vivo and shown their safety at a high dose with LD > 2000mg/kg BW. A cell-based toxicity evaluation was performed to determine the safety of compounds on liver cells, using the MTT assay against HepG2 cells, and the results shown that all compounds have non-toxic impact against cell viability and proliferation compared to reference drug (Pioglitazone). Furthermore, the molecular homology analysis, SAR and the molecular binding properties of compound with the active site of α-amylase and α-glucosidase were confirmed through computational analysis. This study has identified the inhibitory potential of a new class of synthesized isoxazoline-thiazolidine-2,4-dione derivatives in controlling both hyperglycemia and type 2 diabetes mellitus without any hepatic toxicity.Communicated by Ramaswamy H. Sarma.

Structure-activity relationships and the underlying mechanism of α-amylase inhibition by hyperoside and quercetin: Multi-spectroscopy and molecular docking analyses

Inhibiting the activity of α-amylase has been considered an effective strategy to manage hyperglycemia. Hyperoside and quercetin are the main natural flavonoids in various plants, and the inhibition mechanism on α-amylase remains unclear. In this study, the structure-activity relationships between hyperoside/quercetin and α-amylase were evaluated by enzyme kinetic analysis, multi-spectroscopic techniques, and molecular docking analysis. Results showed that hyperoside and quercetin exhibited significant α-amylase inhibitory activities with IC₅₀ values of 0.491 and 0.325 mg/mL, respectively. The α-amylase activity decreased in the presence of hyperoside and quercetin in a competitive and noncompetitive manner, respectively. UV-vis spectra suggested that the aromatic amino acid residues (Trp and Tyr) microenvironment of α-amylase changed in the presence of these two flavonoids. FTIR and CD spectra showed the vibrations of the amide bands and the secondary structure content changes. The fluorescence quenching mechanism of α-amylase by hyperoside and quercetin belonged to the static quenching type. Finally, molecular docking intuitively showed that hyperoside/quercetin formed hydrogen bonds with the key active site residues (Asp197, Glu233, and Asp300) in α-amylase. MD simulation indicated hyperoside/quercetin-α-amylase docked complexes had good stability. Taken together, this research provides new sights to developing potent drugs or functional foods with hyperoside and quercetin, offering new avenues for hyperglycemia treatment.

Synthesis, crystal structure, DFT, Hirshfeld surface analysis, energy framework, docking and molecular dynamic simulations of (E)-4-(4-methylbenzyl)-6-styrylpyridazin-3(2H)-one as anticancer agent

In this work, a novel crystal, (E)-4-(4-methylbenzyl)-6-styrylpyridazin-3(2H)-one (E-BSP) was synthesized via Knoevenagel condensation of benzaldehyde and (E)-6-(4-methoxystyryl)-4,5-dihydropyridazin-3(2H)-one. The molecular structure of E-BSP was confirmed by using FT-IR, 1H-NMR, 13C-NMR, UV-vis, ESI-MS, TGA/DTA thermal analyses and single crystal X-ray diffraction. The DFT/B3LYP methods with the 6-311++G(d,p) basis set were used to determine the vibrational modes over the optimized structure. Potential energy distribution (PED) and the VEDA 4 software were used to establish the theoretical mode assignments. The same approach was used to compute the energies of frontier molecular orbitals (HOMO-LUMO), global reactivity descriptors, and molecular electrostatic potential (MEP). Additionally, experimental and computed UV spectral parameters were determined in methanol and the obtained outputs were supported by FMO analysis. Molecular docking and molecular dynamics (MD) simulation analyses of the E-BSP against six proteins obtained from different cancer pathways were carried out. The proteins include; epidermal growth factor receptor (EGFR), Estrogen receptor (ERα), Mammalian target of rapamycin (mTOR), Progesterone receptor (PR) (Breast cancer), Human cyclin-dependent kinase 2 (CDK2) (Colorectal cancer), and Survivin (Squamous cell carcinoma/Non-small cell lung cancer). The results of the analyses showed that the compound had less binding energies ranging between -6.30 to -9.09 kcal/mol and formed stable complexes at the substrate-binding site of the proteins after the 50 ns MD simulation. Therefore, E-BSP was considered a potential inhibitor of different cancer pathways and should be used for the treatment of cancer after experimental validation and clinical trial.Communicated by Ramaswamy H. Sarma.

Synthesis, characterization, anticancer and in silico studies of a pyrazole-tethered thiazolidine-2,4-dione derivative

A new pyrazole-tethered thiazolidine-2,4-dione derivative (8) has been synthesized by the Knoevenagel condensation of 3-(4-nitrophenyl)-1-phenyl-1H-pyrazole-4-carbaldehyde (4) and 3-(2,4-dioxothiazolidin-3-yl)propanenitrile (7). The structure of the final compound was confirmed by standard spectroscopic techniques including IR spectroscopy, ¹H-NMR spectroscopy, and ESI-MS mass spectrometry. Molecular features including frontier molecular orbital (HOMO-LUMO) energies, reactivity descriptors and molecular electrostatic potential (ESP) of the title molecule were determined using density functional theory (DFT) calculation. The in vitro cytotoxicity of both the intermediate (4) and final (8) compounds were investigated against cancerous (SW-480 and MCF-7) and normal (HEK-293) cell lines by MTT assay. Compound (8) displayed higher activity than (4) with higher sensitivity against breast cancer cell line and lesser toxicity. The experimental data were further complemented by docking and absorption, distribution, metabolism, and excretion (ADME) studies.Communicated by Ramaswamy H. Sarma.

Comparative antibacterial analysis of the anthraquinone compounds based on the AIM theory, molecular docking, and dynamics simulation analysis

BACKGROUND

Hydroxyanthraquinones and anthraquinone glucoside derivatives are always considered as the active antibacterial components.

METHODS

Comparison of structure characteristics and antibacterial effect of these compounds was performed by applying quantum chemical calculations, atoms in molecules theory, molecular docking, and dynamics simulation procedure. Density functional theory calculation with B3LYP using 6-31G (d, p) basis set has been used to determine ground state molecular geometries.

RESULTS

The molecular geometric stability, electrostatic potential, frontier orbital energies, and topological properties were analyzed at the active site. Once glucose ring is introduced into the hydroxyanthraquinone rings, almost all of the positive molecular potentials are distributed among the hydroxyl hydrogen atoms of the glucose rings. In addition, low electron density ρ (r) and positive Laplacian value of the O-H bond of the anthraquinone glucoside are the evidences of the highly polarized and covalently decreased bonding interactions. The anthraquinone glucoside compounds have generally higher intermolecular binding energies than the corresponding aglycones due to the strong interaction between the glucose rings and the surrounding amino acids. Molecular dynamics simulations further explored the stability and dynamic behavior of the anthraquinone compound and protein complexes through RMSD, RMSF, SASA, and Rg.

CONCLUSION

The type of carboxyl, hydroxyl, and hydroxymethyl groups on phenyl ring and the substituent glucose rings is important to the interactions with the topoisomerase type II enzyme DNA gyrase B.

Facile synthesis, crystal structure, biological evaluation, and molecular modeling studies of N-((4-acetyl phenyl) carbamothioyl) pivalamide as the multitarget-directed ligand

The crystal structure of N-((4-acetylphenyl)carbamothioyl)pivalamide (3) was synthesized by inert refluxing pivaloyl isothiocyanate (2) and 4-aminoacetophenone in dry acetone. The spectroscopic characterization (¹H-NMR, ¹³CNMR, FT-IR) and single crystal assays determined the structure of synthesized compound (3). Systematic experimental and theoretical studies were conducted to determine the molecular characteristics of the synthesized crystal. The biological examination of (3) was conducted against a variety of enzymes i.e., acetyl cholinesterase (AChE), butyl cholinesterase (BChE), alpha amylase, and urease enzyme were evaluated. The crystal exhibited approximately 85% enzyme inhibition activity against BChE and AChE, but only 73.8 % and 57.9% inhibition activity against urease and alpha amylase was observed respectively. The theoretical calculations were conducted using density functional theory studies (DFTs) with the 6–31G (d, p) basis set and B3LYP functional correlation. The Frontier molecular orbital analysis revealed that the HOMO/LUMO energy gap was smaller, which corresponds to the molecule’s reactivity. In terms of reactivity, the chemical softness value was found to be in good agreement with experimental values. In Crystal structure analysis, the intramolecular N—H•••O hydrogen bond generates a S 6) ring motif and N—H•••O interactions exist in crystal structure between the centroids of neighboring parallel aromatic (C4-C9) rings with a centroid to centroid distance of 3.9766 (7)Å. These intermolecular interactions were useful in structural stabilization. The Hirshfeld surfaces and their related two-dimensional fingerprint plots were used for thorough investigation of intermolecular interactions. According to Hirshfeld surface analysis of the crystal structure the most substantial contributions to the crystal packing are from H ••• O and H ••• N/N ••• H interactions. Molecular docking studies were conducted to evaluate the binding orientation of synthesized crystal with multiple targets. The compound exhibited stronger interactions with AChE and BChE with binding energies of -7.5 and -7.6 kcal/mol, respectively. On the basis of in-vitro and in-silico findings, it is deduced that N-((4-acetylphenyl)carbamothioyl)pivalamide 3) possesses reactive and potent multiple target inhibitory properties.

Gallium (III) Complexes with 5-Bromosalicylaldehyde Benzoylhydrazones: In Silico Studies and In Vitro Cytotoxic Activity

Gallium (III) complexes with the ligands 5-bromosalicylaldehyde-4-hydroxybenzoylhydrazone and 5-bromosalicylaldehyde isonicotinoylhydrazone were synthesized to receive compounds with improved antiproliferative action. Compounds were characterized by elemental analysis, IR, and NMR spectroscopy. Density functional theory calculations with Becke’s 3-parameter hybrid functional and 6-31+G(d,p) basis set were carried out to investigate the structural features of the ligands and Ga(III) complexes. Cytotoxic screening by MTT-dye reduction assay was carried out using cisplatin and melphalan as reference cytotoxic agents. A general formula [Ga(HL)₂]NO₃ for the complexes obtained was suggested. The complexes are mononuclear with the Ga(III) ions being surrounded by two ligands. The ligands acted as monoanionic tridentate (ONO) donor molecules. The analysis revealed coordination binding through deprotonated phenolic-oxygen, azomethine-nitrogen, and amide-oxygen atoms. The bioassay demonstrated that all compounds exhibited concentration-dependent antiproliferative activity at low micromolar concentrations against the acute myeloid leukemia HL-60 and T-cell leukemia SKW-3 cell lines. IC₅₀ values of 5-bromo-derivative ligands and gallium (III) complexes are lower than those of cisplatin and much lower than these of melphalan. The coordination to gallium (III) additionally increased the cytotoxicity compared to the metal-free hydrazones.

Metal-Doped Al12N12X (X = Na, Mg, K) Nanoclusters as Nanosensors for Carboplatin: Insight from First-Principles Computation

This theoretical study focuses on the adsorption, reactivity, topological analysis, and sensing behavior of metal-doped (K, Na, and Mg) aluminum nitride (Al12N12) nanoclusters using the first-principle density functional theory (DFT). All quantum chemical reactivity, natural bond orbital (NBO), free energies (ΔG, ΔH), and sensor parameters were investigated using the ωB97XD functional with the 6-311++G(d,p) basis set. The trapping of carboplatin (cbp) onto the surfaces of doped Al12N12 was studied using four functionals PBE0-D3, M062X-D3, ωB97XD, and B3LYP-D3 at the 6-311++G(d,p) basis set. Overall, the substantial change in the energy gap of the surfaces after the adsorption process affects the work function, field emission, and the electrical conductivity of the doped clusters, hence making the studied surfaces a better sensor material for detecting carboplatin. Higher free energies of solvation were obtained in polar solvents compared to nonpolar solvents. Moreover, negative solvation energies and adsorption energies were obtained, which therefore shows that the engineered surfaces are highly efficient in trapping carboplatin. The relatively strong adsorption energies show that the mechanism of adsorption is by chemisorption, and K- and Na-doped metal clusters acted as better sensors for carboplatin. Also, the topological analysis in comparison to previous studies shows that the nanoclusters exhibited very high stability with regard to their relevant binding energies and hydrogen bond interactions.

Synthesis, crystal structure and in silico studies of novel 2,4-dimethoxy-tetrahydropyrimido[4,5-b]quinolin-6(7H)-ones

Herein, acetic acid mediated multicomponent synthesis of novel 2,4-dimethoxy-tetrahydropyrimido[4,5-b]quinolin-6(7H)-one (2,4-dimethoxy-THPQs) was reported. Single-crystal XRD analysis of four newly developed crystals of 2,4-dimethoxy-THPQs and their DFT study were also reported. The structure of all molecules was optimized using DFT B3LYP/6-31G(d) level and compared with the corresponding single-crystal XRD data. As a result, the theoretical and experimental geometrical parameters (bond lengths and bond angles) were found to be in good agreement. Frontier molecular orbital (FMO) and molecule electrostatic potential (MEP) analyses were used to investigate the physicochemical properties and relative reactivity of 2,4-dimethoxy-THPQs. The formation of strong C–H⋯O and N–H⋯O interaction was investigated by Hirshfeld analysis. Furthermore, electronic charge density concentration in 2,4-dimethoxy-THPQs was analysed by the Mulliken atomic charges which helps to predict the ability of 2,4-dimethoxy-THPQs to bind in the receptor. The molecular docking of the crystal structure of 2,4-dimethoxy-THPQs in the main protease (M^pro) of SARS-CoV-2 suggested that all four 2,4-dimethoxy-THPQs efficiently docked in M^pro. Furthermore, 2,4-dimethoxy-THPQs with a 3-chloro substitution in the phenyl ring have the highest binding affinity because of the additional formation of halogen bonds and highest dipole moment.

Single-crystal XRD analysis of 2,4-dimethoxy THPQs and their relative reactivity with properties were investigated using DFT calculation. Molecular docking studies show they effectively docked with main protease of SARS-CoV-2.

Synthesis, Characterization, Biological Evaluation and DNA Interaction Studies of 4-Aminophenol Derivatives: Theoretical and Experimental Approach

In the present study, five 4-aminophenol derivatives (4-chloro-2-(((4-hydroxyphenyl)imino)methyl)phenol(S-1), 4-((4-(dimethylamino)benzylidene)amino)phenol(S-2), 4-((3-nitrobenzylidene)amino)phenol(S-3), 4-((thiophen-2-ylmethylene)amino)phenol(S-4) and 4-(((E)-3-phenylallylidene)amino)phenol(S-5)) were synthesized and characterized by FT-IR, ¹H-NMR, ¹³C-NMR and elemental analyses. The synthesized compounds were tested for their antimicrobial (Gram-positive and Gram-negative bacteria and Saccharomyces cervesea fungus) and antidiabetic (α-amylase and α-glucosidase inhibitory) activities. All the compounds showed broad-spectrum activities against the Staphylococcus aureus (ATCC 6538), Micrococcus luteus (ATCC 4698), Staphylococcus epidermidis (ATCC 12228), Bacillus subtilis sub. sp spizizenii (ATCC 6633), Bordetella bronchiseptica (ATCC 4617) and Saccharomyces cerevisiae (ATCC 9763) strains. The newly synthesized compounds showed a significant inhibition of amylase (93.2%) and glucosidase (73.7%) in a concentration-dependent manner. Interaction studies of Human DNA with the synthesized Schiff bases were also performed. The spectral bands of S-1, S-2, S-3 and S-5 all showed hyperchromism, whereas the spectral band of S-4 showed a hypochromic effect. Moreover, the spectral bands of the S-2, S-3 and S-4 compounds were also found to exhibit a bathochromic shift (red shift). The present studies delineate broad-spectrum antimicrobial and antidiabetic activities of the synthesized compounds. Additionally, DNA interaction studies highlight the potential of synthetic compounds as anticancer agents. The DNA interaction studies, as well as the antidiabetic activities articulated by the molecular docking methods, showed the promising aspects of synthetic compounds.

Steric and energetic characterizations of mouse and human musk receptors activated by nitro musk smelling compounds at molecular level: Statistical physics treatment and molecular docking analysis

Understanding olfaction process at a microscopic or molecular level needs more elucidation of the multiple stages involved in the olfaction mechanism. A worth full elucidation and a better understanding of this molecular mechanism, a necessary preamble should be achieved. The content of this work is a preamble for that. A study of the mouse and human olfactory receptors activation in response to two nitro musks stimuli, which are the musk xylol and the musk ketone, are considered here, first, for their wide expanded use in perfumery, but also to show some particular aspects of this process in the case of these two stimuli, which could help to deduce more details and more general aspects in the global olfactory mechanism. A statistical physics modeling using the monolayer model with two independent types of receptor binding sites of the response of the mouse olfactory receptor MOR215-1 and the human olfactory receptor OR5AN1, which are identified as specifically responding to musk compounds, is used to characterize the interaction between the two nitro musk molecules, the mouse and the human olfactory receptors and to determine the olfactory band of these two odorants through the determination of the molar adsorption energies and the adsorption energy distributions. The physico-chemical model parameters can be used for the steric characterization via the calculation of the receptor site size distributions. The docking computation between these two nitro musks and the human olfactory receptor OR5AN1 is performed demonstrating a large similarity in receptor-ligand detection process. Thus, docking finding results prove that the calculated binding affinities were belonging to the spectrum of adsorption energies.

Synthesis, Spectroscopic Characterization (FT-IR, NMR, UV), NPA, NBO, NLO, Thermochemical Analysis and Molecular Docking Studies of 2-((4-hydroxyphenyl)(piperidin-1-yl)methyl)phenol

In this study, a new alkylaminophenol compound was synthesized and characterized by spectroscopic techniques (FT-IR, NMR, UV). The optimized molecular geometry and the vibrational wavenumbers were calculated using density functional theory (DFT) B3LYP/WB97XD and HF methods with 6-311++ G([Formula: see text], [Formula: see text]) basis set. Thus, theoretical data were compared within themselves before comparing with experimental data. The detailed interpretation of the vibrational spectra has been carried out by VEDA program. 1H-NMR and [Formula: see text]C-NMR chemical shifts of the compound were calculated using GIAO/IEFPCM method in CDCl3. Using time-dependent (TD-DFT) approach electronic properties such as HOMO and LUMO energies, the electronic spectrum of the title compound has been studied and reported. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Linear polarizability, anisotropic linear polarizability and hyperpolarizability values of the title compound were found to be higher than the values of the pNA compound that are used as a standard substance in the NLO analysis. Molecular electrostatic potential (MEP), the thermodynamic properties (heat capacity, entropy and enthalpy) were calculated. Also, to investigate the biological properties of the title compound, molecular docking was done with DNA(PDB ID: 414D). It has been observed that the effective interaction is hydrogen bonds.