Synthesis of a novel phenytoin derivative: Crystal structure, Hirshfeld surface analysis and DFT calculations

Discovery of potential anti- Staphylococcus aureus natural products and their mechanistic studies using machine learning and molecular dynamic simulations

The structure-activity analysis (SAR) and machine learning were used to investigate potential anti-S. aureus agents in a faster method. In this study, 24 oxygenated benzene ring components with S. aureus inhibition capacity were confirmed by literature exploring and in-house experiments, and the SAR analysis suggested that the hydroxyl group position may affect the anti-S. aureus activity. The 2D-MLR-QSAR model with 9 descriptors was further evaluated as the best model among the 21 models. After that, hesperetic acid and 2-HTPA were further explored and evaluated as the potential anti-S. aureus agents screening in the natural product clustering library through the best QSAR model calculation. The antibacterial capacities of hesperetic acid and 2-HTPA had been investigated and proved the similar predictive pMIC value resulting from the QSAR model. Besides, the two novel components were able to inhibit the growth of S. aureus by disrupting the cell membrane through the molecular dynamics simulation (MD), which further evidenced by scanning electron microscopy (SEM) test and PI dye results. Overall, these results are highly suggested that QSAR can be used to predict the antibacterial agents targeting S. aureus, which provides a new paradigm to research the molecular structure-antibacterial capacity relationship.

Phytochemical investigation, molecular docking studies and DFT calculations on the antidiabetic and cytotoxic activities of Gmelina philippensis CHAM

ETHNOPHARMACOLOGICAL RELEVANCE

Gmelina philippensis CHAM is an ornamental plant that is distributed in South Asia and warm regions of the Mediterranean area. The plant is traditionally applied in folk medicine for the treatment of diabetes.

AIM OF THE STUDY

To evaluate the cytotoxic and the antidiabetic activities of the ethanolic extract of G. philippensis aerial parts. To isolate the metabolite(s) responsible for these activities and to elucidate the mechanism of action by molecular docking study.

MATERIALS AND METHODS

Compounds (1-11) were isolated using various chromatographic techniques and their structures were determined by NMR spectroscopic and mass spectrometric analysis. The cytotoxic effect was tested using viability test and MTT assay. Antidiabetic activity was evaluated by measuring the inhibitory activity of the ethanolic extracts and compounds against α-glucosidase and α-amylase activities. Modeling and docking simulations were performed using Molecular Operating Environment software and the crystal structure of protein kinases CDK2, (1PYE) and AKT1 (4GV1), in addition to α-glucosidase (3TOP) and α-amylase (2QV4).

RESULTS

Compounds 2, 3 and 8 were isolated for the first time from the plant and identified as: gmelinol (2), apigenin (3) and tyrosol (8). While β-sitosterol-3-O- β-D-glucopyranoside (4) vicenin-II (7), rhoifolin (9), isorhoifolin (11) were isolated for the first time from the genus, along with and the new iridoid 6-O-α-L-(2″-O-benzoyl-4″-O-trans-p-methoxycinnamoyl)rhamnopyranosyl-1α- β-D-glucopyranoside catalpolgenin (6). In addition, to the previously reported compounds: mixture of β -sitosterol and stigmasterol (1), and 6- O- α-L-(2″,3″,4″-tri-O -benzoyl)rhamnopyranosylcatalpol (5) and 6-O-α-L-(2″-O-trans-p-methoxycinnamoyl)rhamnopyranosylcatalpol (10). The cytotoxic activity against hepatocellular carcinoma (HepG-2) cell lines for compounds 2, 5, 7, 9 and 11 was conducted using cisplatin as a standard. Gmelinol (2) exhibited strong cytotoxic activity against HepG-2 cell lines with IC ₅₀ value of 3.6 ± 0.1 μg/ml which is more potent than the standard cisplatin IC ₅₀ = 8.7 ± 0.9 μg/ml. Molecular modeling of 2 against diverse targets of protein kinases suggested that CDK-2 and AKT-1 could be the dual probable kinase targets for its cytotoxic action. Compound 2 showed α-amylase inhibition activity with IC ₅₀ value of 60.9 (μg/ml) while, compounds 5 showed strong α-glucosidase inhibition activity with IC ₅₀ values of 41.7 (μg/ml) compared to acarbose with IC ₅₀ value of 34.7, 30.6 (μg/ml). Molecular docking of compounds 2 and 5 on α-glucosidase (3TOP) and α-amylase (2QV4) enzymes revealed high binding affinity and active site interactions comparable to native ligand acarbose.

CONCLUSION

The ethanolic extract of G. philippensis CHAM aerial parts is effective against HepG-2 cell lines, α-amylase and α-glucocidase activities. Biologically guided isolation indicated that compounds 2 and 5 are responsible for these activities. These results were supported by DMF calculations that detected the molecular areas responsible for protein interactions shown via docking studies.

3-(2-Bromo-eth-yl)-5,5-di-phenyl-imidazolidine-2,4-dione

The imidazolidine ring in the title mol-ecule, C₁₇H₁₅BrN₂O₂, is slightly ruffled [r.m.s. deviation = 0.0192 Å], while the attached phenyl rings at the C atom at the position between the amine and carbonyl centres are rotated well out of its mean plane [dihedral angles with the imidazolidine ring = 63.60 (8) and 76.4 (1)°]. In the crystal, a three-dimensional network features N-H⋯O and C-H⋯O hydrogen bonds together with C-H⋯π(ring) inter-actions.

3-Isobutyl-5,5-diphenylimidazolidine-2,4-dione

The imidazolidine ring in the title molecule, C19H20N2O2, is slightly `ruffled'. In the crystal, a layer structure is generated by N—H...O and C—H...O hydrogen bonds plus C—H...π(ring) interactions.

Preparation, DFT calculations, docking studies, antioxidant, and anticancer properties of new pyrazole and pyridine derivatives

Seven novel pyrazole derivatives (4a-g) and four novel starting compounds incorporating substituted pyridine moieties were synthesized successfully. Cell viability assay for the tested compounds was performed, and the inhibitory concentrationlogarithmic 50 (LogIC₅₀ ) values of the compounds were calculated after a 24-h treatment. Four of the examined compounds (3d, 3g, 4f, and 4g) showed comparable cytotoxic activity against CaCo-2 compared to the standard drug docetaxel at 0.1 and 1 μM concentrations. Although the LogIC₅₀  of docetaxel was -0.678 μM for CaCo-2 cells at 24 h, the LogIC₅₀ values of compounds were -0.794, -0.567, -0.657, and -0.498 μM, respectively. Five of the compounds (2d, 2g, 3d, 3g, and 4e) showed comparable cytotoxic activity against MCF-7 at 0.1 μM concentration compared to docetaxel (p < 0.05). Docking studies revealed the compounds have a good affinity to the active site of the human topoisomerase II β enzyme. The antioxidant capacities of all compounds were determined using both 1,1-diphenyl-2-picrylhydrazyl and metal chelation methods. Although the compounds did not show significant antioxidant activity, relatively effective are compounds 3c, 3d, and 3g, which are hydrazine derivatives with approximately 50% antioxidant activity of standard antioxidants at concentrations of 62.5 and 125 μg/ml.

A possible potential COVID-19 drug candidate: Diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate: Docking of disordered independent molecules of a novel crystal structure, HSA/DFT/XRD and cytotoxicity

This study reports the synthesis, characterization and importance of a novel diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate (MQOAHM). Two independent molecular structures of the disordered MQOAHM have been established by XRD‑single‑crystal analysis in a ratio of 0.596(3)/0.404(3), MQOAHM (a) and MQOAHM (b), respectively. MQOAHM was characterized by means of various spectroscopic tools ESI-MS, IR, ¹H &¹³C NMR analyses. Density Functional Theory (DFT) method, B3LYP, 6-311++G(d,p) basis set was used to optimize MQOAHM molecule. The obtained theoretical structure and experimental structure were superimposed on each other, and the correlation between them was calculated. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) were created, and the energy gap between these orbitals was calculated. For analyzing intermolecular interactions, Molecular Electrostatic Potential (MEP) and Hirshfeld Surface Analysis were studied. For a fair comparative study, the two forms of the title compound were docked together with 18 approved drugs and N3 under precisely the same conditions. The disordered molecule structure's binding scores against 7BQY were -7.0 and -6.9 kcal/mol^-1 for MQOAHM (a) and MQOAHM (b), respectively. Both the forms show almost identical superimposed structures and scores indicating that the disorder of the molecule, in this study, has no obvious effect. The high binding score of the molecule was attributed to the multi-hydrogen bond and hydrophobic interactions between the ligand and the receptor's active amino acid residues. Worth pointing out here that the aim of using the free energy in Silico molecular docking approach is to rank the title molecule compared to the wide range of approved drugs and a well-established ligand N3. The binding scores of all the molecules used in this study are ranged from -9.9 to -4.5 kcal/mol^-1. These results and the supporting statistical analyses suggest that this malonate-based ligand merits further research in the context of possible therapeutic agents for COVID-19. Cheap computational techniques, PASS, Way2drug and ADMET, online software tools, were used in this study to uncover the title compound's potential biological activities and cytotoxicity.

Pyrolyzed carbon derived from red soil as an efficient catalyst for cephalexin removal

Red soil, a typical soil type in southern China, has been deemed infertile or nutrient-deficient. In this study, red soil was firstly utilized as a substrate for preparing catalysts, which were then successfully applied to the catalytic wet peroxide oxidation (CWPO) of cephalexin. The highest cephalexin removal was 95.23% and TOC removal was 60.58%, with the catalyst pyrolyzed at 500 °C (RC500). The high iron content and proportion of Fe(II) on the surface of RC500 was responsible for the decomposition of H₂O₂ into· OH. Moreover, the porous structure and existence of other minerals (such as SiO₂ and Al₂O₃) in the catalyst were also significant for enhancing the catalytic activity of RC500. Afterwards, the influencing parameters, including temperature, pH, the dose of H₂O₂, and catalyst, were examined for cephalexin degradation. It was noteworthy that RC500 was efficient in treating hospital wastewater when using a self-design pilot device. A density functional theory analysis of cephalexin was conducted to establish the possible position attacked by ·OH, and the possibly ruptured one. Meanwhile, the intermediates generated during CWPO were identified. Finally, a reliable degradation pathway of cephalexin was proposed on the basis of the results.

Spectroscopic, density functional theoretical study, molecular docking, and in vitro studies based on anticancer activity studies against A549 lung cancer cell line of diphenylhydantoin adsorbed on AuNPs surface

The optimized geometry, FT-Raman, FT-IR, surface-enhanced Raman scattering, UV-Vis spectra, frontier molecular orbital analysis, molecular electrostatic potential analysis, and local and global reactivity descriptors of diphenylhydantoin (DPH) and diphenylhydantoin@AuNPs (DPHA) molecule have been investigated with the help of density functional theory method (B3LYP/6-31++G [d,p] together with LANL2DZ) and was compared and analyzed with the corresponding experimental data in order to identify their structural and bonding features responsible for their bioactivity. In-silico (molecular docking) biological activity screening of the molecules together with the in-vitro (SERS and MTT assay) analysis confirms the anticancer activity of DPH and DPHA molecules. The results of the structure-activity studies and bioactivity studies signify that the DPHA molecule is more active than the DPH molecule against lung cancer.

Crystal structure and Hirshfeld surface analysis of 2-(2-oxo-3-phenyl-1,2,3,8a-tetra-hydro-quinoxalin-1-yl)ethyl acetate

In the title mol-ecule, C18H16N2O3, the di-hydro-quinoxaline moiety, with the exception of the N atom is essentially planar with the inner part of the methyl-propano-ate group (CH2-CH2-O) nearly perpendicular to it. In the crystal, inversion dimers formed by C-H⋯O hydrogen bonds are connected into oblique stacks by π-stacking and C-H⋯π(ring) inter-actions.

Design, synthesis, structural and molecular characterization, toxicity, psychotropic activity and molecular docking evaluation of a novel phenytoin derivative: 3-decyl-5,5-diphenylimidazolidine-2,4-dione

The hydantoin scaffold is of substantial importance and it is commonly used in drug discovery. Herein, we report the synthesis of a novel phenytoine (a hydantoin derivative) with high yield by the reaction of phenytoin with 1-bromodecyl agent. Namely, 3-decyl-5,5- diphenylimidazolidine-2,4-dione (3DDID). The optimized geometry of the compound was calculated using density functional theory (DFT) method by B3LYP with 6-311++G(d,p) basis set. For this calculation, the X-ray data were used as initial values. Molecular electrostatic potential (MEP) surface and Frontier molecular orbitals (FOMs) were prepared for the compound. The crystal structure of the title compound contains intermolecular N-H···O, C-H···O hydrogen bonds and weak C-H···π interactions. Hirshfeld surface analysis and 2D fingerprint plots of the molecule aid comparison of intermolecular interactions and these analysis reveals that two close contacts are associated with intermolecular hydrogen bonds. The psychotropic activity evaluation of the synthesized compound was further explored using hole bored test for exploratory behaviors, dark//light box test for anxiolytic activity and Rota-road, traction, chimney testes were used to assess the myrelaxant effect. In addition, molecular modeling study was also conducted to rationalize the potential as neurotherapeutic drugs of our synthesized compound by predicting their binding modes, binding affinities and optimal orientation at the active site of the GABA-A receptor and Na⁺ channel. Finally, in silico ADMET predictions was also examined. HighlightsSynthesis, structural, and molecular characterization of a novel phenytoin derivative.DFT, XRD, and the Hirshfeld surface analysis of crystal structure was studied.Acute toxicity and psychotropic activity evaluation of 3-decyl-5,5 diphenylimidazolidine-2,4-dione (3DDID).Molecular modeling studies have been conducted to rationalize the obtained data and to determine the probable binding mode.Communicated by Ramaswamy H. Sarma.

Molecular modeling, density functional theory, ADME prediction and antimicrobial activity studies of 2-(substituted)oxazolo[4,5-b]pyridine derivatives

Molecular docking, molecular dynamics, DFT, ADME prediction, and antimicrobial activity studies of some 2-(substituted)oxazolo[4,5-b]pyridine derivatives were carried out.

Synthesis and crystal structure of 3-octyl-5,5-diphenylimidazolidine-2,4-dione, C23H28N2O2

C23H28N2O2, orthorhombic, Pbca (no. 61), a = 10.713(2) Å, b = 15.689(3) Å, c = 24.485(5) Å, V = 4115.2(14) Å3, Z = 8, Rgt(F) = 0.0581, wRref(F2) = 0.1734, T = 120(2) K.