Synthesis, Characterization, DFT, and In Silico Investigation of Two Newly Synthesized ß-Diketone Derivatives as Potent COX-2 Inhibitors.

Despite extensive genetic and biochemical characterization, the molecular genetic basis underlying the biosynthesis of ß-diketones remains largely unexplored. ß-Diketones and their complexes find broad applications as biologically active compounds. In this study, in silico molecular docking results revealed that two ß-diketone derivatives, namely 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione and 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione, exhibit anti-COX-2 activities. However, recent docking results indicated that the relative anti-COX-2 activity of these two studied ß-diketones was influenced by the employed docking programs. For improved design of COX-2 inhibitors from ß-diketones, we conducted molecular dynamics simulations, density functional theory (DFT) calculations, Hirshfeld surface analysis, energy framework, and ADMET studies. The goal was to understand the interaction mechanisms and evaluate the inhibitory characteristics. The results indicate that 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione shows greater anti-COX-2 activity compared to 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione.

Crystal structure, Hirshfeld surface analysis and DFT study of (5E,5'E,6Z,6'Z)-6,6'-[ethane-1,2-diyl-bis(aza-nylyl-idene)]bis-{5-[2-(4-fluoro-phen-yl)hydra-zono]-3,3-di-methyl-cyclo-hexa-none} 2.5-hydrate.

The title compound, C30H34F2N6O2·2.5H2O, was obtained by condensation of 2-[2-(4-fluoro-phen-yl)hydrazono]-5,5-di-methyl-cyclo-hexan-1,3-dione with ethyl-enedi-amine in ethanol and crystallized as a 1:2.5 hydrate in space group C2/c. The two independent mol-ecules, with approximate crystallographic C 2 symmetries, have different conformations and packing environments, are stabilized by intra-molecular N-H⋯N hydrogen bonds and linked by O-H⋯O hydrogen bonds involving the water mol-ecules. A Hirshfeld surface analysis showed that H⋯H contacts make by far the largest (48-50%) contribution to the crystal packing. From DFT calculations, the LUMO-HOMO energy gap of the mol-ecule is 0.827 eV.

Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA.

In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.

One-pot synthesis, X-ray crystal structure, and identification of potential molecules against COVID-19 main protease through structure-guided modeling and simulation approach.

Although antimicrobial resistance before the Covid-19 pandemic is a top priority for global public health, research is already ongoing on novel organic compounds with antimicrobial and antiviral properties in changing medical environments in connection with Covid 19. Thanks to the Biginelli reaction, which allows the synthesis of pyrimidine compounds, blockers of calcium channels, antibodies, antiviral, antimicrobial, anti-inflammatory, or antioxidant therapeutic compounds were investigated. In this paper, we aim to present Biginelli's synthesis, its therapeutic properties, and the structural-functional relationship in the test compounds that allows the synthesis of antimicrobial compounds. Both the DFT and TD-DFT computations of spectral data, molecular orbitals (HOMO, LUMO) analysis, and electrostatic potential (MEP) surfaces are carried out as an add-on to synthetic research. Hirshfeld surface analysis was also used to segregate the different intermolecular hydrogen bonds involved in the molecular packing strength. Natural Bond Orbital (NBO) investigation endorses the existence of intermolecular interactions mediated by lone pair, bonding, and anti-bonding orbitals. The dipole moment, linear polarizability, and first hyperpolarizabilities have been explored as molecular parameters. All findings based on DFT exhibit the best consistency with experimental findings, implying that synthesized molecules are highly stable. To better understand the binding mechanism of the SARS-CoV-2 Mpro, we performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations.

Molecular docking study and molecular dynamics simulation of ethyl 3,5-diphenyl-1H-pyrrole-2-carboxylate and (Z)-ethyl-2-(3-oxo-1,3-diphenylprop-1-enylamino)acetate.

The present analysis has been performed in the wet-lab and computational environments. First, the synthesis of the latest heterocyclic compounds containing the alkyl organic compound fragment of acetate and glycine acid were obtained and then their crystal structure and biological activity were studied. (Z)-ethyl-2-(3-oxo-1,3-diphenylprop-1-enylamino) acetate (1) was initially retrieved on the supported reaction of dibenzene gas with glycine alkyl organic compound-complex within the presence of Y(OTF)3 catalyst in liquid medium. At an identical time, ethyl-3,5-diphenyl-1H-pyrrole-2-carboxylate (2) was synthesized from the interaction of amino alkane with tert-BuOK in the presence of tert-BuOH/DMFA solvent. The structure of the latest compounds has been studied by 1 H, 13 C NMR. Additionally, the crystal structure of ethyl-3,5-diphenyl-1H-pyrrole-2-carboxylate (2) is conferred. Moreover, computational drug-likeness and pharmacokinetics indicated the compounds' good drug-like molecules and friendly pharmacokinetics, making the compound valuable candidates to be explored for additional structural modification to act as a potential inhibitor of AChE and α-glycosidase enzymes.

Synthesis, crystal structure, and biological evaluation of optically active 2-amino-4-aryl-7,7-dimethyl-5-oxo-5,6,7,8-tetrahydro-4H-chromen-3-carbonitriles: Antiepileptic, antidiabetic, and anticholinergics potentials.

In the presence of chiral organic catalysts, the optically active 4H-chromine was synthesized from the multicomponent condensation of 5,5-dimethylcyclohexane-1,3-dione with malononitrile and methylene-active compound, and the specific angle of rotation of the compounds was determined in the AUTOPOL-III polarimeter and their structures were confirmed by the X-ray spectroscopic analysis method. These optically active 2-amino-4-aryl-7,7-dimethyl-5-oxo-5,6,7,8-tetrahydro-4H-chromen-3-carbonitriles were effective inhibitors of α-glycosidase, the cytosolic carbonic anhydrase I and II isoforms (hCA I and II), and acetylcholinesterase (AChE) enzymes with Ki values in the range of 21.33 ± 1.11 to 40.24 ± 10.78 µM for hCA I, 28.91 ± 6.51 to 59.97 ± 15.62 µM for hCA II, 18.16 ± 3.18 to 66.57 ± 1.36 µM for α-glycosidase, and 8.68 ± 0.93 to 102.61 ± 24.96 µM for AChE.

Ethyl 4-(5-bromo-2-hy-droxy-phen-yl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate.

In the title compound, C21H24BrNO4, the dihedral angle between the heterocyclic ring and the pendant aromatic ring is 80.20 (13)°. The hexahydroquinone [i.e. the one with the C=O group] ring adopts a sofa conformation. An intra-molecular O-H⋯O hydrogen bond generates an S(6) ring motif. The ethyl group is disordered over two sets of sites with a refined site occupancy ratio of 0.633 (10):0.366 (10). In the crystal, mol-ecules are linked by N-H⋯O inter-actions, forming chains parallel to [101]. There are no significant C-H⋯π or π-π inter-actions in the crystal structure.

Ethyl 2,7,7-trimethyl-5-oxo-4-phenyl-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate.

In the title compound, C(21)H(25)NO(3), the hydro-pyridine ring that constitutes a part of the hexa-hydro-quinoline fused-ring system adopts a sofa conformation; the methine C atom deviates from the least-squares plane defined by the remaining five non-H atoms (r.m.s. deviation = 0.088 Å) by 0.454 (3) Å. The phenyl ring is aligned at 85.5 (1)° with respect to this mean plane. In the crystal, adjacent molecules are linked via an N-H⋯O hydrogen bond, involving the amino group and the carbonyl O atom of the fused-ring system, forming chains running along [100]. The ethyl group is disordered over two positions in a 0.609 (6):0.391 (6) ratio.

9-(2-Hy-droxy-4,4-dimethyl-6-oxocyclo-hex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetra-hydro-1H-xanthen-1-one.

The cyclo-hexene ring that constitutes a part of the tetra-hydroxanthene fused-ring system of the title compound, C(23)H(26)O(4), adopts a flattened half-chair conformation that approximates an envelope conformation (in which the methyl-ene C atom bearing the two methyl substituents represents the flap) as five of the six atoms lie approximately on a plane (r.m.s. deviation = 0.020 Å). The mean plane of the cyclo-hexene ring with the hy-droxy substituent is approximately perpendicular to the mean plane of the tetra-hydroxanthene system. In the crystal, adjacent mol-ecules are linked by O-H⋯O(carbon-yl) hydrogen bonds into a chain running along the b axis.

1-(9-Methyl-11-sulfanyl-idene-8-oxa-10,12-diaza-tricyclo-[7.3.1.0]trideca-2,4,6-trien-13-yl)ethanone.

The six-membered oxacyclo-hexene ring of the title compound, C(13)H(14)N(2)O(2)S, is fused with the benzene ring and the quarternary C atom lies above the plane of the benzene ring by 0.229 (8) Å, whereas the methine C atom (which bears the acetyl substituent) lies below this plane by 0.595 (8) Å. The oxacyclo-hexene ring is also fused with the sofa-shaped 2,6-diaza-cyclo-hexa-none ring. The methine C atom that belongs to both six-membered rings lies above the mean plane of the other five atoms (r.m.s. deviation = 0.077 Å) by 0.759 (5) Å. In the crystal, N-H⋯S hydrogen bonds link adjacent mol-ecules into a linear chain.

1-(2-Oxo-3,4-dihydro-2H-1,3-benzoxazin-4-yl)urea monohydrate.

The organic molecule in the title hydrate, C(9)H(9)N(3)O(3)·H(2)O, was obtained by the condenstation of salicylic aldehyde with urea in acetonitrile. The oxazine ring adopts a slightly distorted sofa conformation, with the N atom deviating from the plane passing through the other atoms of the ring by 0.267 (2) Å. The crystal structure displays inter-molecular N-H⋯O and O-H⋯O hydrogen bonding.