Synthesis, crystal structure, spectroscopic characterization, DFT calculations, Hirshfeld surface analysis, molecular docking, and molecular dynamics simulation investigations of novel pyrazolopyranopyrimidine derivatives.

A series of new pyrazolopyranopyrimidine derivatives (3-9) were synthesized from 5-amino-2,4-dihydro-3-methyl-4-phenylpyrano-[2,3-c]pyrazole-5-carbonitrile (2) by multicomponent reactions (MCR) involving malononitrile, benzaldehyde, and pyrazolone under refluxing ethanol in the presence of piperidine. Compound (2) was then converted to 2-acetylpyrazolopyranopyrimidine (3) through a reaction with acetic anhydride. The deprotection of 3 using ammonium hydroxide in ethanol, leads to 4. Subsequent chlorination of 4 by phosphorus oxychloride affords 5 which was alkylated using methyl iodide and ethyl bromoacetate in DMF, leading to regioisomers 6-9. The products were characterized by spectroscopic techniques (1H and 13C NMR) and confirmed by single crystal X-ray diffraction (XRD) studies for 2, 5, 6, and 9. Moreover, the geometrical parameters, molecular orbital calculations, and spectral data of 2, 5, 6, and 9 were compared by DFT at the B3LYP/6-311G(d,p) level of theory. There is good agreement between the calculated results and the experimental data. The intermolecular contacts for 2, 5, 6, and 9 were studied by Hirshfeld surface analysis. In addition, the molecular docky study was conducted to investigate the binding patterns of 2, 5, 6, and 9 within the binding site of cyclin-dependent kinase 2 (CDK2) and penicillin-binding protein 1 A. After the docking process, molecular dynamics (MD) simulations for 100 ns were performed on CDK2 and PBP 1 A proteins in the complex with 5.Communicated by Ramaswamy H. Sarma.

Discovery of a new Bcl-2 inhibitor through synthesis, anticancer activity, docking and MD simulations.

A database of 300 compounds was virtually screened and docked against Bcl-2 protein; the stability of the best-formed complex was evaluated through Molecular dynamics, the top ten compounds with the best in-silico complexation affinities were synthesized, and their In-vitro cytotoxic activity was examined. Thiazolidinone (4e) and isoxazoline (4a-d) were evaluated in-silico. For further evaluation and examination, we designed and synthesized from naturally occurring (R)-carvone and characterized it via spectroscopic analysis, as well as tested for their anticancer activities towards human cancer cell lines such as HT-1080 (fibrosarcome cancer), MCF-7 and MDA-MB-231 (breast cancer) and A-549 (lung cancer) by using MTT method with Doxorubicin as standard drug. Among them, compound 4d showed the most promising anticancer activity against HT-1080, A-549, MCF-7, and MDA-MB-231 cell lines with IC50 values of 15.59 ± 3.21 µM; 18.32 ± 2.73 µM; 17.28 ± 0.33 µM and 19.27 ± 2.73 µM respectively.Communicated by Ramaswamy H. Sarma.

Hybrids of thiazolidinone with 1,2,3-triazole derivatives: design, synthesis, biological evaluation, in silico studies, molecular docking, molecular dynamics simulations, and ADMET profiling.

A new series of thiazolidinone linked 1,2,3-triazole hybrids 5a-h was designed and synthesized using the copper-catalyzed Huisgen azide-alkyne cycloaddition (CuAAC) between thiazolidinone linked alkyne and aromatic azides. The structures of the newly synthesized compounds were established by NMR (1H and 13C) and HRMS. The targeted thiazolidinone-1,2,3-triazole hybrids were evaluated for their cytotoxic activity against four human cancer cell lines, including fibrosarcoma (HT-1080), lung carcinoma (A-549), and breast carcinoma (MCF-7 and MDA-MB-231) using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliun bromide (MTT). The obtained data showed that most of these compounds have moderate anti-proliferative activity with IC50 values between 10.26 ± 0.71 and 53.93 ± 1.20 µM. The compound 5a exhibited higher activity with an IC50 value of 10.26 ± 0.71 µM, compared to 5d with an IC50 value of 11.56 ± 1.98 µM for the HT-1080 and MCF-7 cancer cells line, respectively. Moreover, Annexin-V apoptosis was assessed by flow cytometry for hybrid compounds 5a and 5d against HT-1080 and MCF-7 competitor cell lines, as they increase the level of active caspase 3/7. The experimental results were further confirmed by docking studies followed by molecular dynamic simulations. Both the potent derivatives i.e. 5a and 5d have comparable docking scores and MD simulations results showed that the docked complex of 5a is somewhat more stable than 5d primarily for protein p53. The ADMET profile of both derivatives established their safety zone and drug-like potential.Communicated by Ramaswamy H. Sarma.

Crystal structure, Hirshfeld surface analysis and inter-action energy calculation of 1-decyl-2,3-di-hydro-1H-benzimidazol-2-one.

The title mol-ecule, C17H26N2O, adopts an L-shaped conformation, with the straight n-decyl chain positioned nearly perpendicular to the di-hydro-benzimidazole moiety. The di-hydro-benzimidazole portion is not quite planar as there is a dihedral angle of 1.20 (6)° between the constituent planes. In the crystal, N-H⋯O hydrogen bonds form inversion dimers, which are connected into the three-dimensional structure by C-H⋯O hydrogen bonds and C-H⋯π(ring) inter-actions. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (75.9%), H⋯C/C⋯H (12.5%) and H⋯O/O⋯H (7.0%) inter-actions. Based on computational chemistry using the CE-B3LYP/6-31 G(d,p) energy model, C-H⋯O hydrogen bond energies are -74.9 (for N-H⋯O) and -42.7 (for C-H⋯O) kJ mol-1.

Crystal structure, Hirshfeld surface analysis and DFT studies of 1-benzyl-3-[(1-benzyl-1H-1,2,3-triazol-5-yl)meth-yl]-2,3-di-hydro-1H-1,3-benzo-diazol-2-one monohydrate.

In the title mol-ecule, C24H21N5O·H2O, the di-hydro-benzo-diazole moiety is not quite planar, while the whole mol-ecule adopts a U-shaped conformation in which there is a close approach of the two benzyl groups. In the crystal, chains of alternating mol-ecules and lattice water extending along [201] are formed by O-HUncoordW⋯ODhyr and O-HUncoordW⋯NTrz (UncoordW = uncoordinated water, Dhyr = di-hydro and Trz = triazole) hydrogen bonds. The chains are connected into layers parallel to (010) by C-HTrz⋯OUncoordW hydrogen bonds with the di-hydro-benzo-diazole units in adjacent layers inter-calating to form head-to-tail π-stacking [centroid-to-centroid distance = 3.5694 (11) Å] inter-actions between them, which generates the overall three-dimensional structure. Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (52.1%), H⋯C/C⋯H (23.8%) and O⋯H/H⋯O (11.2%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Density functional theory (DFT) optimized structures at the B3LYP/ 6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure, Hirshfeld surface analysis and inter-action energy and DFT studies of (2Z)-4-benzyl-2-(2,4-di-chloro-benzyl-idene)-2H-1,4-benzo-thia-zin-3(4H)-one.

The title compound, C22H15Cl2NOS, contains 1,4-benzo-thia-zine and 2,4-di--chloro-benzyl-idene units, where the di-hydro-thia-zine ring adopts a screw-boat conformation. In the crystal, inter-molecular C-HBnz⋯OThz (Bnz = benzene and Thz = thia-zine) hydrogen bonds form corrugated chains extending along the b-axis direction which are connected into layers parallel to the bc plane by inter-molecular C-HMethy⋯SThz (Methy = methyl-ene) hydrogen bonds, en-closing R 4 4(22) ring motifs. Offset π-stacking inter-actions between 2,4-di--chloro-phenyl rings [centroid-centroid = 3.7701 (8) Å] and π-inter-actions which are associated by C-HBnz⋯π(ring) and C-HDchlphy⋯π(ring) (Dchlphy = 2,4-di-chloro-phen-yl) inter-actions may be effective in the stabilization of the crystal structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (29.1%), H⋯C/C⋯H (27.5%), H⋯Cl/Cl⋯H (20.6%) and O⋯H/H⋯O (7.0%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Computational chemistry indicates that in the crystal, the C-HBnz⋯OThz and C-HMethy⋯SThz hydrogen-bond energies are 55.0 and 27.1 kJ mol-1, respectively. Density functional theory (DFT) optimized structures at the B3LYP/6-311G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure, Hirshfeld surface analysis and inter-action energy and DFT studies of 3-{(2Z)-2-[(2,4-di-chloro-phen-yl)methyl-idene]-3-oxo-3,4-di-hydro-2H-1,4-benzo-thia-zin-4-yl}propane-nitrile.

The title compound, C18H12Cl2N2OS, consists of a di-hydro-benzo-thia-zine unit linked by a -CH group to a 2,4-di-chloro-phenyl substituent, and to a propane-nitrile unit is folded along the S⋯N axis and adopts a flattened-boat conformation. The propane-nitrile moiety is nearly perpendicular to the mean plane of the di-hydro-benzo-thia-zine unit. In the crystal, C-HBnz⋯NPrpnit and C-HPrpnit⋯OThz (Bnz = benzene, Prpnit = propane-nitrile and Thz = thia-zine) hydrogen bonds link the mol-ecules into inversion dimers, enclosing R 2 2(16) and R 2 2(12) ring motifs, which are linked into stepped ribbons extending along [110]. The ribbons are linked in pairs by complementary C=O⋯Cl inter-actions. π-π contacts between the benzene and phenyl rings, [centroid-centroid distance = 3.974 (1) Å] may further stabilize the structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (23.4%), H⋯Cl/Cl⋯H (19.5%), H⋯C/C⋯H (13.5%), H⋯N/N⋯H (13.3%), C⋯C (10.4%) and H⋯O/O⋯H (5.1%) inter-actions. Hydrogen bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing. Computational chemistry calculations indicate that the two independent C-HBnz⋯NPrpnit and C-HPrpnit⋯OThz hydrogen bonds in the crystal impart about the same energy (ca 43 kJ mol-1). Density functional theory (DFT) optimized structures at the B3LYP/6-311 G(d,p) level are compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap.

Crystal structure and Hirshfeld surface analysis of 3,4-dihydro-2-(2,4-dioxo-6-methylpyran-3-ylidene)-4-(4-pyridin-4-yl)-1,5-benzodiazepine.

The title compound, C20H17N3O3 [systematic name: 2-(6-methyl-2,4-dioxo-pyran-3-yl-idene)-4-(pyridin-4-yl)-2,3,4,5-tetra-hydro-1H-1,5-benzodiazepine], is built up from a benzodiazepine ring system linked to pyridyl and pendant di-hydro-pyran rings, where the benzene and pyridyl rings are oriented at a dihedral angle of 43.36 (6)°. The pendant di-hydro-pyran ring is rotationally disordered in a 90.899 (3):0.101 (3) ratio with the orientation of each component largely determined by intra-molecular N-HDiazp⋯ODhydp (Diazp = diazepine and Dhydp = di-hydro-pyran) hydrogen bonds. In the crystal, mol-ecules are linked via pairs of weak inter-molecular N-HDiazp⋯ODhydp hydrogen bonds, forming inversion-related dimers with R 2 2(26) ring motifs. The dimers are further connected along the b-axis direction by π-π stacking inter-actions between the pendant di-hydro-pyran and pyridyl rings with centroid-centroid distances of 3.833 (3) Šand a dihedral angle of 14.51 (2)°. Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (50.1%), H⋯C/C⋯H (17.7%), H⋯O/O⋯H (16.8%), C⋯C (7.7%) and H⋯N/N⋯H (5.3%) inter-actions. Hydrogen-bonding and van der Waals inter-actions are the dominant inter-actions in the crystal packing.

Dichlorido(3,5,5'-trimethyl-1,3'-bi-1H-pyrazole-κN,N)copper(II).

In the title complex, [CuCl(2)(C(9)H(12)N(4))], the Cu(II) atom exhibits a distorted square-planar coordination geometry involving two chloride ions and two N-atom donors from the bipyrazole ligand. The chelate ring including the Cu(II) atom is essentially planar, with a maximum deviation of 0.0181 (17) Šfor one of the coordinated N atoms. This plane forms a dihedral angle of 30.75 (6)° with the CuCl(2) plane. In the crystal, each pair of adjacent mol-ecules is linked into a centrosymmetric dimer by N-H⋯Cl hydrogen bonds. The crystal structure is stabilized by inter-molecular C-H⋯N and C-H⋯Cl hydrogen bonds and weak slipped π-π stacking inter-actions between symmetry-related mol-ecules, with an inter-planar separation of 3.439 (19) Šand a centroid-centroid distance of 3.581 (19) Å.