Experimental and theoretical characterization of organic salt: 2-((4-bromophenyl)amino) pyrido[1,2- a ] quinoxalin-11-ium bromide monohydrate synthesized via oxidative cyclization

Identification of Novel Tau-Tubulin Kinase 2 Inhibitors Using Computational Approaches

Tau tubulin kinase 2 (TTBK2) associated with multiple diseases is one of the kinases which phosphorylates tau and tubulin. Numerous efforts have been made to understand the role of TTBK2 in protein folding mechanisms and misfolding behavior. The misfolded protein intermediates form polymers with unwanted aggregation properties that initiate several diseases, including Alzheimer's. The availability of TTBK2 inhibitors can enhance the understanding of the molecular mechanism of action of the kinase and assist in developing novel therapeutics. In the quest for TTBK2 inhibitors, this study focuses on screening two chemical libraries (ChEMBL and ZINC-FDA). The molecular docking, RO5/absorption, distribution, metabolism, and excretion/toxicity, density functional theory, molecular dynamics (MD) simulations, and molecular mechanics with generalized Born and surface area solvation techniques enabled shortlisting of the four most active compounds, namely, ChEMBL1236395, ChEMBL2104398, ChEMBL3427435, and ZINC000000509440. Moreover, 500 ns MD simulation was performed for each complex, which provided valuable insights into the structural changes in the complexes. The relative fluctuation, solvent accessible surface area, atomic gyration, compactness covariance, and free energy landscapes revealed that the compounds could stabilize the TTBK2 protein. Overall, this study would be valuable for the researchers targeting the development of novel TTBK2 inhibitors.

Designing of new tetrahydro-β-carboline-based ABCG2 inhibitors using 3D-QSAR, molecular docking, and DFT tools

Human ATP-binding cassette superfamily G member 2 (ABCG2) protein is a member of the ABC transporter family, which is responsible for multidrug resistance (MDR) in cancerous cells. MDR reduces the effectiveness of chemotherapy in breast cancer, which is one of the leading causes of death in women globally. MDR in cancer cells is one of the immediate signs of progression of resistance; thus, various anticancer drugs can be designed. To reduce MDR, we utilized the tetrahydro-β-carboline (THβC) compound library. We accomplished a three-dimensional quantitative structure-activity relationship (3D-QSAR), scaffold hopping to design a new library of compounds of THβC, and further molecular docking, induced-fit docking (IFD), molecular mechanics energies combined with generalized born and surface area continuum solvation (MM-GBSA), drug-like features, ADMET properties, and density functional theory (DFT) studies were performed. From these studies, the best 3D-QSAR model (r2 = 0.99, q2 = 0.92) was found, and the necessity of electrostatic, steric, and hydrophobic field effects were determined that could modulate bioactivity. Moreover, based on electrostatic, steric, and hydrophobic field notations, new THβC derivatives (3409) were designed. These findings might provide new insight for researchers to perform in vitro and in vivo studies for better antagonists against MDR in treating breast cancer.Communicated by Ramaswamy H. Sarma.

Crystal structure, Hirshfeld surface analysis and DFT studies of (E)-4-methyl-2-{[(2-methyl-3-nitro-phen-yl)imino]-meth-yl}phenol

The title compound, C15H14N2O3, was prepared by condensation of 2-hy-droxy-5-methyl-benzaldehyde and 2-methyl-3-nitro-phenyl-amine in ethanol. The configuration of the C=N bond is E. An intra-molecular O-H⋯N hydrogen bond is present, forming an S(6) ring motif and inducing the phenol ring and the Schiff base to be nearly coplanar [C-C-N-C torsion angle of 178.53 (13)°]. In the crystal, mol-ecules are linked by C-H⋯O inter-actions, forming chains along the b-axis direction. The Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (37.2%), C⋯H (30.7%) and O⋯H (24.9%) inter-actions. The gas phase density functional theory (DFT) optimized structure at the B3LYP/ 6-311 G(d,p) level is compared to 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 DFT studies of (E)-2-{[(3-chloro-4-methyl-phen-yl)imino]-meth-yl}-4-methyl-phenol

The title compound, C15H14ClNO, was synthesized by condensation reaction of 2-hy-droxy-5-methyl-benzaldehyde and 3-chloro-4-methyl-aniline, and crystallizes in the monoclinic space group P21/c. The 3-chloro-benzene ring is inclined to the phenol ring by 9.38 (11)°. The configuration about the C=N bond is E and an intra-molecular O-H⋯N hydrogen bond forms an S(6) ring motif. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the packing arrangement are from H⋯H (43.8%) and C⋯H/H⋯C (26.7%) inter-actions. The density functional theory (DFT) optimized structure at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure and the HOMO-LUMO energy gap is provided.

Synthesis, crystal structure at 219 K and Hirshfeld surface analyses of 1,4,6-tri-methyl-quinoxaline-2,3(1H,4H)-dione monohydrate

The asymmetric unit of the title compound, C11H12N2O2·H2O, contains a mol-ecule of 1,4,6-trimethyl-1,4-di-hydro-quinoxaline-2,3-dione and a solvent water mol-ecule. Four atoms of the benzene ring are disordered over two sets of sites in a 0.706 (7):0.294 (7) ratio while the N-bound methyl groups are rotationally disordered with occupancy ratios of 0.78 (4):0.22 (4) and 0.76 (5):0.24 (5). In the crystal, mol-ecules are linked by O-H⋯O and C-H⋯O hydrogen bonds into layers lying parallel to (10). The Hirshfeld surface analysis indicates that the most important contributions to the packing arrangement are due to H⋯H (51.3%) and O⋯H/H⋯O (28.6%) inter-actions. The mol-ecular structure calculated by density functional theory is compared with the experimentally determined mol-ecular structure, and the HOMO-LUMO energy gap has been calculated.

Crystal structure, Hirshfeld surface analysis and DFT studies of 2-[(2-hy-droxy-5-methyl-benzyl-idene)amino]-benzo-nitrile

The title compound, C15H12N2O, was synthesized by condensation reaction of 2-hy-droxy-5-methyl-benzaldehyde and 2-amino-benzo-nitrile, and crystallizes in the ortho-rhom-bic space group Pbca. The phenol ring is inclined to the benzo-nitrile ring by 25.65 (3)°. The configuration about the C=N bond is E, stabilized by a strong intra-molecular O-H⋯N hydrogen bond that forms an S(6) ring motif. In the crystal, C-H⋯O and C-H⋯N inter-actions lead to the formation of sheets perpendicular to the a axis. C-H⋯π inter-actions, forming polymeric chains along the a-axis direction, connect these sheets into a three-dimensional network. A Hirshfeld surface analysis indicates that the most important contributions for the packing arrangement are from H⋯H and C⋯H/H⋯C inter-actions. The density functional theory (DFT) optimized structure at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure and the HOMO-LUMO energy gap is given.

Crystal structure, Hirshfeld surface analysis and DFT studies of 4-methyl-2-({[4-(tri-fluoro-meth-yl)phen-yl]imino}-meth-yl)phenol

The title compound, C15H12F3NO, crystallizes with one mol-ecule in the asymmetric unit. The configuration of the C=N bond is E and there is an intra-molecular O-H⋯N hydrogen bond present, forming an S(6) ring motif. The dihedral angle between the mean planes of the phenol and the 4-tri-fluoro-methyl-phenyl rings is 44.77 (3)°. In the crystal, mol-ecules are linked by C-H⋯O inter-actions, forming polymeric chains extending along the a-axis direction. The Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from C⋯H/H⋯C (29.2%), H⋯H (28.6%), F⋯H/H⋯F (25.6%), O⋯H/H⋯O (5.7%) and F⋯F (4.6%) inter-actions. The density functional theory (DFT) optimized structure at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure in the solid state. The HOMO-LUMO behaviour was elucidated to determine the energy gap. The crystal studied was refined as an inversion twin.

Crystal structure, Hirshfeld surface analysis and DFT studies of (E)-4-methyl-2-{[(4-methyl-phen-yl)imino]-meth-yl}phenol

In the title compound, C15H15NO, the configuration of the C=N bond of the Schiff base is E, and an intra-molecular O-H⋯N hydrogen bond is observed, forming an intra-molecular S(6) ring motif. The phenol ring is inclined by 45.73 (2)° from the plane of the aniline ring. In the crystal, mol-ecules are linked along the b axis by O-H⋯N and C-H⋯O hydrogen bonds, forming polymeric chains. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the packing arrangement are from H⋯H (56.9%) and H⋯C/C⋯H (31.2%) inter-actions. The density functional theory (DFT) optimized structure at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined mol-ecular structure, and the HOMO-LUMO energy gap is provided. The crystal studied was refined as an inversion twin.

Crystal structure and Hirshfeld surface analysis of 2-{[(4-iodo-phen-yl)imino]-meth-yl}-4-nitro-phenol

The title compound, C13H9IN2O3, was synthesized by a condensation reaction between 2-hy-droxy-5-nitro-benzaldehyde and 4-iodo-aniline, and crystallizes in the ortho-rhom-bic space group Pna21. The 4-iodo-benzene ring is inclined to the phenol ring by a dihedral angle of 39.1 (2)°. The configuration about the C=N double bond is E. The crystal structure features C-H⋯O hydrogen-bonding inter-actions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the packing arrangement are O⋯H/H⋯O (26.9%) and H⋯H (22.0%) inter-actions.

Dichlorido{N,N,N′-trimethyl-N′-(1H-pyrazol-1-yl-κN 2)methyl]ethane-1,2-diamine-κ2 N,N′}copper(II) methanol monosolvate

In the title compound, [CuCl2(C9H18N4)]·CH3OH, the central CuII ion is coordinated by three N atoms from the pyrazole derivative ligand and two chloride co-ligands. The coordination geometry around the CuII ion is distorted trigonal–bipyramidal. In the crystal, the molecules are linked by C—H...O, C—H...Cl and O—H...Cl hydrogen bonds, forming a three-dimensional framework with the lattice solvent molecule.

Crystal structure of 4-(2-hy-droxy-3-meth-oxy-benzyl-amino)-benzoic acid di-methyl-formamide monosolvate monohydrate

The title compound, C15H15NO4·C3H7NO·H2O, a secondary amine mol-ecule, is accompanied by one equivalent of water and one equivalent of di-methyl-formamide (DMF) as solvents. The mol-ecule is non-planar, with a Car-yl-CH2-NH-Car-yl torsion angle of -66.3 (3)°. In the crystal, O-H⋯O and N-H⋯O hydrogen-bonding inter-actions between the amine mol-ecules and the two types of solvent mol-ecule result in the formation of a layered structure extending parallel to (010).

Crystal structure and Hirshfeld surface analysis of (E)-2-[1-hy-droxy-2-(pyridin-2-yl)eth-yl]-4-[2-(4-meth-oxy-phen-yl)diazen-1-yl]phenol

In the title compound, C20H19N3O3, the configuration about the azo N=N bond is E, and the central benzene ring is inclined to the pyridine ring by 31.43 (8)° and to the 4-meth-oxy-phenyl ring by 4.73 (8)°. In the crystal, mol-ecules are linked by pairs of O-H⋯N hydrogen bonds, forming inversion dimers with an R 2 2(12) ring motif. The dimers are linked by O-H⋯O and C-H⋯O hydrogen bonds, forming layers parallel to the ac plane. There are C-H⋯π inter-actions present within the layers and between the layers, leading to the formation of a supra-molecular framework. The layers are also linked by offset π-π inter-actions, with an inter-planar distance of 3.416 (2) Å.

Crystal structure of 4-[(2-hy-droxy-3-meth-oxy-benz-yl)amino]-benzoic acid hemihydrate

In the crystal of the title vanilline derivative, 2C15H15NO4·H2O, the secondary amine mol-ecule is accompanied by half equivalent of water. The mol-ecule is non-planar, with torsion angle Car-yl-CH2-NH-Car-yl of -83.9 (2)°. In the crystal, the system of O-H⋯O hydrogen bonds, including bridging water mol-ecules residing on crystallographic twofold axes, results in a two-dimensional layered structure. Within the layers, there are also weak N-H⋯π inter-actions involving the vanilline benzene ring.

trans-Bis{2-[bis(1H-pyrazol-1-yl)methyl]-1-methyl-1H-benzimidazole}iron(II) bis(perchlorate) acetonitrile disolvate

In the structure of the title complex, [Fe(C15H14N6)2](ClO4)2·2C2H3N, the asymmetric unit contains one complete ligand molecule, one perchlorate and one acetonitrile solvent molecule. The iron(II) atom, situated on an inversion centre, is surrounded by six nitrogen atoms from two ligands in an octahedral coordination sphere in which the two benzimidazole units adopt a trans-configuration. The crystal structure is stablized by extensive weak C—H...O and C—H...N interactions.

Crystal structure of 4-[(3-meth-oxy-2-oxidobenzyl-idene)azaniumyl]-benzoic acid methanol monosolvate

In the crystal of the title compound, C15H13NO4·CH3OH, the Schiff base mol-ecule exists in the zwitterionic form; an intra-molecular N-H⋯O hydrogen bond stabilizes the mol-ecular structure. The benzene rings are nearly co-planar, subtending a dihedral angle of 5.34 (2)°. In the crystal, classical O-H⋯O and weak C-H⋯O hydrogen bonds link the Schiff base mol-ecules and methanol solvent mol-ecules into a three-dimensional supra-molecular architecture. The crystal studied was refined as an inversion twin.

Designing of phenol-based β-carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach

Tuberculosis (Tb) is an airborne infectious disease caused by Mycobacterium tuberculosis. Beta-carbonic anhydrase 1 (β-CA1) has emerged as one of the potential targets for new antitubercular drug development. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulation approaches were performed on a series of natural and synthetic phenol-based β-CA1 inhibitors. The developed 3D-QSAR model (r² = 0.94, q² = 0.86, and pred_r² = 0.74) indicated that the steric and electrostatic factors are important parameters to modulate the bioactivity of phenolic compounds. Based on this indication, we designed 72 new phenolic inhibitors, out of which two compounds (D25 and D50) effectively stabilized β-CA1 receptor and, thus, are potential candidates for new generation antitubercular drug discovery program.