Synthesis, crystal structure, DFT, Hirshfeld surface analysis, energy frameworks and in-Silico drug-targeting PFKFB3 kinase of novel triazolequinoxalin derivative (TZQ) as a therapeutic Strategy against cancer

Overall, drug design is a dynamic and evolving field, with researchers constantly working to improve their understanding of molecular interactions, develop new computational methods, and explore innovative techniques for creating effective and safe medications. The process can involve steps such as the identification of targets, the discovery of lead compounds, lead optimization, preliminary testing, human trials, regulatory approval and finally post-marketing surveillance, all aimed at bringing a new drug from concept to market. In this article, the synthesis of the novel triazolequinoxalin (TZQ) 1-((1-hexyl-1H-1,2,3-triazol-5-yl)methyl)-3-phenylquinoxalin-2(1H)-one (4) is reported. The structure has been identified with a variety of spectroscopic methods (1H, 13C NMR, and LC-MS) and finally, the structure has been determined by X-ray diffraction (XRD) studies. The TZQ molecule has crystallized in the monoclinic space C2/c group with unit cell dimensions a = 41.201(2) Å, b = 10.6339(6) Å, c = 9.4997(4) Å, β = 93.904(4). The crystal structure is stabilized by intermolecular interactions (N-H ⋯ O and N-H … Cg) occurring within the molecule. The presence of these intermolecular interactions is evaluated through analysis of Hirshfeld surfaces (HS) and two-dimensional (2D) chemical fingerprints map. Additionally, energy frameworks were employed to identify the prevailing interaction energy influencing the molecular arrangement. Density Functional Theory (DFT) calculations were computed to establish concurrence between theoretical and experimental results. Furthermore, the HOMO-LUMO energy levels were determined using the B3LYP/6-31+G(d, p) level of theory. Finally, molecular docking was used to predict the anti-cancer activity of the compound (4) against PFKFB3 kinase and presented noticeable hydrophilic and hydrophobic interactions at the active site region.

Diethyl 2,2'-[({2-chloro-5-[(2-eth-oxy-2-oxoeth-yl)(2-methyl-indolin-1-yl)carbamo-yl]phen-yl}sulfon-yl)aza-nedi-yl]di-acetate

The majority of the title mol-ecule, C28H34ClN3O9S, is disordered over two closely spaced sets of sites; the site occupancy of the major component = 0.542 (3). The conformation of each component is approximately U-shaped with the chloro-benzene ring forming the base and the indolinyl and sulfamoyl groups the sides; an intra-molecular C-H⋯Cl hydrogen bond possibly contributes to the stabilization of the conformation. In the crystal, a corrugated layer structure parallel to the ab plane is formed by C-H⋯O and C-H⋯Cl hydrogen bonds together with C-H⋯π(ring) inter-actions.

Synthesis, structural characterization, antioxidant and antidiabetic activities, DFT calculation, and molecular docking of novel substituted phenolic and heterocyclic compounds

The current work describes the preparation of three unexpected compounds: a tetrasubstituted phenolic compound, an isocoumarin, and a pyranopyridine, bearing various substituent groups obtained through the condensation of 6-methyl-4-hydroxypyran-2-one 1 with 2-aminopyridine 2 under mild conditions. Plausible mechanisms explaining the formation of these compounds have been presented. Their structures have been elucidated using spectral data and confirmed by crystallographic studies. Furthermore, optimized geometries of and electronic distribution of FMOs orbitals are investigated in the PCM solvent model at the B3LYP/6-311++G(d,p) level of theory. The compounds were tested for their antioxidant and antidiabetic activities. Moreover, the binding interactions between the compounds and α-glucosidase and α-amylase were determined through their docking into the binding sites of the target enzymes using the Autodock package.Communicated by Ramaswamy H. Sarma.

Crystal structure, Hirshfeld surface analysis and inter-action energy calculation of 4-(furan-2-yl)-2-(6-methyl-2,4-dioxo-pyran-3-yl-idene)-2,3,4,5-tetra-hydro-1H-1,5-benzodiazepine

The title compound {systematic name: (S,E)-3-[4-(furan-2-yl)-2,3,4,5-tetra-hydro-1H-benzo[b][1,4]diazepin-2-yl-idene]-6-methyl-2H-pyran-2,4(3H)-dione}, C19H16N2O4, is constructed from a benzodiazepine ring system linked to furan and pendant di-hydro-pyran rings, where the benzene and furan rings are oriented at a dihedral angle of 48.7 (2)°. The pyran ring is modestly non-planar [largest deviation of 0.029 (4) Å from the least-squares plane] while the tetra-hydro-diazepine ring adopts a boat conformation. The rotational orientation of the pendant di-hydro-pyran ring is partially determined by an intra-molecular N-HDiazp⋯ODhydp (Diazp = diazepine and Dhydp = di-hydro-pyran) hydrogen bond. In the crystal, layers of mol-ecules parallel to the bc plane are formed by N-HDiazp⋯ODhydp hydrogen bonds and slipped π-π stacking inter-actions. The layers are connected by additional slipped π-π stacking inter-actions. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (46.8%), H⋯O/O⋯H (23.5%) and H⋯C/C⋯H (15.8%) inter-actions, indicating that van der Waals inter-actions are the dominant forces in the crystal packing. Computational chemistry indicates that in the crystal the N-H⋯O hydrogen-bond energy is 57.5 kJ mol-1.

Solvent induced supramolecular polymorphism in Cu(II) coordination complex built from 1,2,4-triazolo[1,5-a]pyrimidine: Crystal structures and anti-oxidant activity

Two Cu(II) coordination complexes, C1 and C2 of the formula [Cu(4)₂(H₂O)₂], have been prepared by reaction between CuCl₂·2H₂O and 7-ethoxycarbonylmethyl-5-methyl-1,2,4[1,5-a]pyrimidine (L) in a 1:2 M:L molar ratio. The L molecule decomposes during the reaction process into 7-carboxy-5-methyl-[1,2,4]-triazolo[1,5-a]pyrimidine (4) through an intermediate, ethyl 2,2-dihydroxy-2-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)acetate (5), which has been isolated and its crystal structure determined by X-ray diffraction. The X-ray analysis of the single crystals of [Cu(4)₂(H₂O)₂] obtained from the slow evaporation of EtOH and MeOH, separately, revealed the formation of "solvent induced" polymorphs C1 and C2, respectively. The primary supramolecular synthon for C1 and C2 are six membered ring, and square shaped hydrogen bonded architecture, respectively. The self-assembly of such synthons resulted in a two dimensional hydrogen bonded sheet supported by OH⋯O interactions. In addition, the antioxidant properties of the ligands and its complexes were evaluated in vitro using 1,1-diphenyl-2-picrylhydrazyl acid, 2,2'-azino-bis (3-ethylbenzothiazoline-6 sulfonic acid radical scavenging methods and ferric reducing antioxidant power.

Crystal structure and Hirshfeld surface analysis of N-(tert-but-yl)-2-(phenyl-ethyn-yl)imidazo[1,2-a]pyridin-3-amine

In the title compound, the phenyl ring of the phenyl-ethynyl substituent is inclined to the mean plane of the imidazo[1,2-a]pyridine moiety by 18.2 (1)°.

The bicyclic imidazo[1,2-a]pyridine core of the title compound, C₁₉H₁₉N₃, is relatively planar with an r.m.s. deviation of 0.040 Å. The phenyl ring is inclined to the mean plane of the imidazo[1,2-a]pyridine unit by 18.2 (1)°. In the crystal, mol­ecules are linked by N—H⋯H hydrogen bonds, forming chains along the c-axis direction. The chains are linked by C—H⋯π inter­actions, forming slabs parallel to the ac plane. The Hirshfeld surface analysis and fingerprint plots reveal that the crystal structure is dominated by H⋯H (54%) and C⋯H/H⋯C (35.6%) contacts. The crystal studied was refined as an inversion twin

Crystal structure and Hirshfeld surface analysis of 3-(4-meth-oxy-phen-yl)-1-methyl-4-phenyl-1H-pyrazolo-[3,4-d]pyrimidine

In the title mol-ecule, C19H16N4O, the planar pyrazolo-pyrimidine moiety is inclined to the attached phenyl rings by 35.42 (4) and 54.51 (6)°. In the crystal, adjacent mol-ecules are linked into chains parallel to [110] and [10] by C-H⋯O and C-H⋯N hydrogen bonds. Additional C-H⋯π(ring) inter-actions lead to the formation of the final three-dimensional network structure. The Hirshfeld surface analysis of the title compound suggests that the most significant contributions to the crystal packing are from H⋯H (48.2%), C⋯H/H⋯C (23.9%) and N⋯H/H⋯N (17.4%) contacts.

Crystal structure and Hirshfeld surface analysis of 5-[(5-nitro-1H-indazol-1-yl)meth-yl]-3-phenyl-4,5-di-hydro-isoxazole

In the title compound, C17H14N4O3, the indazole unit is planar to within 0.0171 (10) Å and makes dihedral angles of 6.50 (6) and 6.79 (4)°, respectively, with the nitro and pendant phenyl groups. The conformation of the oxazole ring is best described as an envelope. In the crystal, oblique stacks along the a-axis direction are formed by π-π stacking inter-actions between the indazole unit and the pendant phenyl rings of adjacent mol-ecules. The stacks are linked into pairs through C-H⋯O hydrogen bonds. Hirshfeld surface analysis and two-dimensional fingerprint plots indicate that the most important contributions to the crystal packing are from H⋯H (36.3%), O⋯H/H⋯O (23.4%), C⋯H/H⋯C (13.4%) and N⋯H/H⋯N (11.4%) inter-actions.

1-(3-Hydroxypropyl)-3-phenylquinoxalin-2(1H)-one

In the title molecule, C17H16N2O2, the quinoxaline portion is slightly folded about the N...N axis with an angle of 4.27 (4)°. In the crystal, O—H...O and weak C—H...O hydrogen bonds link molecules along the b-axis direction. In addition, two sets of weak C—H...π(ring) interactions form a two-dimensional `step' motif parallel to the bc plane.

3,4,6-Trimethyl-1-phenyl-5-(thiophen-3-yl)-1H-pyrazolo[3,4-b]pyridine

In the title compound, C19H17N3S, the pyrazolo[3,4-b]pyridine unit is slightly bowed across the C—C bond common to the two rings. In the crystal, ribbons extending along the a-axis direction are formed by C—H...π(ring) interactions. The ribbons are packed into corrugated layers inclined to the ac plane by approximately 22°. The thiophenyl group is rotationally disordered over two sites 180° apart in a 0.606 (2)/0.394 (2) ratio.

2-Amino-5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7(4H)-one

The asymmetric unit of the title compound, C6H7N5O, consists of two molecules with almost identical conformations. In the crystal, inversion dimers linked by pairs of N—H...N hydrogen bonds occur for both molecules; further N—H...N and N—H...O hydrogen bonds connect the dimers into a three-dimensional network.

Ethyl 4-(3,4,6-trimethyl-1-phenyl-1H-pyrazolo[3,4-b]pyridin-5-yl)benzoate

In the title compound, C24H23N3O2, the dihedral angles between the pyrazolopyridine ring system (r.m.s. deviation = 0.001 Å) and the N-bound and C-bound benzene rings are 15.95 (2) and 83.71 (4)°, respectively. The conformation of the former is influenced by an intramolecular C—H...N hydrogen bond, which generates an S(6) ring. In the crystal, stepped layers are generated by three sets of C—H...π interactions.

Ethyl 2-{[2-(2-ethoxy-2-oxoethoxy)quinolin-4-yl]carbonyloxy}acetate

The conformation of the 2-ethoxy-2-oxoethoxy side chain, including a gauche Ce—O—C—C3 [72.46 (16)°] (e = ethoxy) unit, in the title compound, C18H19NO7, is partly determined by an intramolecular C—H...O hydrogen bond. In the crystal, C—H...O hydrogen bonds and C—H...π interactions arising from the same methylene group form chains extending along the a-axis direction.

4-Phenyl-2,5,5a,6,7,8,9,9a-hexahydro-1H-1,5-benzodiazepine-2-thione ethanol monosolvate

In the solvated title compound, C15H18N2S·C2H5OH, the seven-membered ring has a twisted envelope conformation and the cyclohexyl ring has a chair conformation. In the crystal, N—H...O and O—H...S hydrogen bonds as well as C—H...π(ring) interactions form helical chains in which the thione and solvent ethanol molecules alternate. These chains are formed into layers parallel to (101) by inversion-related pairs of N—H...S hydrogen bonds. The ethanol solvent molecule is disordered over two sets of sites [occupancy ratio 0.880 (8): 0.120 (8)] with the oxygen atom in common.

Ethyl 2-(5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7-yl)pent-4-enoate

In the title molecule, C13H16N4O2, the fused triazolopyrimidine ring system is planar. In the crystal, inversion-related C—H...O hydrogen bonds form dimers that are linked into chains extending along the a-axis direction by inversion-related C—H...π(ring) interactions.

1-Methyl-4-phenyl-3-[4-(trifluoromethyl)phenyl]-1H-pyrazolo[3,4-d]pyrimidine

In the title molecule, C19H13F3N4, the pyrazolopyrimidine unit is slightly non-planar [dihedral angle between the five- and six-membered rings = 3.03 (15)°]. In the crystal, offset head-to-tail π-stacking interactions between pyrazolopyrimidine units [centroid–centroid separation = 3.665 (2) Å] together with weak C—H...N hydrogen bonds form stepped chains propagating along the c-axis direction. The structure was refined as a two-component twin.

1-Methyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one

The title molecule, C6H6N4O, is essentially planar [dihedral angle between the rings = 0.46 (9)°]. The crystal structure consists of sheets of molecules lying parallel to (-111) formed by a combination of N—H...O, C—H...O and C—H...H hydrogen bonds. The sheets are connected through π–π stacking interactions.

N,N-Dimethyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine monohydrate

The asymmetric unit of the title compound, C7H9N5·H2O, consists of two formula units differing slightly in the orientation of the dimethylamino groups. In the crystal, a combination of O—H...N and N—H...O hydrogen bonds involving the water molecules of crystallization, as well as slipped π-stacking interactions between pyrazolopyrimidine units form layers parallel to thebcplane.

2-[(Prop-2-yn-1-yl)amino]anilinium chloride

The title compound, C9H11N2+·Cl−, is an anilinium chloride salt, in which the Car—N—C—C (ar = aromatic) torsion angle is −84.95 (18)°. In the crystal, a bilayer of cation–anion sheets runs parallel to (100), primarily through an extensive range of N—H...Cl hydrogen bonds. Weak offset π-stacking interactions between the benzene rings stack molecules alongc.

4-(Prop-2-yn-1-ylsulfanyl)-1H-pyrazolo[3,4-d]pyrimidine

The asymmetric unit of the title compound, C8H6N4S, consists of two independent molecules differing in the orientation of the side chain. In the crystal, molecules form dimers through N—H...N hydrogen bonds. The dimers stack along thea-axis direction with weak π–π stacking interactions [centroid–centroid distances of 3.898 (2) and 3.908 (2) Å]. The crystal studied was refined as a two-component twin.

1-Methyl-3-(2-methylphenyl)-4-phenyl-1H-pyrazolo[3,4-d]pyrimidine

In the title compound, C19H16N4, the pyrazolopyrimidine unit is slightly twisted. A combination of π-stacking and offset π-stacking interactions forms columns along theb-axis direction.

1-Methyl-4-phenyl-1H-pyrazolo[3,4-d]pyrimidine

In the crystal, molecules of the title compound, C12H10N4, stack in a head-to-tail manner along thebdirection through π–π stacking interactions between both portions of the pyrazolopyrimidine ring system.

Ethyl 2-allyl-2-(5-methyl-1,2,4-triazolo[1,5-a]pyrimidin-7-yl)pent-4-enoate

In the title molecule, C16H20N4O2, the dihedral angle between the planes of the fused rings is 2.26 (8)°. In the crystal, [\overline{2}10] chains of molecules linked by C—H...O and C—H...N hydrogen bonds arise, which are further linked by weak C—H...π interactions.

2-(2-Oxo-4-phenyl-2,3-dihydro-1H-1,5-benzodiazepin-1-yl)acetic acid

The asymmetric unit of the title compound, C17H14N2O3, consists of two independent molecules having distinctly different conformations. The components of the asymmetric unit are connected by an O—H...N hydrogen bond, with additional O—H...N hydrogen bonds connecting this assemblage into chains running parallel to thebaxis. Intermolecular C—H...π(ring) interactions are also present.

1-Benzyl-4-phenyl-1H-1,5-benzodiazepin-2(3H)-one

In the title molecule, C22H18N2O, the seven-membered ring adopts a boat conformation with the planes of the pendant phenyl rings nearly perpendicular to the plane of the aromatic portion of the benzodiazepine core. Pairwise C—H...π(ring) interactions form inversion dimers which pack in zigzag layers associated through weak C—H...O hydrogen bonds.

1-Ethyl-5-nitro-1H-indazole

In the title molecule, C9H9N3O2, the nitro substituent is twisted by 4.0 (2)° out of the plane of the indazolyl moiety; the ethyl group is perpendicular to the indazolyl plane, with the N—N—C—C torsion angle being 101.4 (2)°. In the molecular packing, C—H...O hydrogen bonds lead to supramolecular chains along [001]. Globally, molecules assemble into layers in thebcplane. π–π interactions between five- and six-membered rings consolidate the three-dimensional packing [inter-centroid distance = 3.591 (1) Å]. The sample was refined as an inversion twin.

5-Nitro-1-(prop-2-yn-1-yl)-1H-indazole

The packing of the title molecule, C10H7N3O2, features the formation of weak dimersviapairwise C—H...O interactions across centers of symmetry. The prop-2-yn-1-yl moiety is twisted out of the plane of the indazole unit by 78.53 (17)°.