Synthesis, crystal structure investigation and computational approach to discover potential hydrazide derivatives as a potent inhibitor of cyclooxygenase-2 enzyme.

This study reports the synthesis of two new hydrazide derivatives, namely, (E)-N'-(4- bromobenzylidene)-2-(4-isobutylphenyl)propanehydrazide (4a) and (E)-N'-benzylidene-2-(4-isobutylphenyl)propanehydrazide (4b), respectively. The compounds were synthesized by the reaction of benzaldehyde with Ibuprofen acid hydrazide. Their structures were confirmed by X-ray crystallography. To try to do a more detailed investigation, computational studies including Hirshfeld surface analyses, energy frameworks, density functional theory (DFT) optimizations, frontier orbital analyses, molecular electrostatic potential analyses, and natural bond orbital analyses of the studied compounds are performed. Moreover, molecular docking and dynamics simulations of complexes of the compounds with the cyclooxygenase-2 (COX-2) enzyme were performed to determine the anti-inflammatory potential of the compounds. These analyses predicted the compounds to show maximum chemical interactions and be dynamically stable during simulation time. Furthermore, estimation of binding free energies confirmed the high binding affinity of the compounds for the COX-2 enzyme.

Synthesis, crystal structure, and a molecular modeling approach to identify effective antiviral hydrazide derivative against the main protease of SARS-CoV-2.

In the fall of 2019, a new type of coronavirus took place in Wuhan city, China, and rapidly spread across the world and urges the scientific community to develop antiviral therapeutic agents. In our effort we have synthesized a new hydrazide derivative, (E)-N'-(1-(4-bromophenyl)ethylidene)-2-(6-methoxynaphthalen-2-yl)propanehydrazide for this purpose because of its potential inhibitory proprieties. The asymmetric unit of the title molecule consists of two independent molecules differing noticeably in conformation. In the crystal, the independent molecules are linked by N-H···O and C-H···O hydrogen bonds and C-H···π(ring) interactions into helical chains extending along the b-axis direction. The chains are further joined by additional C-H···π(ring) interactions into the full 3-D structure. To obtain a structure-activity relationship, the DFT-NBO analysis is performed to study the intrinsic electronic properties of the title compound. Molecular modeling studies were also conducted to examine the binding affinity of the compound for the SARS-CoV-2 main protease enzyme and to determine intermolecular binding interactions. The compound revealed a stable binding mode at the enzyme active pocket with a binding energy value of -8.1 kcal/mol. Further, stable dynamics were revealed for the enzyme-compound complex and reported highly favorable binding energies. The net MMGBSA binding energy of the complex is -37.41 kcal/mol while the net MMPBSA binding energy is -40.5 kcal/mol. Overall, the compound disclosed the strongest bond of ing the main protease enzyme and might be a good lead for further structural optimization.

4-Phenyl-1,2,4-tri-aza-spiro-[4.4]non-1-ene-3-thione.

In the title compound, C12H13N3S, the 4,5-di-hydro-3H-1,2,4-triazole system is nearly planar [maximum deviation = 0.014 (2) Å], while the cyclo-pentane ring adopts a half-chair conformation. The dihedral angle between the mean plane of the 4,5-di-hydro-3H-1,2,4-triazole-3-thione ring and the phenyl ring is 85.49 (14)°, with the S atom 0.046 (1) Šout of the former plane. The crystal structure is stabilized only by van der Waals inter-actions. The investigated crystal was found to be a non-merohedral two-component twin by a 180° rotation about c*, with a refined value of the minor twin fraction of 0.12203 (18).

Methyl 2-((2Z,5Z)-4-oxo-3-phenyl-2-{2-[(1E)-1,2,3,4-tetra-hydro-naphthalen-1-yl-idene]hydrazin-1-yl-idene}-1,3-thia-zolidin-5-yl-idene)acetate.

In the title compound, C22H19N3O3S, the six-membered ring of the 1,2,3,4-tetra-hydro-naphthalene ring system adopts an envelope conformation with the central CH2 C atom as the flap. The mol-ecular conformation is stabilized by an S⋯O contact, forming a pseudo-five-membered ring. In the crystal, mol-ecules are linked via C-H⋯O hydrogen bonds into chains propagating along [102].

2-((1E)-1-{2-[(2Z)-3,4-Diphenyl-2,3-di-hydro-1,3-thia-zol-2-yl-idene]hydrazin-1-yl-idene}eth-yl)pyridin-1-ium bromide monohydrate.

In the title compound, C22H19N4S(+)·Br(-)·H2O, the dihedral angles between the phenyl groups and the mean plane of the thia-zolyl-idene ring are 34.69 (13) and 64.27 (13)°, respectively, while that between the thia-zolyl-idene and pyridinium rings is 14.73 (13)°. In the crystal, zigzag chains of alternating bromide ions and water mol-ecules associate through O-H⋯Br inter-actions run in channels approximately parallel to the b axis. These chains help form parallel chains of cations through N-H⋯O, C-H⋯N and C-H⋯Br hydrogen bonds.

2-((1E)-1-{2-[(2Z)-4-(4-Bromo-phen-yl)-3-phenyl-2,3-di-hydro-1,3-thia-zol-2-yl-idene]hydrazin-1-yl-idene}eth-yl)pyridin-1-ium bromide monohydrate.

In the title hydrated molecular salt, C22H18BrN4S(+)·Br(-)·H2O, the aromatic rings make dihedral angles of 14.20 (12), 34.29 (10) and 68.75 (11)° with the thia-zole ring. In the crystal, mol-ecules are linked into chains running parallel to the a axis by association of the bromide ions and the water mol-ecules of crystallization with the cations via N-H⋯O, O-H⋯Br, C-H⋯N and C-H⋯Br hydrogen-bonding inter-actions. C-H⋯π and C-Br⋯π [3.7426 (11) Å, 161.73 (7)°] inter-actions are also observed, forming infinite chains extending along the b-axis direction.

Bis(2-amino-5-benzyl-3-eth-oxy-carbonyl-4,5,6,7-tetra-hydro-thieno[3,2-c]pyridin-5-ium) bis-(4-meth-oxy-phen-yl)di-phos-phon-ate.

The asymmetric unit of the title salt, 2C17H21N2O2S(+)·C14H14O7P2 (2-), contains half of a centrosymmetric bis-(4-meth-oxy-phen-yl)di-phospho-nate anion and one 2-amino-5-benzyl-3-eth-oxy-carbonyl-4,5,6,7-tetra-hydro-thieno[3,2-c]pyri-din-5-ium cation. In the anion, the O atoms of the di-phospho-nate group are disordered over two positions with equal occupancies. In the cation, the ethyl group is disordered over two orientations with a refined occupancy ratio of 0.753 (5):0.247 (5), and the tetra-hydro-pyridinium ring adopts a distorted half-chair conformation. In the crystal, the ions are linked by C-H⋯O, N-H⋯O and C-H⋯S hydrogen bonds into a three-dimensional network.

N'-[(E)-(Furan-2-yl)methyl-idene]-2-[4-(2-methyl-prop-yl)phen-yl]propano-hydrazide.

In the title mol-ecule, C18H22N2O2, the furan and benzene rings form a dihedral angle of 70.17 (14)°. In the crystal, strong N-H⋯O and weak C-H⋯O hydrogen bonds link the mol-ecules into chains running parallel to [010].

2-Cyclo-heptyl-idene-N-phenyl-hydrazine-carbo-thio-amide.

In the title compound, C14H19N3S, the seven-membered cyclo-heptane ring adopts a chair conformation. An intra-molecular N-H⋯N hydrogen bond [graph-set motif S(5)] is present in the N-N-C-N chain between the ring systems. An intra-molecular C-H⋯S contact also occurs. In the crystal, pairs of mol-ecules form centrosymmetric dimers through N-H⋯S hydrogen bonds [graph-set R 2 (2)(8)]. These dimers are connected by C-H⋯S inter-actions with an R 2 (2)(14) motif.

Methyl (2Z)-2-{(2Z)-3-[(cyclo-pentyl-idene)amino]-4-oxo-2-phenyl-imino-1,3-thia-zol-idin-5-yl-idene}acetate.

In the title compound, C17H17N3O3S, the thia-zole ring is nearly planar [maximum deviation = 0.015 (1) Šfor the ring N atom] and the cyclo-pentane ring has a twist conformation. The mol-ecular conformation is stabilized by a hypervalent inter-action between the S atom and the ester group carbonyl O atom, with an S⋯O distance of 2.7931 (10) Å. In the crystal, C-H⋯O inter-actions generate chains of mol-ecules propagating along [110] and π-π stacking inter-actions [centroid-centroid distance = 3.4677 (7) Å] between the thia-zole rings organize these chains into (001) layers.

1-{[(Z)-Cyclo-pentyl-idene]amino}-3-phenyl-thio-urea.

The sample of the title compound, C12H15N3S, chosen for study consisted of triclinic crystals twinned by a 180° rotation about the a axis. The five-membered ring adopts a twisted conformation. The dihedral angle between the phenyl ring and the mean plane of the thio-urea unit is 78.22 (8)°. In the crystal, molecules are linked via pairs of N-H⋯S hydrogen bonds forming inversion dimers.

4-Chloro-N'-[(E)-2-chloro-benzyl-idene]benzohydrazide monohydrate.

The title compound, C14H10Cl2N2O·H2O, has a nearly planar extended conformation [C-N-N-C = -173.66 (15)°]. The dihedral angle between the aromatic rings is 4.6 (2)°. The water mol-ecules alternate with benzohydrazide mol-ecules in chains formed by O-H⋯O hydrogen bonds which run parallel to the a axis. These chains are linked to neighboring chains through N-H⋯O and C-H⋯O inter-actions, forming a layer parallel to (001).

3,6-Di-chloro-9-(prop-2-yn-1-yl)-9H-carbazole.

The tricyclic aromatic ring system of the title compound, C15H9Cl2N, is essentially planar (r.m.s. deviation = 0.002 Å). The two Cl atoms lie slightly out of the plane of the carbazole ring system, with the C-Cl bonds forming angles of 1.23 (8) and 1.14 (8)° with the plane. The acetylene group has a syn orientation with respect to the ring system. In the crystal, no weak hydrogen bonds nor any π-π stacking inter-actions are observed.

4-Chloro-N'-[(3Z)-2-oxo-2,3-di-hydro-1H-indol-3-yl-idene]benzohydrazide.

In the title compound, C15H10ClN3O2, the benzene ring is slightly twisted out of the plane of the 2,3-di-hydro-1H-indole ring system (r.m.s. deviation = 0.007 Å), forming a dihedral angle of 7.4 (3)°. An intra-molecular N-H⋯O hydrogen bond forms a six-membered ring. In the crystal, mol-ecules are linked via N-H⋯O and C-H⋯O hydrogen bonds, forming layers alternately perpendicular to [011] and [0-11].

(2E)-2-(1,3-Benzo-thia-zol-2-yl)-3-(di-methyl-amino)-prop-2-ene-nitrile.

The mol-ecular conformation of title compound, C12H11N3S, is almost planar [maximum deviation = 0.063 (2) Å]; an intra-molecular C-H⋯N hydrogen bond is noted. In the crystal, mol-ecules inter-act with each other via π-π stacking inter-actions between thia-zole rings [centroid-centroid distance = 3.7475 (9) Å] and methyl-H⋯π(C6) inter-actions, forming columns along the a axis.

N-(2-Hy-droxy-phen-yl)-4-methyl-benzene-sulfonamide.

In the title compound, C13H13NO3S, the dihedral angle between the benzene rings is 64.15 (7)° and the C-S-N-C torsion angle is -57.18 (12)°. An intra-molecular N-H⋯O hydrogen bond closes an S(5) ring. In the crystal, O-H⋯O hydrogen bonds link the mol-ecules into C(8) chains propagating in [100]. Weak C-H⋯π inter-actions are also observed.

Ethyl 2-[({[4-amino-5-cyano-6-(methyl-sulfan-yl)pyridin-2-yl]carbamo-yl}meth-yl)sulfan-yl]acetate monohydrate.

The title compound, C13H16N4O3S2·H2O, crystallizes in a 'folded' conformation with the ester group lying over the carbamoyl moiety, with one solvent water mol-ecule. The mol-ecular conformation is stabilized by an intra-molecular C-H⋯O hydrogen bond, and an N-H⋯O hydrogen-bonding inter-action involving the lattice water mol-ecule. The packing involves N-H⋯N, N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds and consists of tilted layers running approximately parallel to the c axis, with the ester groups on the outer sides of the layers and with channels running parallel to (101).

3,4,6-Tri-amino-N-phenyl-thieno[2,3-b]pyridine-2-carboxamide.

In the title compound, C14H13N5OS, the dihedral angle between the fused ring system (r.m.s. deviation = 0.028 Å) and the phenyl ring is 48.24 (4)°. The mol-ecule features both an intra-molecular N-H⋯O and an N-H⋯N hydrogen bond. In the crystal, mol-ecules are linked by N-H⋯O and N-H⋯N hydrogen bonds, generating a three-dimensional network. A weak N-H⋯π inter-action is also observed.

3-Oxo-N',2-diphenyl-2,3-di-hydro-1H-pyrazole-4-carbohydrazide.

In the title compound, C16H14N4O2, the pyrazole ring makes a dihedral angle of 10.49 (8)° with its N-bound phenyl group, while it is nearly perpendicular to the other phenyl ring [dihedral angle = 88.47 (5)°]. The mol-ecular conformation is stabilized by intra-molecular C-H⋯O and N-H⋯O hydrogen bonds. In the crystal, the packing involves sheets of mol-ecules parallel to (100) linked by N-H⋯O hydrogen bonds. A C-H⋯O interaction is also observed.

1-[(Cyclo-hexyl-idene)amino]-3-(prop-2-en-1-yl)thio-urea.

The asymmetric unit of the title compound, C10H17N3S, consists of three symmetry-independent mol-ecules with distinctly different conformations, as indicated for example by the C-N-C-C torsion angles of -155.9 (3), 89.9 (3) and 81.1 (4)° along the bond between thio-urea and allyl units. In the crystal, mol-ecules are connected via N-H⋯N and N-H⋯S hydrogen bonds into chains extending along [110] that are further associated through C-H⋯N inter-actions into layers parallel to (001). The allyl group in one of the independent mol-ecules is disordered over two sets of sites with an occupancy ratio of 0.853 (6):0.147 (6).