Pyrazolone-type compounds: synthesis and in silico assessment of antiviral potential against key viral proteins of SARS-CoV-2.

Coronavirus outbreak is still a major public health concern. The high mutation ability of SARS-CoV-2 periodically delivers more transmissible and dangerous variants. Hence, the necessity for an efficient and inexpensive antiviral agent is urgent. In this work, pyrazolone-type compounds were synthesised, characterised using spectroscopic methods and theoretical tools, and evaluated in silico against proteins of SARS-CoV-2 responsible for host cell entry and reproduction processes, i.e., spike protein (S), Mpro, and PLpro. Five of twenty compounds are newly synthesised. In addition, the crystal structure of a pyrazolone derivative bearing a vanillin moiety is determined. The obtained in silico results indicate a more favourable binding affinity of pyrazolone analogues towards Mpro, and PLpro in comparison to drugs lopinavir, remdesivir, chloroquine, and favipiravir, while in the case of S protein only lopinavir exerted higher binding affinity. Also, the investigations were performed on ACE2 and the spike RBD-ACE2 complex. The obtained results for these proteins suggest that selected compounds could express antiviral properties by blocking the binding to the host cell and viral spreading, also. Moreover, several derivatives expressed multitarget antiviral action, blocking both binding and reproduction processes. Additionally, in silico ADME/T calculations predicted favourable features of the synthesised compounds, i.e., drug-likeness, oral bioavailability, as well as good pharmacokinetic parameters related to absorption, metabolism, and toxicity. The obtained results imply the great potential of synthesised pyrazolones as multitarget agents against SARS-CoV-2 and represent a valuable background for further in vitro investigations.

Pyrazole Derivatives of Medically Relevant Phenolic Acids: Insight into Antioxidative and Anti-LOX Activity.

BACKGROUND: From the point of view of medicinal chemistry, compounds containing phenolic and pyrazolic moiety are significant since they are often constituents of bioactive compounds. OBJECTIVE: The aims of this study were to synthesize pyrazole derivatives of medically relevant phenolic acids, confirm their structure, and evaluate their antioxidative and anti-LOX activities. METHODS: Phenolic pyrazole derivatives were obtained, starting from esters of medically relevant phenolic acids. The structures of all obtained compounds were determined by NMR and IR spectroscopy, and UV-Vis spectrophotometry. In addition, the single-crystal X-ray diffraction was used. Pyrazole derivatives were tested for their in vitro antioxidative (DPPH assay), and lipoxygenase (LOX) inhibitory activities. Radical quenching mechanism was estimated using DFT and thermodynamic approach, while molecular docking was used to estimate the binding mode within the enzyme. RESULTS: Pyrazole derivatives were obtained in high yields. The crystal structure of a new compound 3e was determined. Pyrazole derivative with catechol moiety 3d exhibited excellent radical scavenging activity, while compound 3b exhibited the best anti-LOX activity. Molecular docking study revealed that there is no direct interaction of any ligand with the active site of LOX-Ib, but pyrazoles 3a-e behave as inhibitors blocking the approach of linoleic acid to the active site. CONCLUSION: In this research, protocatechuic and vanillic acid pyrazole derivatives have been obtained for the first time. In vitro antioxidative assay suggests that pyrazole derivate of protocatechuic acid is a powerful radical scavenger, while anti-LOX assay indicates a pyrazole derivative with 4-hydroxyphenyl moiety.

Chemoselective synthesis of multifunctional ferrocene-containing derivatives by the cross Rauhut-Currier reaction.

A simple protocol has been developed for the chemoselective synthesis of ferrocene-containing Rauhut-Currier adducts from 1-ferrocenyl-2-nitroethene and vinyl ketones using 20 mol% of triphenylphosphine. Multifunctional ferrocene derivatives were obtained in moderate to high yields (51-92%) by the coupling between the α-position of vinyl ketones and the ß-position of the nitroalkene. The study of the Rauhut-Currier reaction under the described conditions showed that the strong electron-donating group at the ß-position of nitroalkenes plays a significant role in the reaction outcome due to prevention of polymerization and stabilization of the zwitterionic intermediate. Additionally, a preparative synthesis of 4-ferrocenyl-3-methylene-5-nitropentan-2-one was carried out and its synthetic transformations showed easy conversion to other useful building blocks.

Electrochemical characterization and estimation of DNA-binding capacity of a series of novel ferrocene derivatives.

The synthesis of a series of methyl 2-alkyl-5-aryl-4-ferrocenoylpyrrolidine-2-carboxylates has been achieved by [3 + 2] dipolar cycloaddition of azomethine ylides to acryloylferrocene. The electrochemical properties of novel products were examined by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). These techniques revealed the quasi-reversible one-electron oxidation process. The DNA-binding capacity of all the products was also studied using CV and DPV, and significant interactions between synthesized compounds and nucleic acid, mostly of the electrostatic type, were disclosed. DFT calculations and molecular docking tests were carried out to gain a more exhaustive insight into the interactions of the obtained products with nucleic acid. A detailed characterization of the new compounds was performed by IR, NMR and elemental analyses, followed by single-crystal X-ray diffraction experiments for two representatives.

Synthesis, characterization, anticancer evaluation and mechanisms of cytotoxic activity of novel 3-hydroxy-3-pyrrolin-2-ones bearing thenoyl fragment: DNA, BSA interactions and molecular docking study.

In order to make a progress in discovering a new agents for chemotherapy with improved properties and bearing in mind the fact that substituted 3-hydroxy-3-pyrrolin-2-ones belong to a class of biologically active compounds, series of novel 1,5-diaryl-4-(2-thienylcarbonyl)-3-hydroxy-3-pyrrolin-2-ones were synthesized and characterized by spectral (UV-Vis, IR, NMR, ESI-MS), X-ray and elemental analysis. All compounds were examined for their cytotoxic effect on human cancer cell lines HeLa and MDA-MB 231 and normal fibroblasts (MRC-5). Four compounds, 3-hydroxy-1-(p-tolyl)-4-(2-thienylcarbonyl)-5-(4-chlorophenyl)-2,5-dihydro-1H-pyrrol-2-one (D10), 3-hydroxy-1-(3-nitrophenyl)-4-(2-thienylcarbonyl)-5-(4-(benzyloxy)phenyl)-2,5-dihydro-1H-pyrrol-2-one (D13), 3-hydroxy-1-(4-nitrophenyl)-4-(2-thienylcarbonyl)-5-(4-(benzyloxy)phenyl)-2,5-dihydro-1H-pyrrol-2-one (D14), and 3-hydroxy-1-(4-chlorophenyl)-4-(2-thienylcarbonyl)-5-(4-(benzyloxy)phenyl)-2,5-dihydro-1H-pyrrol-2-one (D15), that showed the highest cytotoxicity against malignant cells and the best selectivity towards normal cells were selected for further experiments. Results obtained by investigating mechanisms of cytotoxic activity suggest that selected 3-hydroxy-3-pyrrolin-2-one derivatives in HeLa cells induce apoptosis that is associated with S phase arrest (D13, D15, and D10) or unrelated to cell cycle distribution (D14). Additionally, to better understand their suitability for potential use as anticancer medicaments we studied the interactions between biomacromolecules (DNA or BSA) and D13 and D15. The results indicated that D13 and D15 have great affinity to displace EB from the EB-DNA complex through intercalation [Ksv = (3.7 ±â€¯0.1) and (3.4 ±â€¯0.1) × 103 M-1, respectively], an intercalative mode also confirmed through viscosity measurements. Ka values, obtained as result of fluorescence titration of BSA with D13 and D15 [Ka = (4.2 ±â€¯0.2) and (2.6 ±â€¯0.2) × 105 M, respectively], support the fact that a significant amount of the tested compounds could be transported and distributed through the cells. In addition, by DNA and BSA molecular docking study for D13, D14 and D15 is determined and predicted the binding mode and the interaction region.

First crystal structures of metal complexes with a 4-nitropyrazole-3-carboxylic acid ligand and the third crystal form of the ligand.

Pyrazole (pz)-derived ligands can, besides exhibiting a strong coordination ability toward different metal ions, exhibit a great diversity in their coordination geometry and nuclearity, which can be achieved by varying the type and position of the pz substituents. The present study reports the synthesis and crystal structure of two binuclear complexes, namely bis(µ-4-nitro-1H-imidazol-1-ide-5-carboxylato)-κ3N1,O:N2;κ3N2:N1,O-bis[aqua(dimethylformamide-κO)copper(II)], [Cu2(C4HN3O4)2(C3H7NO)2(H2O)2], (II), and bis(µ-4-nitro-1H-imidazol-1-ide-5-carboxylato)-κ2N1,O:N2;κ2N2:N1,O-bis[triaquacobalt(II)] dihydrate, [Co2(C4HN3O4)2(H2O)6]·2H2O, (III). These compounds represent rare examples of metal complexes comprising 3,4-substituted pz derivatives as a bridging ligand and also the first crystal structures of transition-metal complexes with ligands derived from 4-nitropyrazole-3-carboxylic acid. Recently, the crystal structures of the same ligand in the neutral and mixed neutral/anionic forms have been reported. We present here the third form of this ligand, where it is present in a fully deprotonated anionic form within a salt, i.e. ammonium 4-nitropyrazole-3-carboxylate, NH4+·C4H2N3O4-, (I). Single-crystal X-ray diffraction revealed that in the present complexes, the CuII and CoII centres adopt distorted square-pyramidal and octahedral geometries, respectively. In both cases, the N,N',O-coordinated pz ligand shows simultaneously chelating and bridging coordination modes, leading to the formation of a nearly planar six-membered M2N4 metallocycle. In all three crystal structures, the supramolecular arrangement is controlled by strong hydrogen bonds which primarily engage the carboxylate O atoms as acceptors, while the nitro group adopts the role of an acceptor only in structures with an increased number of donors, as is the case with CoII complex (III). The electrostatic potential, as a descriptor of reactivity, was also calculated in order to examine the changes in ligand electrostatic preferences upon coordination to metal ions.

Discovery of the Biginelli hybrids as novel caspase-9 activators in apoptotic machines: Lipophilicity, molecular docking study, influence on angiogenesis gene and miR-21 expression levels.

In order to investigate potential therapeutically agents, novel products of Biginelli reaction (4a-l) were synthesized and exposed to cytotoxic and caspase activities, angiogenesis, cell cycle distribution, gene and microRNA expression levels, lipophilicity assessment and docking study. Among the twelve novel compounds (4a-l) evaluated for the cytotoxic activity, five of them (4c, 4d, 4f, 4k and 4l) that showed excellent activity on the tested cell lines (HeLa, LS174 and A549) were selected for further evaluation. Interestingly, compound 4f has up to three times higher selectivity index (SI) towards cancer cells than cisplatin (on HeLa, LS174 and A549 SI = 18.2, 13.5 and 11.2, respectively). The obtained results from cell cycle distribution and caspase activity indicate that tested compounds (4c, 4d, 4f, 4k and 4l) promoted caspase-9 activation, implicated in the intrinsic pathway of apoptosis. Lipophilicity of 4a-l was determinate by using reversed-phase high-performance liquid chromatography.

A new efficient domino approach for the synthesis of pyrazolyl-phthalazine-diones. Antiradical activity of novel phenolic products.

Pyrazolyl-phthalazine-dione derivatives (PPDs) were synthetized in the ionic liquid catalyzed one-pot multicomponent reaction of acetylacetone, 2,3-dihydrophthalazine-1,4-dione, and different aldehydes in moderate to good yields. Six new PPDs were obtained, and the crystal structure of 2-acetyl-1-(4-fluorophenyl)-3-methyl-1H-pyrazolo[1,2-b]phthalazine-5,10-dione (PPD-4) was determined. The most interesting structural features of the novel PPD-4 is the formation of a rather short intermolecular distance between the F atom of one molecule and the midpoint of the neighbouring six-membered heterocyclic ring. This interaction arranges all molecules into parallel supramolecular chains. UV-Vis spectra of all PPDs were acquired and compared to the simulated ones obtained with TD-DFT. All synthetized compounds were subjected to evaluation of their in vitro antioxidative activity using a stable DPPH radical. It was shown that PPD-7, with a catechol motive, is the most active antioxidant, while PPD-9, with two neighbouring methoxy groups to the phenolic OH, exerted a somewhat lower, but significant antioxidative potential. The results of DFT thermodynamical study are in agreement with experimental findings that PPD-7 and PPD-9 should be considered as powerful radical scavengers. In addition, the obtained theoretical results (bond dissociation and proton abstraction energies) specify SPLET as a prevailing radical scavenging mechanism in polar solvents, and HAT in solvents with lower polarity. On the other hand, the obtained reaction enthalpies for inactivation of free radicals suggest competition between HAT and SPLET mechanisms, except in the case of the ˙OH radical in polar solvents, where HAT is labeled as prefered.

Vanillic aldehydes for the one-pot synthesis of novel 2-oxo-1,2,3,4-tetrahydropyrimidines.

A small library of novel 2-oxo-1,2,3,4-tetrahydropyrimidines was synthesized via a one-pot multicomponent Biginelli reaction. Copper complex [Formula: see text] which was used for the first time as a homogeneous and heterogeneous catalyst, makes this a facile and efficient reaction at room temperature. All the obtained products fall out of the solution in pure form and are easily isolated via filtration in good-to-excellent yields. The molecular structure of one of the products, ethyl 6-methyl-2-oxo-4-(4[Formula: see text]-isopropoxy-3[Formula: see text]-methoxyphenyl) - 1,2,3,4 - tetrahydropyrimidine-5- carboxylate, has been determined by X-ray crystallography. All non-hydrogen atoms in the heterocyclic, six-membered ring are determined to be approximately coplanar.

Ferrier rearrangement promoted by an electrochemically generated zirconium catalyst.

In situ generated zirconium catalyst from a sacrificial zirconium anode was successfully applied to promote Ferrier rearrangement of 3,4,5-tri-O-acetyl-D-glucal and 6-deoxy-3,4-di-O-acetyl-L-glucal (3,4-di-O-acetyl-L-rhamnal) in the presence of three thiols and eleven thiophenols as nucleophiles. A simple constant current electrolysis (20 mA, 0.4 F mol(-1)) of an acetonitrile solution of lithium perchlorate (0.1 M) containing the corresponding glycal and S-nucleophiles, using a zirconium anode and a platinum cathode resulted in the successful synthesis of the corresponding 2,3-unsaturated peracetylated thioglycosides (with an average anomer ratio α/ß=4.129 in the case of peracetylated D-glucal and 8.740 in the case of L-rhamnal). The same procedure proved to be appropriate in synthesizing dihydropyran derivatives ('C-glycosides') using allyltrimethylsilane as the nucleophile (only 'α-anomers' were obtained). All new compounds were fully characterized by spectral data, whereas single-crystal X-ray analysis was performed for two thioglycosides.

Charge-density distribution and electrostatic flexibility of ZIF-8 based on high-resolution X-ray diffraction data and periodic calculations.

The electron-density distribution in a prototypical porous coordination polymer ZIF-8 has been obtained in an approach combining high-resolution X-ray diffraction data and Invariom refinement. In addition, the periodic quantum-chemical calculation has been used to describe the theoretical density features of ZIF-8 in the same geometry (m1) and also in a "high-pressure" form of ZIF-8 (m2) characterized by conformational change with respect to the methylimidazolate linker. A thorough comparison of the electronic and electrostatic properties in two limiting structural forms of ZIF-8 proposes additional aspects on diffusion and adsorption processes occurring within the framework. The dimensions of the four-membered (FM) and six-membered (SM) apertures of the ß cage are reliably determined from the total electron-density distribution. The analysis shows that FM in m2 becomes competitive in size to the SM aperture and should be considered for the diffusion of small molecules and cations. Bader's topological analysis (quantum theory of atoms in molecules) shows similar properties of both ZIF-8 forms. On the other hand, analysis of their electrostatic properties reveals tremendous differences. The study suggests exceptional electrostatic flexibility of the ZIF-8 framework, where small conformational changes lead to a significantly different electrostatic potential (EP) distribution, a feature that could be important for the function and dynamics of the ZIF-8 framework. The cavity surface in m1 contains 38 distinct regions with moderately positive, negative, or neutral EP and weakly positive EP in the cavity volume. In contrast to m1, the m2 form displays only two regions of different EP, with the positive one taking the whole cavity surface and the strong negative one localized entirely in the FM apertures. The EP in the cavity volume is also more positive than that in m1. A pronounced influence of the linker reorientation on the EP of the ZIF-8 forms is related to the high symmetry of the system and to an amplification of the electrostatic properties by cooperative effects of the proximally arranged structural fragments.

Monomolecular sheets of propeller-shaped triethyl 4,4',4''-[benzene-1,3,5-triyltris(ethyne-2,1-diyl)]tribenzoate deuterochloroform monosolvate.

The title compound, C39H30O6·CDCl3, has a chemical threefold axis and an approximately planar structure, with an ethoxycarbonyl substituent on each of the terminal benzenes oriented in the same direction, thus forming a propeller-shaped molecule. This molecule is of particular interest in the field of metal-organic frameworks (MOFs), where its hydrolyzed analogue forms MOF structures with high surface areas. The benzene ring which occupies the centre of the molecule forms π-π interactions to the equivalent benzene ring at a perpendicular distance of 3.32 (1) Å. Centrosymmetric dimers formed in this way are interconnected by intermolecular C-H···π interactions with a rather short H···CgA distance of 2.51 Š(CgA is the centroid of the central benzene ring). The molecules are arranged in regular parallel sheets. Within a sheet, molecules are interconnected via C-H···O interactions where all carbonyl O atoms participate in weak hydrogen bonds as hydrogen-bond acceptors. Neighbouring sheets are connected through the above-mentioned π-π and C-H···π interactions.

Discovery of anxiolytic 2-ferrocenyl-1,3-thiazolidin-4-ones exerting GABAA receptor interaction via the benzodiazepine-binding site.

Herein, we report on the synthesis, spectral, crystallographic and electrochemical properties of a small library of N-substituted 2-ferrocenyl-1,3-thiazolidin-4-ones, designed as novel GABAA benzodiazepine-binding site ligands. The anxiolytic properties of the title compounds were evaluated in several different in vivo models, whereas the involvement of the GABAA receptor complex in the activity of the most potent compound, 2-ferrocenyl-3-(4-methoxyphenylethyl)-1,3-thiazolidin-4-one, was inferred from experiments with known GABAA-targeting agents. Ligand docking experiments revealed that the high, dose-dependent, anxiolytic activity of the new compounds might be due to their favorable interactions with the benzodiazepine-binding site of the GABAA receptor complex. The incorporation of the ferrocene core and fine tuning of the distance between the thiazolidinone core and an additional aromatic ring were judged to be crucial structural requirements for the observed anxiolytic effect.

Synthesis, characterization, and antimicrobial evaluation of a small library of ferrocene-containing acetoacetates and phenyl analogs: the discovery of a potent anticandidal agent.

A library of 16 2-substituted methyl acetoacetates containing ferrocenyl or phenyl units was designed to disclose differences in the antimicrobial activity of ferrocene-containing compounds and their phenyl analogs. Two methyl acetoacetates, whose structures do not contain an aromatic nucleus, were also included in order to probe the inherent activity of the scaffold itself. The acetoacetates were synthesized (low-to-good yields) and fully characterized by spectral (MS, IR, UV-Vis, 1D and 2D NMR) and electrochemical (cyclic voltammetry) techniques. Single-crystal X-ray analysis has been performed for methyl 2-acetyl-2-(ferrocenylmethyl)-5-methylhex-4-enoate. All compounds have demonstrated in vitro antimicrobial activity against six bacterial (three Gram-positive and three Gram-negative) and two fungal strains with minimal inhibitory concentration values of 0.0050-20.6 µmol mL(-1). The most active compound was 2-acetyl-2-(ferrocenylmethyl)-4-methylpent-4-enoate whose activity was comparable to that of nystatin against the yeast Candida albicans. Agglomerative hierarchical clustering statistical analysis of the antimicrobial assay data demonstrated that ferrocene-containing compounds have statistically different and greater antimicrobial activity when compared to their phenyl analogs.

(E)-4-[(2-carbamoylhydrazinylidene)methyl]-3-hydroxy-5-hydroxymethyl-2-methylpyridin-1-ium nitrate.

The title compound, C9H13N4O3(+)·NO3(-), is the first structurally characterized Schiff base derived from semicarbazide and pyridoxal. Unusually for an unsubstituted semicarbazone, the compound adopts a syn conformation, in which the carbonyl O atom is in a cis disposition relative to the azomethine N atom. This arrangement is supported by a pair of hydrogen bonds between the organic cation and the nitrate anion. The cation is essentially planar, with only a hydroxymethyl O atom deviating significantly from the mean plane of the remaining atoms (r.m.s. deviation of the remaining non-H atoms = 0.01 Å). The molecules are linked into flat layers by N-H···O and C-H···O hydrogen bonds. O-H···O hydrogen bonds involving the hydroxymethyl group as a donor interconnect the layers into a three-dimensional structure.

Benzyl 2-(benzylsulfanyl)benzoate.

In the title compound, C(21)H(18)O(2)S, the central aromatic ring makes dihedral angles of 5.86 (12) and 72.02 (6)° with the rings of the terminal O-benzyl and S-benzyl groups, respectively. The dihedral angle between the peripheral phenyl rings is 66.16 (6)°. In the crystal, mol-ecules are linked by pairs of C-H⋯O hydrogen bonds, forming inversion dimers. These dimers are linked via C-H⋯π inter-actions, forming a three-dimensional network.

4-[(4-Methyl-phen-yl)sulfan-yl]butan-2-one.

In the title compound, C11H14OS, all non-H atoms are essentially coplanar, with a mean deviation of 0.023 Å. In the crystal, centrosymmetrically related mol-ecules are weakly connected into dimers by pairs of C-H⋯O inter-actions. The dimers are further linked along the a axis by weak C-H⋯π and C-H⋯S inter-actions.

4-Eth-oxy-3-meth-oxy-benzaldehyde.

In the title compound, C10H12O3, all non-H atoms are approximately coplanar, with an r.m.s. deviation of 0.046 Å. In the crystal, very weak C-H⋯O inter-actions link the mol-ecules into sheets parallel to (101).

4-[(2E)-2-(2-Hy-droxy-benzyl-idene)hydrazin-1-yl]benzonitrile.

The asymmetric unit of the title Schiff base, C(14)H(11)N(3)O, contains two independent mol-ecules which have similar conformations. The dihedral angles between the benzene rings are 4.19 (9) and 14.18 (9)° in the two mol-ecules. An intra-molecular O-H⋯N hydrogen bond stabilizes the mol-ecular conformation of each mol-ecules. The crystal packing is dominated by pairs of equivalent N-H⋯N and C-H⋯O hydrogen bonds which arrange the mol-ecules into layers parallel to (-111).

2-(1,3-Dioxoisoindolin-2-yl)acetic acid-N'-[(E)-4-meth-oxy-benzyl-idene]pyridine-4-carbohydrazide (2/1).

In the crystal structure of the title compound, 2C(10)H(7)NO(4)·C(14)H(13)N(3)O(2), the two independent acid mol-ecules are connected through strong O-H⋯N and O-H⋯O hydrogen bonds to the central mol-ecule of the anti-tubercular drug N'-[(E)-4-meth-oxy-benzyl-idene]pyridine-4-carbohydrazide. Two such trimolecular units related by an inversion centre inter-act through a pair of N-H⋯O hydrogen bonds, forming a 3 + 3 mol-ecular aggregate. The dihedral angle between the aromatic rings of the hydrazone mol-ecule is 1.99 (12)°. The crystal packing features weak C-H⋯O and π-π stacking inter-actions, with centroid-centroid distances of 3.8460 (19) and 3.8703 (13) Å.