Synthesis, conformational studies and NBO analysis of (4-chloro-3,5-dimethyl-1H-pyrazol- 1-yl)(p-tolyl)methanone

Novel pyrazoline linked acyl thiourea pharmacophores as antimicrobial, urease, amylase and α-glucosidase inhibitors: design, synthesis, SAR and molecular docking studies

In the present work, a small library of novel pyrazolinyl-acyl thiourea (5a-j) was designed and synthesized through a multistep sequence and the synthesized compounds were screened for their antifungal, antibacterial and antioxidant activities as well as urease, amylase and α-glucosidase inhibitory activities. The synthesized series (5a-o) was characterized using a combination of spectroscopic techniques, including FT-IR, 1H NMR and 13C NMR. All compounds (5a-j) were found to have significant potency against urease, α-glucosidase, α-amylase, and DPPH. The synthesized compounds were also screened for potential antibacterial and anti-fungal inhibition activities. IC50 values for all the prepared compounds for urease, α-glucosidase, amylase, and DPPH inhibition were determined and derivatives 5b and 5g were found to be the most potent urease inhibitors with IC50 values of 54.2 ± 0.32 and 43.6 ± 0.25 μM, respectively. Whilst compound 5b (IC50 = 68.3 ± 0.11 μM) is a potent α-glucosidase inhibitor, compound 5f (90.3 ± 1.08 μM) is a potent amylase inhibitor and compound 5b (103.4 ± 1.15 μM) is a potent antioxidant. The different substitutions on the phenyl ring were the basis for structure-activity relationship (SAR) study. The molecular docking study was performed for the confirmation of binding interactions.

Molecular properties and In silico bioactivity evaluation of (4-fluorophenyl)[5)-3-phen-(4-nitrophenyl yl-4,5-dihydro-1H-pyrazol-1-yl]methanone derivatives: DFT and molecular docking approaches

Objectives

Molecular structures, spectroscopic properties, charge distributions, frontier orbital energies, nonlinear optical (NLO) properties and molecular docking simulations were analyzed to examine the bio-usefulness of a series of (4-fluorophenyl)[5-(4-nitrophenyl)-3-phenyl-4,5-dihydro-1H-pyrazol-1-yl]methanone derivatives.

Methods

The compounds were studied through computational methods. Equilibrium optimization of the compounds was performed at the B3LYP/6-31G(d,p) level of theory, and geometric parameters, frequency vibration, UV-vis spectroscopy and reactivity properties were predicted on the basis of density functional theory (DFT) calculations.

Results

The energy gap (ΔEg), electron donating/accepting power (ω-/ω+) and electron density response toward electrophiles/nucleophiles calculated for M1 and M2 revealed the importance of substituent positioning on compound chemical behavior. In addition, ω-/ω+ and ΔEn/ΔEe indicated that M6 is more electrophilic because of the presence of two NO₂ groups, which enhanced its NLO properties. The hyperpolarizability (β₀) of the compounds ranged from 5.21 × 10^-30 to 7.26 × 10^-30 esu and was greater than that of urea; thus, M1-M6 were considered possible candidates for NLO applications. Docking simulation was also performed on the studied compounds and targets (PDB ID: 5ADH and 1RO6), and the calculated binding affinity and non-bonding interactions are reported.

Conclusion

The calculated ω^- and ω⁺ indicated the electrophilic nature of the compounds; M6, a compound with two NO₂ groups, showed enhanced effects. Molecular electrostatic potential (MEP) analysis indicated that amide and nitro groups on the compounds were centers of electrophilic attacks. The magnitude of the molecular hyperpolarizability suggested that the entire compound had good NLO properties and therefore could be explored as a candidate NLO material. The docking results indicated that these compounds have excellent antioxidant and anti-inflammatory properties.

New bis hydrazone: Synthesis, X-ray crystal structure, DFT computations, conformational study and in silico study of the inhibition activity of SARS-CoV-2

The aim of this work was to synthesize new bis hydrazone derived from benzil in good yield, namely: (1Z,2Z)-1,2-bis (3-Chlorophenyl Hydrazino) Benzil, encoded by 3-Cl BHB. The benzil (or 1,2-diphenyl ethanedione) reacts with 3-Cl phenyl hydrazine by reflux method using ethanol as solvent to obtain the target compound. The obtained product is depicted by UV-Vis, IR spectroscopy and XRD-crystals analysis. All various contacts intra and intermolecular found in 3-Cl BHB were determined by the X-ray diffraction technique performed on single crystals. On the other hand, the optimized geometric structure of 3-Cl BHB was computed by the DFT/B3LYP method with 6-31 G (d, p) level. So, the bond lengths and angles, frontier molecular orbitals (FMO), surface electrostatic potential of the molecule (MEP), global reactivity descriptors, Mulliken atomic charges, computed vibrational analysis and electronic absorption spectrum were determined to get a good understanding of the electronic properties and the active sites of 3-Cl BHB, then to compare them with experimental data. Additionally, a conformational study was carried out using the same method (DFT). The structure-activity relationships established through molecular docking studies showed that 3-Cl BHB structure strongly binds to the receptors M^pro (-8.90 Kcal/mol) and RdRp (-8.60 Kcal/mol) which confirm its inhibition activity against COVID-19.

Synthesis, conformation and Hirshfeld surface analysis of benzoxazole methyl ester as a versatile building block for heterocycles

Solventless cyclocondensation of 2-aminothiophenol with thiourea afforded the benzo[d]oxazole-2-thiol (3a) capable of existing also in the tautomeric form benzo[d]oxazole-2(3H)-thione (3b). Acylation with methyl chloroacetate in dry ethanol in absence of any base or catalyst selectively afforded the S-substituted ester 2-(methoxycarbonylmethylthio)benzo[d]oxazole (4a) in preference to the corresponding N-substituted ester N-(methoxycarbonylmethyl)thioxobenzoxazole (4b). Quantum chemical calculations were conducted to determine the conformational landscape and NBO population analysis showed the strong electronic delocalization via resonance interactions on the 2-mercaptobenzaxazole group. The anomeric effect and the occurrence of a 1,4-S···O intramolecular interactions suggest the relevance of chalcogen bonding in the conformational preference. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (33.2%), H⋯O/O⋯H (19.9%) and H⋯C/C⋯H (17.8%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. Computational chemistry indicates that in the crystal, the C-H⋯O hydrogen-bond energy is 44.8 kJ mol-1.

Novel 1,2,3-Triazole Derivatives as Potential Inhibitors against Covid-19 Main Protease: Synthesis, Characterization, Molecular Docking and DFT Studies

The highly contagious nature of Covid-19 attracted us to this challenging area of research, mainly because the disease is spreading very fast and until now, no effective method of a safe treatment or a vaccine is developed. A library of novel 1,2,3-triazoles based 1,2,4-triazole, 1,3,4-oxadiazole and/or 1,3,4-thiadiazole scaffolds were designed and successfully synthesized. Different spectroscopic tools efficiently characterized all the newly synthesized hybrid molecules. An interesting finding is that some of the newly designed compounds revealed two isomeric forms. The ratio is affected by the size of the attached group as well as the type of the heteroatom forming the side ring attached to the central 1,2,3-triazole ring. The experimental spectroscopic data is in agreement with the DFT calculations at B3LYP 6-31G (d,p) with regard to the geometrical conformation of the prepared compounds. The DFT results revealed that the stability of one isomeric form over the other in the range of 0.057-0.161 Kcal mol-1. A docking study was performed using PyRx and AutoDockVina to investigate the activity of the prepared 1,2,3-triazoles as antiviral agents. Bond affinity scores of the 1,2,3-triazole derivatives were detected in the range of -6.0 to -8.8 kcal/mol showing binding to the active sites of the 6LU7 protease and hence could be anticipated to inhibit the activity of the enzyme. Verification of the docking results was performed using the Mpro alignment of coronaviruses substrate-binding pockets of COVID-19 against the ligands. As per these results, it can be proposed that the title hybrid molecules are acceptable candidates against COVID-19 for possible medicinal agents.