Synthesis, quantum mechanical calculations, antimicrobial activities and molecular docking studies of five novel 2,5-disubstituted benzoxazole derivatives

Synthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies

We have synthesized the pyrazole-bearing Schiff base derivatives (5a-5e) and (6a-6h) then the structural confirmation was supported by various spectral analyses. The antibacterial activity of all analogs was screened against bacterial strains Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Klebsiella pneumonieae and Pseudomonas aeruginosa. In comparison to the reference drug ciprofloxacin, the lead analogs 5c and 6c showed potent activity, with MIC values of 64 µg/mL against E. coli and B. subtilis. Compound 5c showed a moderate effect with a MIC value of 128 µg/mL against B. subtilis, P. aeruginosa and K. pneumonieae, while compound 6c was against E. coli and P. aeruginosa. Furthermore, the compounds 5c and 6c displayed groove binding mode towards CT-DNA by absorption, emission, competitive fluorescence studies using EtBr, CD and time-resolved fluorescence studies. Thermodynamic parameters of analogs 5c and 6c with CT-DNA were also calculated at 298, 303 and 308K temperatures by UV-visible spectroscopy. The molecular docking studies give the docking score for all compounds with PDB codes: 1BNA and 2XCT. The MD simulation study of analogs 5c and 6c was also carried out. The pharmacokinetic and ADME properties were calculated for all of the synthesized analogs (5a-5e) and (6a-6h).Communicated by Ramaswamy H. Sarma.

Density functional modeling, and molecular docking with SARS-CoV-2 spike protein (Wuhan) and omicron S protein (variant) studies of new heterocyclic compounds including a pyrazoline nucleus

Nowadays, different vaccines and antiviral drugs have been developed and their effectiveness has been proven against SARS-CoV-2. Pyrazoline derivatives are biologically active molecules and exhibit broad-spectrum biological activity properties. In this scope, four new molecules (4a-d) including a pyrazoline core were synthesized in order to predict their antiviral properties theoretically. Compounds 4a-d were purified by the crystallization method. The structures of 4a-d were completely characterized by NMR, IR, and elemental analysis. The molecular structures of the compounds in the ground state have been optimized using density functional theory with the B3LYP/6-31++G(d,p) level. The quantum chemical parameters were predicted by density functional theory calculations. Moreover, the molecular docking studies of 4a-d with SARS-CoV-2 Spike protein (Wuhan) and omicron S protein (variant) were presented to investigate and predict potential interactions. The binding sites, binding types and energies, bond distances of the non-covalent interactions and calculated inhibition constants (calc. Ki) as a consequence of molecular docking for 4a-d were presented in this study. Furthermore, the stability of the protein-4a complex obtained from the docking was investigated through molecular dynamics simulation.Communicated by Ramaswamy H. Sarma.

A New Benzoxazole-Based Fluorescent Macrocyclic Chemosensor for Optical Detection of Zn2+ and Cd2+

Background: Benzoxazole-containing ligands find many applications both in medicinal chemistry, catalysis and fluorescence chemosensing. Benzoxazole-containing macrocycles could be therefore a good strategy to achieve stable and selective fluorescent complexes with suitable metal ions. In this work, the synthesis, binding, and photochemical properties of a new fluorescent ligand (L) are reported. L is a cyclophane macrocycle containing the 1,3-bis(benzo[d]oxazol-2-yl)phenyl (BBzB) fluorophore and an aliphatic tetra-amine chain to form the macrocyclic skeleton. Methods: Spectrophotometric and spectrofluorimetric measurements, 1H NMR analysis, and DFT calculations were performed. Results: L behaves as a PET-mediated chemosensor, being emissive at 390 nm at acidic pH and non-emissive at basic pH. The chemosensor is able to detect Zn2+ and Cd2+ in an aqueous medium (acetonitrile–water, 4:1 v/v) at neutral pH through a CHEF effect upon metal ion coordination. Paramagnetic metal ions (Cu2+) and heavy atoms (Pb2+, Hg2+) resulted in a quenching of fluorescence or very low emission. Conclusions: The new cyclophane macrocycle L was revealed to be a selective PET-regulated chemosensor for Zn2+ and Cd2+ in an aqueous medium, being able to bind up to two and one metal cations, respectively. The molecule showed a shifted emission towards the visible region compared to similar systems, suggesting a co-planar conformation of the aromatic fragment upon metal coordination. All these data are supported by both experimental measurements and theoretical calculations.