Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative

D-Mannoside FimH Inhibitors as Non-Antibiotic Alternatives for Uropathogenic Escherichia coli

FimH is a type I fimbria of uropathogenic Escherichia coli (UPEC), recognized for its ability to adhere and infect epithelial urinary tissue. Due to its role in the virulence of UPEC, several therapeutic strategies have focused on the study of FimH, including vaccines, mannosides, and molecules that inhibit their assembly. This work has focused on the ability of a set of monosubstituted and disubstituted phenyl mannosides to inhibit FimH. To determine the 3D structure of FimH for our in silico studies, we obtained fifteen sequences by PCR amplification of the fimH gene from 102 UPEC isolates. The fimH sequences in BLAST had a high homology (97–100%) to our UPEC fimH sequences. A search for the three-dimensional crystallographic structure of FimH proteins in the PDB server showed that proteins 4X5P and 4XO9 were found in 10 of the 15 isolates, presenting a 67% influx among our UPEC isolates. We focused on these two proteins to study the stability, free energy, and the interactions with different mannoside ligands. We found that the interactions with the residues of aspartic acid (ASP 54) and glutamine (GLN 133) were significant to the binding stability. The ligands assessed demonstrated high binding affinity and stability with the lectin domain of FimH proteins during the molecular dynamic simulations, based on MM-PBSA analysis. Therefore, our results suggest the potential utility of phenyl mannoside derivatives as FimH inhibitors to mitigate urinary tract infections produced by UPEC; thus, decreasing colonization, disease burden, and the costs of medical care.

Investigation of the reactivity properties of a thiourea derivative with anticancer activity by DFT and MD simulations

Spectroscopic analysis of 1-(2-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (FPTT) is reported. Experimental and theoretical analyses of FPTT, with molecular dynamics (MD) simulations, are reported for finding different parameters like identification of suitable excipients, interactions with water, and sensitivity towards autoxidation. Molecular dynamics and docking show that FPTT can act as a potential inhibitor for new drug. Additionally, local reactivity, interactivity with water, and compatibility of FPTT molecule with frequently used excipients have been studied by combined application of density functional theory (DFT) and MD simulations. Analysis of local reactivity has been performed based on selected fundamental quantum-molecular descriptors, while interactivity with water was studied by calculations of radial distribution functions (RDFs). Compatibility with excipients has been assessed through calculations of solubility parameters, applying MD simulations. Graphical abstract Reactive sites identified.

Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative

Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of (E)-N'-(5-chloro-2-hydroxybenzylidene)-4-trifluoromethyl) benzohydrazide (CHTB) have been studied on different silver colloids in order to know the particular chemical species responsible for the spectra. Very significant shifts are observed for Raman and SERS wavenumbers. Observed changes in the υ-ring modes may be due to surface interaction of the π-electrons and the presence of this suggested that RingII is more tilted in both cases than RingI and the molecule assumes a tilted orientation for the concentration 10^-3 M. Orientation changes are seen in concentration dependent SERS spectra. The molecular electrostatic potential has also been constructed to determine the electron rich and poor site of CHTB. The molecular docking studies indicate that the binding affinity and hydrogen bond interactions with the receptors may be supporting evidence for further studies in designing other pharmaceutical applications of CHTB.Communicated by Ramaswamy H. Sarma.

DFT computational study towards investigating psychotropic drugs, promazine and trifluoperazine adsorption on graphene, fullerene and carbon cyclic ring nanoclusters

Detection and qualification process related to impurities assume importance in pharmacological drug development programmes and the present article gives the structural and spectral characterisation of phenothiazine derivatives, promazine (PME) and trifluoperazine (TPE) and their self-assembly with graphene/fullerene/carbon ring (CG/CF/CR) systems theoretically. The investigation of adsorption behaviour of these compounds can provide valuable information about its reactivity, electronic and structural properties. Three-dimensional electrostatic potential diagrams were mapped. The frontier orbital energies and energy band gaps of the molecules were computed. Delocalization of charge density between the bonding or lone pair and antibonding orbitals is calculated by NBO analysis. Docking was executed to investigate binding areas of chemical compounds. Bioactivity scores show that the pharmacokinetic and pharmacological properties of the ligands are appropriate leading to be considered potential drug agents. The obtained theoretical wavenumber results of the present study were fully compatible with the experimental results.

Synthesis, Crystal Structure, Biological Evaluation and in Silico Studies on Novel (E)-1-(Substituted Benzylidene)-4-(3-isopropylphenyl)thiosemicarbazone Derivatives

A series of (E)-1-(substituted benzylidene)-4-(3-isopropylphenyl)thiosemicarbazone derivatives were synthesized and characterized by FT-IR spectrum, elemental analysis, NMR spectrum, HR-MS spectrum, and X-ray single crystal diffraction technology. The crystal structures and packing of (E)-1-(4-fluorobenzylidene)-4-(3-isopropylphenyl)thiosemicarbazone and (E)-1-(3-fluorobenzylidene)-4-(3-isopropylphenyl)thiosemicarbazone were maintained through the intramolecular hydrogen bond (N3-H6⋅⋅⋅N1) and intermolecular hydrogen bonds (N2-H4⋅⋅⋅S1, C14-H14⋅⋅⋅F1 and C7-H7⋅⋅⋅S1). The results obtained by employing the DPPH free radicals scavenging assay indicated that (E)-1-(4-methoxylbenzylidene)-4-(3-isopropylphenyl)thiosemicarbazone had a more significant antioxidant activity compared with other compounds. The results measured by adopting the disc diffusion method elucidated that (E)-1-(4-trifluoromethylbenzylidene)-4-(3-isopropylphenyl)thiosemicarbazone possessed a more prominent antifungal activity than other compounds. Molecular docking showed that (E)-1-(4-chlorobenzylidene)-4-(3-isopropylphenyl)thiosemicarbazone had the highest affinity with receptor protein (1NMT). Moreover, the drug-likeness characteristic, physicochemical properties, pharmacokinetic profiles, and bioactivity scores of all the compounds were predicted through in silico studies. The results illustrated that (E)-1-(4-fluorobenzylidene)-4-(3-isopropylphenyl)thiosemicarbazone had the drug-likeness characteristic and all the compounds were considered as moderately biological active molecules.