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

Multifunctional in vitro, in silico and DFT analyses on antimicrobial BagremycinA biosynthesized by Micromonospora chokoriensis CR3 from Hieracium canadense

Among the actinomycetes in the rare genera, Micromonospora is of great interest since it has been shown to produce novel therapeutic compounds. Particular emphasis is now on its isolation from plants since its population from soil has been extensively explored. The strain CR3 was isolated as an endophyte from the roots of Hieracium canadense, and it was identified as Micromonospora chokoriensis through 16S gene sequencing and phylogenetic analysis. The in-vitro analysis of its extract revealed it to be active against the clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Candida tropicalis (15 mm). No bioactivity was observed against Gram-negative bacteria, Escherichia coli ATCC 25922, and Klebsiella pneumoniae ATCC 706003. The Micromonospora chokoriensis CR3 extract was also analyzed through the HPLC-DAD-UV-VIS resident database, and it gave a maximum match factor of 997.334 with the specialized metabolite BagremycinA (BagA). The in-silico analysis indicated that BagA strongly interacted with the active site residues of the sterol 14-α demethylase and thymidylate kinase enzymes, with the lowest binding energies of - 9.7 and - 8.3 kcal/mol, respectively. Furthermore, the normal mode analysis indicated that the interaction between these proteins and BagA was stable. The DFT quantum chemical properties depicted BagA to be reasonably reactive with a HOMO-LUMO gap of (ΔE) of 4.390 eV. BagA also passed the drug-likeness test with a synthetic accessibility score of 2.06, whereas Protox-II classified it as a class V toxicity compound with high LD50 of 2644 mg/kg. The current study reports an endophytic actinomycete, M. chokoriensis, associated with H. canadense producing the bioactive metabolite BagA with promising antimicrobial activity, which can be further modified and developed into a safe antimicrobial drug.

TD-DFT, DFT, docking, MD simulations, and concentration-dependent SERS investigations of a bioactive trifluoromethyl derivative having human acetylcholinesterase and butyrylcholinesterase in silver colloids

CONTEXT

Various concentrations of (E)-4-methoxy-N'-(2-(trifluoromethyl)benzylidene) benzohydrazide (EMT) adsorbed on colloidal silver nanoparticles were studied using SERS and results were compared to the normal Raman spectrum. DFT calculations were used to validate experimental findings. Theoretically, the structures of the EMT and EMT-Ag6 systems were optimized. The UV-Vis spectral analysis's red shift and lower intensity behavior show that EMT has chemisorbed onto Ag nanoparticles. Charge transfer (CT) from Ag to EMT is highlighted by FMO analysis. The CT interaction in EMT and EMT-Ag6 was further verified by MEP and Mulliken charge analyses. The EMT was adsorbed on Ag nanoparticles with tilted orientation and orientation changes with colloidal concentration, according to SERS spectrum analysis. Docking EMT with 4PQE and 5DYW binding affinities are found to be -9.7 and -8.1 kcal/mol. MD simulations give the competence of 5DYW-EMT and 4PQE-EMT in their intended binding interactions and their ability to establish enduring associations with the protein of interest.

METHODS

DFT was used to optimize the molecular structures of EMT and EMT-Ag6 using B3LYP/6-311++G* (LANL2DZ basis set for Ag). A molecular dynamics simulation study was conducted on the 4PQE-EMT and 5DYW-EMT systems using the Desmond software for 100 ns.

Schiff-base ligands containing phenanthroline terminals: Synthesis, characterization, biological activities and molecular docking study

Three new phenanthroline-derived ligands were synthesized by the Schiff base condensation method. The first ligand was the result of 1,10-phenanthroline-2-carboxyaldehyde reaction with 1,4-diaminobutane (L1). The other ligands were obtained 1,6-diaminohexane (L2) and 1,8-diaminooctane (L3) with the phenanthroline aldehyde in separate reactions. The structures of all ligands were elucidated using spectral techniques such as FT-IR, ¹³C NMR, ¹H NMR and LC ESI/MS. The geometric properties of ligands such as bond lengths, bond angles, dihedral angles, electronic properties, HOMO and LUMO energies were calculated by using the Gaussian 09w programme. Ligands were optimized with B3LYP and 6-311++G(2d,p) basis set and NMR and FT-IR spectra were calculated. Experimental and theoretical spectrum data were compared. All of the ligands showed antibacterial activity against Staphylococcus aureus ATCC 25923 and Bacillus cereus ATCC 11778. The anticancer activities of the ligands were also determined against human breast cancer (MCF7) and prostate cancer (DU145) cell lines. In addition, which conformation of the ligands was determined by the theoretical calculations. Docking studies of ligands with bovine serum albumin (BSA) were performed using Autock Tools 1.5.6 programme.

Molecular–substrate interaction on dynamic SERS detection of butylated hydroxyanisole on a silver nano-tripod substrate

A SERS enhancement model with a surface adsorption effect is proposed by dynamical SERS analysis of butylated hydroxyanisole on a silver nano-tripod substrate.

Silver Flowerlike Structures for Surface-Enhanced Raman Spectroscopy

Micro- and nanoflowers are a class of materials composed of particles with high surface-to-volume ratio. They have been extensively studied in the last decade due to simple preparation protocols and promising applications in biosensing, as drug delivery agents, for water purification, and so on. Flowerlike objects, due to their highly irregular surface, may act also as plasmonic materials, providing resonant coupling between optical waves and surface plasmon excitations. This fact allows us to infer the possibility to use micro- and nanoflowers as effective surface-enhanced Raman scattering (SERS) substrate materials. Here, we report on the design and Raman enhancement properties of silver flowerlike structures, deposited on aluminum surface. A simple and cost-effective fabrication method is described, which leads to SERS substrates of high developed surface area. The morphology of the silver flowers on a nanoscale is characterized by self-organized quasiperiodic stacks of nanosheets, which act as plasmonic cavity resonators. The substrates were tested against rhodamine-6G (R6G) water solutions of concentration varying between 10⁻³ M and 10⁻⁷ M. Optimal SERS enhancement factors of up to 10⁵ were established at R6G concentrations in the 10⁻⁶–10⁻⁷ M range.

Adsorption of the drug bempedoic acid over different 2D/3D nanosurfaces and enhancement of Raman activity enabling ultrasensitive detection: First principle analysis

The nanocluster-based drug delivery system is of much importance, now days. This manuscript studies the interaction of pristine/substituted/doped GQDs, fullerene, helicene and CNT with bempedoic acid, which is an effective alternative of statins in the treatment of hypercholesteremia. The adsorption energies are calculated at B3LYP-D3/6-311G+(2d,p) level in order to study the adsorption of bempedoic acid over the surfaces of the nanoclusters incorporating Grimme's dispersion correction. Surface enhanced Raman scattering (SERS), which is a sound approach to vibrational spectroscopy, is used in order to detect bempedoic acid. All the studies signify that bempedoic acid can be detected with these nanoclusters and the negative adsorption energies advocate for the possible use of these nanoclusters as effective drug delivery system in case of bempedoic acid. Adsorption energy of bempedoic acid over helicene was found to be the most negative among the mentioned nanocluster systems, while adsorption on the surface of CNT was found to be the least negative.