Spectroscopic investigation (FT-IR, FT-Raman), HOMO-LUMO, NBO, and molecular docking analysis of N -ethyl- N -nitrosourea, a potential anticancer agent

Theoretical Study on Spectrum and Luminescence Mechanism of Cy5.5 and Cy7.5 Dye Based on Density Functional Theory (DFT)

Cy5.5 and 7.5 are the most commonly used NIR 2-region fluoresceins, which have good luminescence properties and important biomedical tracer applications. In this paper, their molecular non-covalent interactions, UV-Vis absorption spectra, main bond lengths, electrostatic potential distributions, frontier molecular orbitals (HOMO and LUMO) and energy gaps were calculated by density functional theory (DFT). We found that the differences in the luminescence properties and energy gaps of Cy5.5 and Cy7.5 molecules may be caused by the length of the conjugated chains between the two aromatic rings in the molecule. By calculating the relevant molecular characteristics, this paper can provide ideas and theoretical basis for the relevant modification and application, as well as the development of new fluorescent dyes.

Combination of bendamustine-azacitidine against Syk target of breast cancer: an in silico study

Breast cancer (BC) is the most serious and second leading cause of death in women worldwide. When breast cancer is diagnosed and treated early, the chance of long-term survival is up to 90%. On the other hand, 90% of BC patient deaths are due to metastasis and a lack of effective early diagnosis. The existing conventional chemotherapy provides negative feedback due to transportation barriers towards the action sites, multidrug resistance, poor bio-availability, non-specific delivery and systemic side effects on the healthy tissue. Syk protein Kinase has been reported in BC, as a tumor modulator, providing a pro-survival signal and also by restricting epithelial-mesenchymal transition, enhancing cell-cell interactions and inhibiting migration. In the present study, we explored the possibility of targeting BC by attenuating Syk protein Kinase. Hence, we have conjugated the hydrophobic Bendamustine (BEN) and hydrophilic Azacitidine (AZA) anticancer drugs to evaluate their efficacy against BC. The native drugs (BEN and AZA) and designed drug-drug conjugate (BEN-AZA) were docked with Syk protein. Then, the docked complex was performed for Binding Free Energy and Molecular Dynamics Simulations. Furthermore, DFT and ADME properties were carried out. The results revealed that the designed drug-drug conjugate has a better docking score, ΔGbind and admirable stability throughout the simulation when compared with native drugs. In DFT and ADME analyses, the designed drug-drug conjugate has shown good stereo electronic features and pharmaceutical relevant parameters than that of native drugs. The overall results suggested that the designed drug-drug conjugate may be a suitable candidate for BC treatment.Communicated by Ramaswamy H. Sarma.

Theoretical Study on Spectrum and Luminescence Mechanism of Indocyanine Green Dye Based on Density Functional Theory (DFT)

Indocyanine green is a great near-infrared fluorescence with good luminescent properties and important medical applications. In this paper, the theoretical spectrum and orbital model of its molecular level are established. The two most probable conformations were studied, and their energies, vibrational spectra, UV-Vis absorption spectra, frontier molecular orbitals (HOMO and LUMO), and energy gaps were obtained by density functional theory (DFT) calculations, respectively. This provides a theoretical and design basis for the development of novel dyes similar to indocyanine green dyes and a reference case for improved application methods and synthetic predesign of novel fluorescent dyes.

Acetophenone-Based 3,4-Dihydropyrimidine-2(1H)-Thione as Potential Inhibitor of Tyrosinase and Ribonucleotide Reductase: Facile Synthesis, Crystal Structure, In-Vitro and In-Silico Investigations

The acetophenone-based 3,4-dihydropyrimidine-2(1H)-thione was synthesized by the reaction of 4-methylpent-3-en-2-one (1), 4-acetyl aniline (2) and potassium thiocyanate. The spectroscopic analysis including: FTIR, 1H-NMR, and single crystal analysis proved the structure of synthesized compound (4), with the six-membered nonplanar ring in envelope conformation. In crystal structure, the intermolecular N-H ⋯ S and C-H ⋯ O hydrogen bonds link the molecule in a two-dimensional manner which is parallel to (010) the plane enclosing R22 (8) and R22 (10) ring motifs. After that, the Hirshfeld surfaces and their related two-dimensional fingerprint plots were used for thorough investigation of intermolecular interactions. According to Hirshfeld surface analysis, the most substantial contributions to the crystal packing are from H ⋯ H (59.5%), H ⋯ S/S ⋯ H (16.1%), and H ⋯ C/C ⋯ H (13.1%) interactions. The electronic properties and stability of the compound were investigated through density functional theory (DFT) studies using B3LYP functional and 6-31G* as a basis set. The compound 4 displayed the high chemical reactivity with chemical softness of 2.48. In comparison to the already reported known tyrosinase inhibitor, the newly synthesized derivatives exhibited almost seven-fold better inhibition of tyrosinase (IC50 = 1.97 μM), which was further supported by molecular docking studies. The compound 4 inside the active pocket of ribonucleotide reductase (RNR) exhibited a binding energy of -19.68 kJ/mol, and with mammalian deoxy ribonucleic acid (DNA) it acts as an effective DNA groove binder with a binding energy of -21.32 kJ/mol. The results suggested further exploration of this compound at molecular level to synthesize more potential leads for the treatment of cancer.

Thiazole-Formulated Azomethine Compound for Three-Way Detection of Mercury Ions in Aqueous Media and Application in Living Cells

Heavy metal ions are extremely poisonous and cause long-term harm to living organisms. Among these ions, mercury is the most toxic metal and has no notorious purpose in the human body. In this regard, an elegant azomethine thiazole compound AM1 was synthesized, and it was found to be highly sensitive to three-way detection of mercury ions with detection limits of 0.1126 × 10^-9 M (FL) and 0.64 × 10^-6 M (UV-vis). AM1 highlighted the capability to detect mercury ions through the colorimetric method, the fluorometric method, and via the naked eye in three-way detection. In addition, the structure of AM1 was confirmed by single-crystal X-ray diffraction studies and crystallized in a monoclinic crystal system with a P21/c space group, and it shows numerous noncovalent interactions in the crystal packing. The high sensitivity of AM1 to Hg²⁺ ions was imputed to the quenching mechanism and was estimated by Fourier transform infrared (FT-IR) spectroscopy, nuclear magnetic resonance (¹H-NMR), high-resolution mass spectrometry (HRMS), ultraviolet-visible (UV-vis) absorbance, fluorescence (FL) emission, Job's plot, B-H plot, and DFT calculation. Naked eye color change of AM1 solution to yellow and turn-off FL by the addition of mercury ion is due to complex formation. In addition to mercury ions, the sensor displayed a new absorption peak at around 240 nm. Furthermore, an AM1-coated test strip is used as the solid support sensor, and real-time detection of Hg²⁺ ions in the HeLa cell line by fluorescence microscopy is performed.

Co(II), Ni(II), and Zn(II) complexes based on new hybrid imine-pyrazole ligands: structural, spectroscopic, and electronic properties

The present work reports the theoretical investigation of Co(II), Ni(II), and Zn(II) complexes containing Schiff bases (used as ligands) derived from the reaction of 2-hydroxy-1-naphthaldehyde with N-(2-aminoethyl) pyrazoles. The spectral analyses were carried out using infrared, Raman, and UV-Vis spectroscopy. Vibrational analyses were performed in order to investigate the mechanisms involving metal-ligand and intra-ligand vibrations and indicated the possibility of charge transfer related to the transitions n[Formula: see text]* and [Formula: see text]*. Structure optimizations and normal coordinate force field calculations were performed via the density functional theory (DFT) method at the HSE06/6-311G(d,p)/LanL2DZ level. A thorough analysis was also conducted regarding the nonlinear optical (NLO) properties and the natural bond orbital (NBO) of the complexes. The results show that these complexes have prospective application as materials for NLO. Furthermore, the NBO analysis confirms the coordination between the lone pair (LP) electrons of the donor atoms (O and N) and the metal acceptors. Finally, studies were conducted regarding the electronic properties of the complexes; among the properties investigated included the frontier molecular orbitals (FMO) and the molecular electrostatic potential (MEP), allowing to determine the energy gap and charge distribution.

Quantum chemical calculation, performance of selective antimicrobial activity using molecular docking analysis, RDG and experimental (FT-IR, FT-Raman) investigation of 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro- 1H- pyrazol-1-yl]-4-oxo-1, 3- thiazol-5(4H)-ylidene} methyl] benzonitrile

The research received a great deal of worldwide attention due to the nature of interpretation before the experimental process. Based on the systematic process the structure of thiazole -pyrazole compound 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro- 1H- pyrazol-1-yl]-4-oxo-1, 3- thiazol-5(4H)-ylidene} methyl] benzonitrile [CPTBN] was investigated. In the first level, the spectral statistics on experimental FT-IR and FT- Raman was reported. At the next level, geometrical parameters was theoretically acquired from density functional theory (DFT) using B3LPY/6-31G and 6-311G basis set. The computed Wavenumber were collected and compared with the experimental data. The vibrational modes were interpreted in terms of potential energy distribution (PED) results. The FMO, MEP, and NBO analysis further validated the electrophilic and nucleophilic interaction in the molecular systems. Two grams-positive bacteria: staphylococcus aureus, Bacillus subtilis and two gram-negative bacteria: Esherichia coli, Pseudomonas aeruginosa was performed for antibacterial activity. Two fungal strain Candida albicans and Aspergillus Niger was carried out against a ligand using anti-fungal activity. The molecular docking analysis explores the antimicrobial and selective potential inhibitory nature of the binding molecule. Besides, RDG and ELF analysis were also performed to show the nature of interactions between the molecule.

Lipophilicity, Pharmacokinetic Properties, and Molecular Docking Study on SARS-CoV-2 Target for Betulin Triazole Derivatives with Attached 1,4-Quinone

A key parameter in the design of new active compounds is lipophilicity, which influences the solubility and permeability through membranes. Lipophilicity affects the pharmacodynamic and toxicological profiles of compounds. These parameters can be determined experimentally or by using different calculation methods. The aim of the research was to determine the lipophilicity of betulin triazole derivatives with attached 1,4-quinone using thin layer chromatography in a reverse phase system and a computer program to calculate its theoretical model. The physiochemical and pharmacokinetic properties were also determined by computer programs. For all obtained parameters, the similarity analysis and multilinear regression were determined. The analyses showed that there is a relationship between structure and properties under study. The molecular docking study showed that betulin triazole derivatives with attached 1,4-quinone could inhibit selected SARS-CoV-2 proteins. The MLR regression showed that there is a correlation between affinity scoring values (ΔG) and the physicochemical properties of the tested compounds.

Spectroscopic Investigations, Computational Analysis and Molecular Docking to SAR-Cov-2 Targets Studies of 5,8-Quinolinedione Attached to Betulin Derivatives

The 5,8-quinolinedione-betulin hybrids were investigated using spectroscopic methods as well as a variety of quantum chemical calculations in order to characterize their molecular structure. We used FT-IR and NMR spectroscopy supplemented by the density functional theory (DFT) calculations, molecular electrostatic potential (MEP) and molecular orbital (HOMO, LUMO) analyses. The experimental and calculated FT-IR spectra showed a good correlation for all compounds. Analysis of carbonyl band showed that the compounds are the 7-mono substituted. The calculated 1H NMR and 13C NMR spectra of hybrids reproduced well the experimental ones. Identification of C-6 and C-7 carbon atoms of 5,8-quinolinedione revealed the position of betulin moiety at the C-7 of 5,8-quinolinedione. Molecular electrostatic potential maps of hybrids allowed to recognize the electrophilic and nucleophilic regions within the molecules. The molecular docking study was used to examine the interaction between the 5,8-quinolinedione-betulin hybrids and the SARS-CoV-2 protein, like: Mpro and PLpro. The obtained results showed that compounds with the highest Dock Score are good anti-SARS-CoV-2 potential drug candidates.