DFT/TD-DFT calculations, spectroscopic characterizations (FTIR, NMR, UV–vis), molecular docking and enzyme inhibition study of 7-benzoyloxycoumarin

New Insight into the Pharmacological Importance of Atropine as the Potential Inhibitor of AKR1B1 via Detailed Computational Investigations: DFTs, ADMET, Molecular Docking, and Molecular Dynamics Studies

The aim of this research is to investigate the quantum geometric properties and chemical reactivity of atropine, a pharmaceutically active tropane alkaloid. Using density functional theory (DFT) computations with the B3LYP/SVP functional theory basis set, the most stable geometry of atropine was determined. Additionally, a variety of energetic molecular parameters were calculated, such as the optimized energy, atomic charges, dipole moment, frontier molecular orbital energies, HOMO-LUMO energy gap, molecular electrostatic potential, chemical reactivity descriptors, and molecular polarizability. To determine atropine's inhibitory potential, molecular docking was used to analyze ligand interactions within the active pockets of aldo-keto reductase (AKR1B1 and AKR1B10). The results of these studies showed that atropine has greater inhibitory action against AKR1B1 than AKR1B10, which was further validated through molecular dynamic simulations by analyzing root mean square deviation (RMSD) and root mean square fluctuations (RMSF). The results of the molecular docking simulation were supplemented with simulation data, and the ADMET characteristics were also determined to predict the drug likeness of a potential compound. In conclusion, the research suggests that atropine has potential as an inhibitor of AKR1B1 and could be used as a parent compound for the synthesis of more potent leads for the treatment of colon cancer associated with the sudden expression of AKR1B1.

Theoretical analysis of OLED performances of some aromatic nitrogen-containing ligands

It is well-known that tris(8-hydroxyquinoline) aluminum (Alq3) complex and N,N'diphenyl-N,N'-bis(3-methylphenyl)-1,1'-diphenyl-4,4'-diamine compound (TPD) are widely used as electron transfer material (ETL) and hole transfer material (HTL) in organic light emitting diode (OLED) structure, respectively. Considering the reference materials, in the present work, the OLED performances of some cyclic aromatic structures such as 4,4'azopyridine [AZPY], 4,4'-bipyridine [BIPY], 1,2-bis[4'-(4-methylphenyl)2,2':6'2″-terpyridin6-yl]ethyne (BISTERPY), 5,5'-diamino-2,2'-bipyridine (DABP), dipyrido[3,2-a:2',3'c]phenazine (DPP), 4,7-phenanthroline (PHEN) including nitrogen atom have been theoretically analyzed. It is important to note that B3LYP/6-31G(d) and B3LYP/TZP levels of the theory were taken into account for the calculations about monomeric and dimeric structures, respectively. Additionally, the calculations of the mentioned monomeric form were performed at B3LYP-D3/6-31G, CAM-B3LYP/6-31G and ωB97X-D/6-31G(d) levels. For a detailed theoretical analysis, the reorganization energies (λe and λh), adiabatic and vertical ionization potentials and electron affinities, the effective transfer integrals (Ve and Vh), and the charge transfer rates (We and Wh) of all compounds were computed by means of computational chemistry tools. In the light of calculated parameters, it is determined that these mentioned aromatic cyclic structures will be used in which layers of OLED structure. The results obtained in this study will be helpful in the design and applications of new molecules as OLED materials in the future.

Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach

During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.

Exploring of antioxidant and antibacterial properties of novel 1,3,4-thiadiazole derivatives: Facile synthesis, structural elucidation and DFT approach to antioxidant characteristics

In recent years, compounds containing thiophene and 1,3,4-thiadiazole skeletons have become important cyclic compounds, especially in medicinal chemistry. In this manner, we synthesized and isolated seven 1,3,4-thiadiazole derivatives with thiophene groups and fully characterized by elemental analysis and general spectroscopic methods such as ¹H NMR, ¹³C NMR, and FT-IR. Antibacterial activities of the title compounds were investigated by using TLC-Dot blot, macro dilution, well diffusion, and growth curve analysis methods. Compounds 1 and 6 showed inhibitory activities against all tested gram-negative and gram-positive bacteria. TLC-DPPH and DPPH assays, on the other hand, were performed to detect the antioxidant activities of the 1,3,4-thiadiazole derivatives and compound 1 exhibited the highest antioxidant activity at all tested concentrations. QTAIM and NCI calculations were performed as well as structural, electronic, and spectral analyzes using density functional theory (DFT). Calculations were carried out at the B3lyp/6-311 + +g(2d,2p) level of theory, and the data were used to examine the antioxidant activity of the compounds.

Synthesis, density functional theory (DFT) studies and urease inhibition activity of chiral benzimidazoles

A variety of benzimidazole by the heterocyclization of orthophenylenediamine were synthesized in 69–86% yields. The synthesized compounds 3a-f and 6a-f were characterized and further investigated as jack bean urease inhibitors. Density functional theory (DFT) studies were performed utilizing the basis set B3LYP/6-31G (d, p) to acquire perception into their structural properties. Frontier molecular orbital (FMO) analysis of all compounds 3a–f and 6a-f was computed at the same level of theory to get a notion about their chemical reactivity and stability. The mapping of the molecular electrostatic potential (MEP) over the entire stabilized molecular geometry indicated the reactive centers. They exhibited urease inhibition activity with IC50 between 22 and 99 μM. Compounds containing withdrawing groups on the benzene ring (3d, 6d) were not showing significant urease inhibition. The value obtained for 3a, 3b, 3f had shown their significant urease inhibition for both theoretical and experimental. Notably, the compound having S-configuration (3a) (22.26 ± 6.2 μM) was good as compared to its R enantiomer 3f (31.42 ± 23.3 μM). Despite this, we elaborated the computational studies of the corresponding compounds, to highlight electronic effect which include HOMO, LUMO, Molecular electrostatic potential (MEP) and molecular docking.

Substitution Effects on the Optoelectronic Properties of Coumarin Derivatives

Coumarin derivatives have gathered major attention largely due to their versatile utility in a wide range of applications. In this framework, we report a comparative computational investigation on the optoelectronic properties of 3-phenylcoumarin and 3-heteroarylcoumarin derivatives established as enzyme inhibitors. Specifically, we concentrate on the variation in the optoelectronic characteristics for the hydroxyl group substitutions within the coumarin moiety. In order to realize our aims, all-electron density functional theory and time dependent density functional theory calculations were performed with a localized Gaussian basis-set matched with a hybrid exchange–correlation functionals. Molecular properties such as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, vertical ionization (IEV) and electron affinity energies, absorption spectra, quasi-particle gap, and exciton binding energy values are examined. Furthermore, the influence of solvent on the optical properties of the molecules is considered. We found a good agreement between the experimental (8.72 eV) and calculated (8.71 eV) IEV energy values for coumarin. The computed exciton binding energy of the investigated molecules indicated their potential optoelectronics application.

Expression, purification and characterization of diguanylate cyclase from Rhodococcus ruber

Diguanylate cyclases (DGCs) were responsible for the synthesis of second messenger cyclic di-guanosine monophosphate (c-di-GMP), which were involved in various physiological activities of bacterial species. Here, a full-length DGC from Rhodococcus ruber SD3 fused with glutathione-S-transferase (GST) was expressed in E. coli and purified by glutathione agarose resin. The apparent molecular mass of one subunit of the purified diguanylate cyclase with GST tag (GST-DGC) was estimated to be 71.9 kDa by SDS-PAGE, which was approximately in accordance with the theoretical value of 73.0 kDa. The sequence of GST-DGC was confirmed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The blue native PAGE indicated that GST-DGC formed octamer. The optimum pH and temperature for GST-DGC activity were 8.0 and 47 °C, respectively. The fusion protein exhibited high thermostability, and 94% of activity was retained when the protein was incubated at 87 °C for 1 h. Moreover, the fusion protein showed pH stability. The Km, Vmax and Kcat values for GST-DGC enzyme were 9.8 μM, 0.7 μM/min and 1.3 S^-1. Some ions such as Zn²⁺, Mn²⁺, Fe²⁺, Ni²⁺ and Co²⁺ had inhibitory effects on the activity of the protein, while other ions such as Mg²⁺, K⁺ and Na⁺ slightly activated the protein. The fusion protein also showed rather high stability in the presence of toluene, cyclohexane and n-hexane.

Synthesis, computational quantum chemical study, in silico ADMET and molecular docking analysis, in vitro biological evaluation of a novel sulfur heterocyclic thiophene derivative containing 1,2,3-triazole and pyridine moieties as a potential human topoisomerase IIα inhibiting anticancer agent

Computational quantum chemical study and biological evaluation of a synthesized novel sulfur heterocyclic thiophene derivative containing 1,2,3-triazole and pyridine moieties namely BTPT [2-(1-benzyl-5-methyl-1H-1,2,3-triazol-4-yl)-6-methoxy-4-(thiophen-2-yl) pyridine] was presented in this study. The crystal structure was determined by SCXRD method. For the title compound BTPT, spectroscopic characterization like ¹H NMR, ¹³C NMR, FTIR, UV-vis were carried out theoretically by computational DFT method and compared with experimental data. Druglikeness parameters of BTPT were found through in silico pharmacological ADMET properties estimation. The molecular docking investigation was performed with human topoisomerase IIα (PDB ID:1ZXM) targeting ATP binding site. In vitro cytotoxicity activity of BTPT/doxorubicin were examined by MTT assay procedure against three human cancer cell lines A549, PC-3, MDAMB-231 with IC50 values of 0.68/0.70, 1.03/0.77 and 0.88/0.98 μM, respectively. Our title compound BTPT reveals notable cytotoxicity against breast cancer cell (MDAMB-231), moderate activity with human lung cancer cell (A-549) and less inhibition with human prostate cancer cell (PC-3) compared to familiar cancer medicine doxorubicin. From the results, BTPT could be observed as a potential candidate for novel anticancer drug development process.

Molecular structure and spectral characteristics of hyperoside and analysis of its molecular imprinting adsorption properties based on density functional theory

The structure of hyperoside was optimized according to the skeletal types of different galactopyranosides in hyperoside at the DFT/B3LYP/6-31++G(d,p) level, and the frequencies were calculated. The accuracy of the theoretical calculations of the ¹H and ¹³C NMR signals was evaluated by linear correlation. The excited state was calculated via time-dependent density functional theory (TD-DFT). The stable conformation, NMR, UV-vis, natural bond orbital (NBO), molecular electrostatic potential (MEP) and thermodynamic information were obtained. In the most stable conformation of hyperoside, seven intramolecular hydrogen bonds are formed, which affect the imprinting efficiency. The theoretical ¹H and ¹³C NMR results are in good agreement with the experimental results. The B3PW91 function is more suitable than B3LYP for TD-DFT calculations. Combining the UV-vis and NBO analyses, the HOMO→LUMO transition mainly results from the n→π^∗ transition of the phenolic hydroxyl groups and the π→π^∗ transition of the benzene ring on the B ring in ethanol. The HOMO-1→LUMO+1 transition mainly results from the n→π^∗ and π→π^∗ transition on the A ring. The MEP and NBO calculations indicate that the imprinted active sites are mainly located on the carbonyl oxygen atom and the hydroxyl hydrogen atoms. As the temperature increases, the molecular heat capacity, entropy, enthalpy, and activity of the imprinting sites increase. The obtained results provide strong theoretical guidance for hyperoside in the synthesis of molecularly imprinted polymers and separation techniques.

Combined molecular modeling and cholinesterase inhibition studies on some natural and semisynthetic O-alkylcoumarin derivatives

Coumarins of synthetic or natural origins are an important chemical class exerting diverse pharmacological activities. In the present study, 26 novel O-alkylcoumarin derivatives were synthesized and have been tested at 100 µM for their in vitro inhibitory potential against acetylcholinesterase (AChE) and butyrlcholinesterase (BChE) targets which are the key enzymes playing role in the pathogenesis of Alzheimer's disease. Among the tested coumarins, none of them could inhibit AChE, whereas 12 of them exerted a marked and selective inhibition against BChE as compared to the reference (galanthamine, IC₅₀ = 46.58 ± 0.91 µM). In fact, 10 of the active coumarins showed higher inhibition (IC₅₀ = 7.01 ± 0.28 µM - 43.31 ± 3.63 µM) than that of galanthamine. The most active ones were revealed to be 7-styryloxycoumarin (IC₅₀ = 7.01 ± 0.28 µM) and 7-isopentenyloxy-4-methylcoumarin (IC₅₀ = 8.18 ± 0.74 µM). In addition to the in vitro tests, MetaCore/MetaDrug binary QSAR models and docking simulations were applied to evaluate the active compounds by ligand-based and target-driven approaches. The predicted pharmacokinetic profiles of the compounds suggested that the compounds reveal lipophilic character and permeate blood brain barrier (BBB) and the ADME models predict higher human serum protein binding percentages (>50%) for the compounds. The calculated docking scores indicated that the coumarins showing remarkable BChE inhibition possessed favorable free binding energies in interacting with the ligand-binding domain of the target. Therefore, our results disclose that O-alkylcoumarins are promising selective inhibitors of cholinesterase enzymes, particularly BChE in our case, which definitely deserve further studies.

Synthesis, Structural Characterization and Antimicrobial Activity of Cu(II) and Fe(III) Complexes Incorporating Azo-Azomethine Ligand

We are reporting a novel azo-azomethine ligand, HL and its complexes with Cu(II) and Fe(III) ions. The ligand and its complexes are characterized by various physico-chemical techniques using C,H,N analyses, FT-IR, ¹H-NMR, ESI-MS and UV-Vis studies. TGA analyses reveal complexes are sufficiently stable and undergo two-step degradation processes. The redox behavior of the complexes was evaluated by cyclic voltammetry. Furthermore, the ligand and its complexes were tested for antimicrobial activity against bacterial and fungal strains by determining inhibition zone, minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC). The complexes showed moderate antimicrobial activity when tested against Gram +ve and Gram −ve bacterial strains. To obtain insights into the structure of ligand, DFT studies are recorded. The results obtained are quite close to the experimental results. In addition, the energy gap, chemical hardness, softness, electronegativity, electrophilic index and chemical potential were calculated using HOMO, LUMO energy value of ligand.