Comparative assessment of some benzodiazepine drugs based on Density Functional Theory, molecular docking, and ADMET studies

Benzodiazepines are widely used to treat anxiety, insomnia, agitation, seizures, and muscle spasms. It works through the GABAA receptors to promote sleep by inhibiting brainstem monoaminergic arousal pathways. It is safe and effective for short-term use, and arises some crucial side effects based on dose and physical condition. In this investigation, physicochemical properties, molecular docking, and ADMET properties have been studied. Density functional theory with B3LYP/6-311G+(d,p) level of theory was set for geometry optimization and elucidate their thermodynamic, orbital, dipole moment, and electrostatic potential properties. Molecular docking and interaction calculations have performed against human GABAA receptor protein (PDB ID: 4COF) to search the binding affinity and effective interactions of drugs with the receptor protein. ADMET prediction has performed to investigate their absorption, metabolism, and toxic properties. Thermochemical data suggest the thermal stability; the docking result predicts effecting bindings and ADMET calculation disclose non-carcinogenic and relatively harmless phenomena for oral administration of all drugs.

Synthesis and structural analysis of cis-bis(1,10-phenanthroline)dicarbonyl ruthenium(II) 1.72-trifluoromethanesulfonate 0.28-hexafluoridophosphate

Ruthenium(II) complexes containing both 1,10-phenanthroline (Phen) and carbonyl (CO) ligands are important molecules for various applications including catalysis. In this work, the molecular structure of [Ru(Phen)2(CO)2]2+ was determined via X-ray diffraction analysis for the first time. The complex exhibits substitutional disorder of one of counter-anions in the asymmetric unit, with different occupancies for CF3SO3- (0.72) and PF6- (0.28). The ruthenium atom is coordinated in a distorted octahedral environment by two carbonyl carbon atoms and four nitrogen atoms from bis-Phen ligands. The cation displays a cis configuration of the carbonyl ligands. Several hydrogen bonds and π-π interactions are present in the crystal. In addition to structural characterization, IR spectral data for the complex is compared with calculated values. These results provide fundamental data for understanding various properties of related ruthenium complexes.

Synthesis and in vitro drug release of primaquine phosphate loaded PLGA nanoparticles

Plasmodium falciparum is one of the most common resistant Plasmodium species responsible for high rates of morbidity and mortality in malaria patients. Clinical guidelines for the management of Plasmodium falciparum include the use of a dose of primaquine phosphate resulting intolerable side effects. Therefore, the aim of this work was to formulate primaquine phosphate-loaded PLGA nanoparticles by using a nanoprecipitation method in order to increase its bioavailability to minimize drug intake. This leads to reduced toxicity and better therapeutic efficacy of the drug. The synthesized nanoparticles were characterized by using dynamic light scattering (DLS), transmission electron microscopy (TEM), scanning electron microscopy (SEM), atomic force microscopy (AFM), Fourier transformed infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and powder X-ray diffraction (XRD). TEM analysis revealed the presence of smooth spherical-shaped nanoparticles. The drug DLS analysis confirmed the presence of negatively charged nanoparticles with particle size in the range of 100-400 nm. The drug release study was performed to analyses different kinetic models like zero-order model, first-order model, Higuchi model, Hixson-Crowell model, and Korsmeyer-Peppas model.

Highly efficient fluorescence resonance energy transfer in co-encapsulated BODIPY nanoparticles

Fluorescence resonance energy transfer (FRET) is a powerful tool used in a wide range of applications due to its high sensitivity and many other advantages. Co-encapsulation of a donor and an acceptor in nanoparticles is a useful strategy to bring the donor-acceptor pair in proximity for FRET. A highly efficient FRET system based on BODIPY-BODIPY (BODIPY: boron-dipyrromethene) donor-acceptor pair in nanoparticles was synthesized. Nanoparticles were formed by co-encapsulating a green emitting BODIPY derivative (FRET donor, lmax = 501 nm) and a red emitting BODIPY derivative (FRET acceptor, lmax = 601 nm) in an amphiphilic polymer using the precipitation method. Fluorescence measurements of encapsulated BODIPY in water following 501 nm excitation caused a 3.6 fold enhancement of the acceptor BODIPY emission at 601 nm indicating efficient energy transfer between the green emitting donor BODIPY and the red emitting BODIPY acceptor with a 100 nm Stokes shift. The calculated FRET efficiency was 96.5%. Encapsulated BODIPY derivatives were highly stable under our experimental conditions.

Investigations on spectroscopic characterizations, molecular docking, NBO, drug-Likeness, and ADME properties of 4H-1,2,4-triazol-4-amine by combined computational approach

In this study, the spectroscopic characterization, frontier molecular orbital analysis, and natural bond orbital analysis (NBO) analysis were executed to determine the movement of electrons within the molecule and the stability, and charge delocalization of the 4H-1,2,4-triazol-4-amine (4-AHT) through density functional theory (DFT) approach and B3LYP/6-311++G(d,p) level of theory. Surface plots of the hybrids’ Molecular Electrostatic Potential (MEP) revealed probable electrophilic and nucleophilic attacking sites. The discussed ligand were observed to be characterized by various spectral studies (FT-IR, UV-Vis). The calculated IR was found to be correlated with experimental values. The UV-Vis data of the molecule was used to analyze the visible absorption maximum (λmax) using the time-dependent DFT method. Since the principle of drug-likeness is usually used in combinatorial chemistry to minimize depletion in pharmacological investigations and growth, drug-likeness and ADME properties were calculated in this research to establish 4-AHT molecule bioavailability. Furthermore, molecular docking studies were carried out. Molecular docking analysis was performed for the title ligand inside the active site of the Epidermal Growth Factor Receptor (EGFR). The title compound’s anti-tumor activity against the cancer cell, in which EGFR is strongly expressed, prompted us to conduct molecular docking into the ATP binding site of EGFR to predict whether this molecule has an analogous binding mode to the EGFR inhibitors (PDB: ID: 1M17).

The mystery of chemistry behind the mechanism of action of anti-HIV drugs: A docking approach at an atomic level

The effect of HIV-1 on a human’s immune system cannot be ignored. This is the virus that reduces the power of the immune system to fight against any disease. Of course, many anti-HIV drugs are available, and many computational studies have been done to find out their mechanism of action, but the computational study regarding the chemistry behind the mechanism of action was not done yet. Therefore, the main objective of the study was to clarify the chemistry behind the mechanism of action of commercially available anti-HIV drugs. The drugs taken in the presented study were Entry Inhibitors (EIs) and Non-nucleoside reverse transcriptase inhibitors. First, literature data was evaluated computationally to ensure the reliability of the software used for the presented study. It was found that interaction-based experimental results and computationally evaluated results of the literature data were the same. After that, by following the same procedure, a docking study was done on the drugs taken in the current study. In addition, the residues involved in the interactions of EIs and NNRTIs with their receptors were studied to determine the chemistry that acts behind the action of both. It was found that EIs and NNRTIs work differently. It was also predicted that the derivatization of both drugs could make them more effective and active. Therefore, the presented study will be very helpful in the field of medicinal science.

Antimicrobial activity and physicochemical properties of Balanites aegyptiaca seed oil

This study was aimed to assess the antibacterial and antifungal activities of Balanites aegyptiaca seed oil and characterize the physicochemical properties. Seeds were collected from the local central market, Khartoum-Sudan (2019). The samples were dried under shade and grinded, then the oil was extracted with a Soxhlet extractor using n-hexane. The percentage yield of the extract was found to be 25.64%. The seed oil was tested against Pseudomonas aeruginosa (G-), Escherichia coli (G-), Bacillus subtilis (G+), Staphylococcus aureus (G+), and Candida albicans to assess their antimicrobial properties. The extract of B. aegyptiaca seed oil has antimicrobial activity against most of the organisms tested. The fatty acid profile of the B. aegyptiaca seed oil was analyzed by GC/MS. The results revealed that the presence of five fatty acids, including saturated linoleic acid, oleic acid, and unsaturated palmate and stearic acids, also a unique antioxidant compound butylated hydroxytoluene. The physiochemical properties of the seed oil showed that the oil contained kinetic viscosity (57 cp), density (0.917 g/cm3), refractive index (1.472), acid value (49.96 mg/kg), saponification value (248.75 mg/g), ester number (234.79 mg/kg) and peroxide number (0.02 mg/kg). Through physiochemical analysis, it was found that oil can be used for human consumption due to the percentage yield of unsaturated acids (81%). In addition, the results of the antioxidant activity of the seeds oil showed that the seed oil had moderate antioxidant activity.

Crystallographic structure, activity prediction, and hydrogen bonding analysis of some CSD-based 3,3'-bis-indole derivatives: A review

Herein we report crystallographic comparison of some geometrical and structural features for a series of biologically relevant bis-indole derivatives. Selected bond distances and bond angles of interest in a series of bis-indole derivatives have been discussed in detail. The biological activity of the substances has been correlated with based the structure-activity relationships (SAR) base which provides the different possibility of activity (Pa) and possibility of inactivity (Pi). For a better understanding of the packing interactions existing among these derivatives, an overview of crystal structure analysis with emphasis on the intramolecular hydrogen bonding in some bis-indole derivatives is presented. The role of hydrogen bonding in the crystal structure assembly of bis-indole derivatives has been found to be predominant and this observation reveals significant impact of hydrogen bonding in high value of drug-likeness of these bio-molecules.

Synthesis, X-ray crystal structure, Hirshfeld surface analysis, and molecular docking studies of DMSO/H2O solvate of 5-chlorospiro[indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione

The title compound, 5-chlorospiro[indoline-3,7'-pyrano[3,2-c:5,6-c']dichromene]-2,6',8'-trione was synthesized via one-pot pseudo three-component reaction between one equivalent of 5-chloroisatin and two equivalents of 4-hydroxycoumarin using mandelic acid as catalyst in aqueous ethanol at 110 °C. The synthesized compound was characterized by FT-IR, 1H NMR, and HRMS techniques. Single crystals were grown for crystal structure determination by using single X-ray crystallography technique. It was found that the crystals are triclinic with space group P-1 and Z = 1. The crystal structure was solved by direct method and refined by full-matrix least-squares procedures to a final R-value of 0.0688 for 6738 observed reflections. The crystal structure was stabilized by elaborate system of O-H···O, N-H···O, and C-H···O interactions with the formation of supramolecular structures. 3D Hirshfeld surfaces and allied 2D fingerprint plots were analyzed for molecular interactions. Molecular docking studies have been performed to get insights into the inhibition property of this molecule for Human topoisomerase IIα.

Multivariate analysis of images in spectrophotometric methods: Quantification of soil organic matter

Soil organic matter (SOM) is usually quantified by Walkley-Black titration method or using a spectrophotometric method. This study proposes an alternative method for quantification of SOM using digital image from scanner and mathematical algorithms to replace titration and spectrophotometry procedures. For this, after SOM oxidation by potassium dichromate, digital images were acquired. Posteriorly, extraction of RGB color histograms from images have occurred, followed by the use of multivariate calibration method: partial least squares (PLS). Six soil samples were analyzed. We used the Walkley-Black method as reference. SOM was estimated by images using the PLS tool. The new method, besides being a fast, low cost, and more operational alternative, presented statistically equal results in relation to the reference method, as assessed by the Student t-test and F-test at 95 % confidence.