Development and validation of a stability-indicating RP-LC method for the simultaneous determination of otilonium bromide and its expected degradation product in bulk drug and pharmaceutical preparation

A simple, precise, accurate and rapid stability indicating liquid chromatography method had been developed for the simultaneous determination of otilonium bromide (OB) and its expected degradation product; p-aminobenzoic acid (PABA) in bulk powder and pharmaceutical preparation. Chromatographic separation was carried out by isocratic elution on Waters Atlantis C18 column (4.6 × 150 mm, 5 µm) using 2 mM ammonium acetate buffer (pH = 2.35) containing 0.05% TFA: acetonitrile (30:70, v:v) as the mobile phase. The flow rate was 0.8 mL/min with UV detection at 290 nm. Linearity was obtained over a concentration range of 0.5-100 μg/mL with regression coefficient of 1 for OB, and over concentration range of 1-50 μg/mL with regression coefficient of 0.9998 for PABA. The values of LOD and LOQ were found to be 0.0665 and 0.2018 μg/mL for OB and 0.1974 and 0.598 μg/mL for PABA, respectively. The method was validated as per ICH guidelines. The method was successfully applied to the determination of the drug in bulk powder and pharmaceutical preparation

Rational design and synthesis of novel quinazolinone N-acetohydrazides as type II multi-kinase inhibitors and potential anticancer agents

In the current investigation, a new class of quinazolinone N-acetohydrazides 9a-v was designed as type II multi-kinase inhibitors. The target quinazolinones were tailored so that the quinazolinone moiety would occupy the front pocket of the binding sites of VEGFR-2, FGFR-1 and BRAF kinases, meanwhile, the phenyl group at position 2 would act as a spacer which was functionalized at position 4 with an N-acetohydrazide linker that could achieve the key interactions with the essential gate area amino acids. The hydrazide moiety was linked to diverse aryl derivatives to occupy the hydrophobic back pocket of the DFG-out conformation of target kinases. The synthesized quinazolinone derivatives 9a-v demonstrated moderate to potent VEGFR-2 inhibitory activity with IC50 spanning from 0.29 to 5.17 µM. Further evaluation of the most potent derivatives on FGFR-1, BRAFwt and BRAFV600E showed that the quinazolinone N-acetohydrazides 9d, 9e, 9f, 9 L and 9 m have a potent multi-kinase inhibitory activity. Concurrently, 9b, 9d, 9e, 9 k, 9 L, 9o, 9q demonstrated potent mean growth inhibitory activity on NCI cancer cell lines with GI50 reaching 0.72 µM. In addition, compound 9e arrested the cell cycle progression in MDA-MB-231 cell line at the G2/M phase and showed the ability to induce apoptosis

Identification of the Beer Component Hordenine as Food-Derived Dopamine D2 Receptor Agonist by Virtual Screening a 3D Compound Database

The dopamine D2 receptor (D2R) is involved in food reward and compulsive food intake. The present study developed a virtual screening (VS) method to identify food components, which may modulate D2R signalling. In contrast to their common applications in drug discovery, VS methods are rarely applied for the discovery of bioactive food compounds. Here, databases were created that exclusively contain substances occurring in food and natural sources (about 13,000 different compounds in total) as the basis for combined pharmacophore searching, hit-list clustering and molecular docking into D2R homology models. From 17 compounds finally tested in radioligand assays to determine their binding affinities, seven were classified as hits (hit rate = 41%). Functional properties of the five most active compounds were further examined in β-arrestin recruitment and cAMP inhibition experiments. D2R-promoted G-protein activation was observed for hordenine, a constituent of barley and beer, with approximately identical ligand efficacy as dopamine (76%) and a Ki value of 13 μM. Moreover, hordenine antagonised D2-mediated β-arrestin recruitment indicating functional selectivity. Application of our databases provides new perspectives for the discovery of bioactive food constituents using VS methods. Based on its presence in beer, we suggest that hordenine significantly contributes to mood-elevating effects of beer

Predicting the Sites and Energies of Noncovalent Intermolecular Interactions Using Local Properties

Feed-forward artificial neural nets have been used to recognize H-bond donor and acceptor sites on drug-like molecules based on local properties (electron density, molecular electrostatic potential and local ionization energy, electron affinity, and polarizability) calculated at grid points around the molecule. Interaction energies for training were obtained from B97-D and ωB97X-D/aug-cc-pVDZ density-functional theory calculations on a series of model central molecules and H-bond acceptor and donor probes constrained to the grid points used for training. The resulting models provide maps of both classical and unusual H- and halogen-bonding sites. Note that these reactions result even though only classical H-bond donors and acceptors were used as probes around the central molecules. Some examples demonstrate the ability of the models to take the electronics of the central molecule into consideration and to provide semiquantitative estimates of interaction energies at low computational cost

Economical and Accurate Protocol for Calculating Hydrogen-Bond-Acceptor Strengths

A series of density functional/basis set combinations and second-order Møller–Plesset calculations have been used to test their ability to reproduce the trends observed experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques

Quantum Mechanics-Based Properties for 3D-QSAR

We have used a set of four local properties based on semiempirical molecular orbital calculations (electron density (ρ), hydrogen bond donor field (HDF), hydrogen bond acceptor field (HAF), and molecular lipophilicity potential (MLP)) for 3D-QSAR studies to overcome the limitations of the current force field-based molecular interaction fields (MIFs). These properties can be calculated rapidly and are thus amenable to high-throughput industrial applications. Their statistical performance was compared with that of conventional 3D-QSAR approaches using nine data sets (angiotensin converting enzyme inhibitors (ACE), acetylcholinesterase inhibitors (AchE), benzodiazepine receptor ligands (BZR), cyclooxygenase-2 inhibitors (COX2), dihydrofolate reductase inhibitors (DHFR), glycogen phosphorylase b inhibitors (GPB), thermolysin inhibitors (THER), thrombin inhibitors (THR), and serine protease factor Xa inhibitors (fXa)). The 3D-QSAR models generated were tested thoroughly for robustness and predictive ability. The average performance of the quantum mechanical molecular interaction field (QM-MIF) models for the nine data sets is better than that of the conventional force field-based MIFs. In the individual data sets, the QM-MIF models always perform better than, or as well as, the conventional approaches. It is particularly encouraging that the relative performance of the QM-MIF models improves in the external validation. In addition, the models generated showed statistical stability with respect to model building procedure variations such as grid spacing size and grid orientation. QM-MIF contour maps reproduce the features important for ligand binding for the example data set (factor Xa inhibitors), demonstrating the intuitive chemical interpretability of QM-MIFs

Identification of 3-(piperazinylmethyl)benzofuran derivatives as novel type II CDK2 inhibitors: design, synthesis, biological evaluation, and in silico insights.

In the current work, a hybridisation strategy was adopted between the privileged building blocks, benzofuran and piperazine, with the aim of designing novel CDK2 type II inhibitors. The hybrid structures were linked to different aromatic semicarbazide, thiosemicarbazide, or acylhydrazone tails to anchor the designed inhibitors onto the CDK2 kinase domain. The designed compounds showed promising CDK2 inhibitory activity. Compounds 9h, 11d, 11e and 13c showed potent inhibitory activity (IC50 of 40.91, 41.70, 46.88, and 52.63 nM, respectively) compared to staurosporine (IC50 of 56.76 nM). Moreover, benzofurans 9e, 9h, 11d, and 13b showed promising antiproliferative activities towards different cancer cell lines, and non-significant cytotoxicity on normal lung fibroblasts MRC-5 cell line. Furthermore, a cell cycle analysis as well as Annexin V-FITC apoptosis assay on Panc-1 cell line were performed. Molecular docking simulations were performed to explore the ability of target benzofurans to adopt the common binding pattern of CDK2 type II inhibitors

Directional Noncovalent Interactions: Repulsion and Dispersion

The interaction energies between an argon atom and the dihalogens Br₂, BrCl, and BrF have been investigated using frozen core CCSD­(T)­(fc)/aug-cc-pVQZ calculations as reference values for other levels of theory. The potential-energy hypersurfaces show two types of minima: (1) collinear with the dihalogen bond and (2) in a bridging position. The former represent the most stable minima for these systems, and their binding energies decrease in the order Br > Cl > F. Isotropic atom–atom potentials cannot reproduce this binding pattern. Of the other levels of theory, CCSD­(T)­(fc)/aug-cc-pVTZ reproduces the reference data very well, as does MP2­(fc)/aug-cc-pVDZ, which performs better than MP2 with the larger basis sets (aug-cc-pVQZ and aug-cc-pvTZ). B3LYP-D3 and M06-2X reproduce the binding patterns moderately well despite the former using an isotropic dispersion potential correction. B3LYP-D3­(bj) performs even better. The success of the B3LYP-D3 methods is because polar flattening of the halogens allows the argon atom to approach more closely in the direction collinear with the bond, so that the sum of dispersion potential and repulsion is still negative at shorter distances than normally possible and the minimum is deeper at the van der Waals distance. Core polarization functions in the basis set and including the core orbitals in the CCSD­(T)­(full) calculations lead to a uniform decrease of approximately 20% in the magnitudes of the calculated interaction energies. The EXXRPA+@EXX (exact exchange random phase approximation) orbital-dependent density functional also gives interaction energies that correlate well with the highest level of theory but are approximately 10% low. The newly developed EXXRPA+@dRPA functional represents a systematic improvement on EXXRPA+@EXX

Additional file 1 of Discovery of dual kinase inhibitors targeting VEGFR2 and FAK: structure-based pharmacophore modeling, virtual screening, and molecular docking studies

Additional file 1: S1. Training set compounds for VEGFR2 and FAK pharmacophore model generation. S2. Test set compilation. Table S1. VEGFR2 test set active compounds. Table S2. FAK manually collected test set compounds. S3. Pharmacophore model selection and validation. Table S3. Assessment metrics of pharmacophore models performance. Table S4. VEGFR2 pharmacophore model assessment. S4. Molecular docking simulation. S4.1. Self-docking molecular docking validation. S4.1.1. Self-docking validation for VEGFR2. S4.1.2. Self-docking validation for FAK. S4.2. Docking energy score (S) in kcal/mol for the common 13 compounds in VEGFR2 and FAK binding sites