Computer-aided anticancer drug design: In vitro and in silico studies of new iminocoumarin derivative

Production of Prophylactic Nanoformulation for Dental Caries and Investigation of Its Effectiveness by In Vitro and In Silico Methods

Background/Objectives: This study aimed to develop cinnamon bark essential oil (CEO), orange peel essential oil(OEO) and the combination of these two essential oils (OEO-CEO) loaded PLGA nanoparticles to prevent dental caries and to investigate their effectiveness in silico and in vitro methods. Methods: EO loaded PLGA nanoparticles were produced by single emulsion method. Detailed characterization studies were performed using different methods, and the controlled release profile was obtained. The antibacterial activity of the developed formulations was investigated on S. mutans and L. casei strains by in vitro and in silico methods. Additionally, the interaction mechanisms of EOs with DNA were evaluated. Results: Our findings showed that the average droplet size of EO-loaded PLGA nanoparticles varied between 243.1 ± 0.60 nm and 219 ± 4.49 nm, while PdI values varied between 0.069 ± 0.039 and 0.032 ± 0.01. In addition, the developed nanoparticles had high encapsulation efficiency (85.14% to 66.28%) and released the active ingredient in a continuous and controlled manner. Ames test showed that the genotoxicity of EOs was eliminated due to the encapsulation of EOs in PLGA nanoparticles and antibacterial tests showed that OEO-CEO-loaded PLGA nanoparticles were effective on L. casei and S. mutans. The antibacterial activity of EOs was also supported by in silico studies. Finally, it was revealed that EOs showed potential as antibacterial agents by interacting with DNA. Conclusions: The results showed that OEO-CEO-loaded PLGA nanoparticles have the potential to be a suitable nanoformulation for developing mouthwash or toothpaste for the prevention and treatment of dental caries.

Prominent Neuroprotective Potential of Indole-2-N-methylpropargylamine: High Affinity and Irreversible Inhibition Efficiency towards Monoamine Oxidase B Revealed by Computational Scaffold Analysis

Background: Monoamine oxidases (MAO) are flavoenzymes that metabolize a range of brain neurotransmitters, whose dysregulation is closely associated with the development of various neurological disorders. This is why MAOs have been the central target in pharmacological interventions for neurodegeneration for more than 60 years. Still, existing drugs only address symptoms and not the cause of the disease, which underlines the need to develop more efficient inhibitors without adverse effects. Methods: Our drug design strategy relied on docking 25 organic scaffolds to MAO-B, which were extracted from the ChEMBL20 database with the highest cumulative counts of unique member compounds and bioactivity assays. The most promising candidates were substituted with the inactivating propargylamine group, while further affinity adjustment was made by its N-methylation. A total of 46 propargylamines were submitted to the docking and molecular dynamics simulations, while the best binders underwent mechanistic DFT analysis that confirmed the hydride abstraction mechanism of the covalent inhibition reaction. Results: We identified indole-2-propargylamine 4fH and indole-2-N-methylpropargylamine 4fMe as superior MAO-B binders over the clinical drugs rasagiline and selegiline. DFT calculations highlighted 4fMe as more potent over selegiline, evident in a reduced kinetic requirement (ΔΔG‡ = -2.5 kcal mol-1) and an improved reaction exergonicity (ΔΔGR = -4.3 kcal mol-1), together with its higher binding affinity, consistently determined by docking (ΔΔGBIND = -0.1 kcal mol-1) and MM-PBSA analysis (ΔΔGBIND = -1.5 kcal mol-1). Conclusions: Our findings strongly advocate 4fMe as an excellent drug candidate, whose synthesis and biological evaluation are highly recommended. Also, our results reveal the structural determinants that influenced the affinity and inhibition rates that should cooperate when designing further MAO inhibitors, which are of utmost significance and urgency with the increasing prevalence of brain diseases.

Robust Identification of Differential Gene Expression Patterns from Multiple Transcriptomics Datasets for Early Diagnosis, Prognosis, and Therapies for Breast Cancer

Background and Objectives: Breast cancer (BC) is one of the major causes of cancer-related death in women globally. Proper identification of BC-causing hub genes (HubGs) for prognosis, diagnosis, and therapies at an earlier stage may reduce such death rates. However, most of the previous studies detected HubGs through non-robust statistical approaches that are sensitive to outlying observations. Therefore, the main objectives of this study were to explore BC-causing potential HubGs from robustness viewpoints, highlighting their early prognostic, diagnostic, and therapeutic performance. Materials and Methods: Integrated robust statistics and bioinformatics methods and databases were used to obtain the required results. Results: We robustly identified 46 common differentially expressed genes (cDEGs) between BC and control samples from three microarrays (GSE26910, GSE42568, and GSE65194) and one scRNA-seq (GSE235168) dataset. Then, we identified eight cDEGs (COL11A1, COL10A1, CD36, ACACB, CD24, PLK1, UBE2C, and PDK4) as the BC-causing HubGs by the protein-protein interaction (PPI) network analysis of cDEGs. The performance of BC and survival probability prediction models with the expressions of HubGs from two independent datasets (GSE45827 and GSE54002) and the TCGA (The Cancer Genome Atlas) database showed that our proposed HubGs might be considered as diagnostic and prognostic biomarkers, where two genes, COL11A1 and CD24, exhibit better performance. The expression analysis of HubGs by Box plots with the TCGA database in different stages of BC progression indicated their early diagnosis and prognosis ability. The HubGs set enrichment analysis with GO (Gene ontology) terms and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways disclosed some BC-causing biological processes, molecular functions, and pathways. Finally, we suggested the top-ranked six drug molecules (Suramin, Rifaximin, Telmisartan, Tukysa Tucatinib, Lynparza Olaparib, and TG.02) for the treatment of BC by molecular docking analysis with the proposed HubGs-mediated receptors. Molecular docking analysis results also showed that these drug molecules may inhibit cancer-related post-translational modification (PTM) sites (Succinylation, phosphorylation, and ubiquitination) of hub proteins. Conclusions: This study's findings might be valuable resources for diagnosis, prognosis, and therapies at an earlier stage of BC.

Exploring anticancer properties of novel Nano-Formulation of BODIPY Compound, Photophysicochemical, in vitro and in silico evaluations

A new BODIPY complex (C4) composed of meso- thienyl-pyridine substituted core unit diiodinated from 2- and 6- positions and distyryl moieties at 3- and 5- positions is synthesized. Nano-sized formulation of C4 is prepared by single emulsion method using poly(ε-caprolactone)(PCL) polymer. Encapsulation efficiency and loading capacity values of C4 loaded PCL nanoparticles (C4@PCL-NPs) are calculated and in vitro release profile of C4 is determined. The cytotoxicity and anti-cancer activity are conducted on the L929 and MCF-7 cell lines. Cellular uptake study is performed and interaction between C4@PCL-NPs and MCF-7 cell line is investigated. Anti-cancer activity of C4 is predicted with molecular docking studies and the inhibition property on EGFR, ERα, PR and mTOR are investigated for its anticancer properties. Molecular interactions, binding positions and docking score energies between C4 and EGFR, ERα, PR and mTOR targets are revealed using in silico methods. The druglikeness and pharmacokinetic properties of C4 are evaluated using the SwissADME and its bioavailability and toxicity profiles are assessed using the SwissADME, preADMET and pkCSM servers. In conclusion, the potential use of C4 as an anti-cancer agent is evaluated in vitro and in silico methods. Also, photophysicochemical properties are studied to investigate the potential of using Photodynamic Therapy (PDT). In photochemical studies, the calculated singlet oxygen quantum yield (Φ_Δ) value was 0.73 for C4 and in photopysical studies, the calculated fluorescence quantum yield Φ_F value was 0.19 for C4.

Diverse and efficient catalytic applications of new cockscomb flower-like Fe3O4@SiO2@KCC-1@MPTMS@CuII mesoporous nanocomposite in the environmentally benign reduction and reductive acetylation of nitroarenes and one-pot synthesis of some coumarin compounds

In this research, Fe3O4@SiO2@KCC-1@MPTMS@CuII as a new cockscomb flower-like mesoporous nanocomposite was prepared and characterized by various techniques including Fourier transform infrared (FT-IR) spectroscopy, powder X-ray diffraction (PXRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), SEM-based energy-dispersive X-ray (EDX) spectroscopy, inductively coupled plasma-optical emission spectrometry (ICP-OES), thermogravimetric analysis/differential thermal analysis (TGA/DTA), vibrating sample magnetometry (VSM), UV-Vis spectroscopy, and Brunauer-Emmett-Teller (BET) and Barrett-Joyner-Halenda (BJH) analyses. The as-prepared Fe3O4@SiO2@KCC-1@MPTMS@CuII mesoporous nanocomposite exhibited satisfactory catalytic activity in the reduction and reductive acetylation of nitroarenes in a water medium and solvent-free one-pot synthesis of some coumarin compounds including 3,3'-(arylmethylene)bis(4-hydroxy-2H-chromen-2-ones) (namely, bis-coumarins) (3a-n) and 2-amino-4-aryl-7,7-dimethyl-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitriles (6a-n) along with acceptable turnover numbers (TONs) and turnover frequencies (TOFs). Furthermore, the mentioned CuII-containing mesoporous nanocatalyst was conveniently recovered by a magnet from reaction environments and reused for at least seven cycles without any significant loss in activity, which confirms its good stability.

Laurus nobilis L. Essential Oil-Loaded PLGA as a Nanoformulation Candidate for Cancer Treatment

The aim of this study was to obtain essential oil (LNEO) from the Laurus nobilis L. plant, and to prepare LNEO-loaded poly lactic-co-glycolic acid (PLGA) nanoparticles (NPs) as an approach in cancer treatment. The components of the obtained LNEO were analyzed using GC-MS. The LNEO-NPs were synthesized by the single-emulsion method. The LNEO-NPs were characterized using UV-Vis spectrometry, Dynamic Light Scattering (DLS), Scanning Electron Microscopy (SEM), and a DNA binding assay, which was performed via the UV-Vis titration method. According to the results, the LNEO-NPs had a 211.4 ± 4.031 nm average particle size, 0.068 ± 0.016 PdI, and -7.87 ± 1.15 mV zeta potential. The encapsulation efficiency and loading capacity were calculated as 59.25% and 25.65%, respectively, and the in vitro drug release study showed an LNEO release of 93.97 ± 3.78% over the 72 h period. Moreover, the LNEO was intercalatively bound to CT-DNA. In addition, the mechanism of action of LNEO on a dual PI3K/mTOR inhibitor was predicted, and its antiproliferative activity and mechanism were determined using molecular docking analysis. It was concluded that LNEO-loaded PLGA NPs may be used for cancer treatment as a novel phytotherapeutic agent-based controlled-release system.