Investigating the potential of 6-substituted 3-formyl chromone derivatives as anti-diabetic agents using in silico methods.

In exploring nature's potential in addressing diabetes-related conditions, this study investigates the therapeutic capabilities of 3-formyl chromone derivatives. Utilizing in silico methodologies, we focus on 6-substituted 3-formyl chromone derivatives (1-16) to assess their therapeutic potential in treating diabetes. The research examined the formyl group at the chromone's C-3 position. ADMET, biological activities, were conducted along with B3LYP calculations using 3 different basis sets. The analogues were analyzed based on their parent structure obtained from PubChem. The HOMO-LUMO gap confirmed the bioactive nature of the derivatives, NBO analysis was performed to understand the charge transfer. PASS prediction revealed that 3-formyl chromone derivatives are potent aldehyde oxidase inhibitors, insulin inhibitors, HIF1A expression inhibitors, and histidine kinase. Molecular docking studies indicated that the compounds had a strong binding affinity with proteins, including CAD, BHK, IDE, HIF-α, p53, COX, and Mpro of SARS-CoV2. 6-isopropyl-3-formyl chromone (4) displayed the highest affinity for IDE, with a binding energy of - 8.5 kcal mol-1. This result outperformed the affinity of the reference standard dapagliflozin (- 7.9 kcal mol-1) as well as two other compounds that target human IDE, namely vitexin (- 8.3 kcal mol-1) and myricetin (- 8.4 kcal mol-1). MD simulations were revealed RMSD value between 0.2 and 0.5 nm, indicating the strength of the protein-ligand complex at the active site.

Oxidative and Extractive Desulfurization of Fuel Oils Catalyzed by N-Carboxymethyl Pyridinium Acetate and N-Carboxyethyl Pyridinium Acetate Acidic Ionic Liquids: Experimental and Computational DFT Study.

This study reports on the synthesis, characterization, and application of two acidic ionic liquids, namely, N-carboxymethylpyridinium acetate ([HO2CCH2Py][CH3CO2] or AIL1) and N-carboxyethylpyridinium acetate ([HO2C(CH2)2Py][CH3CO2] or AIL2), as both extractants and catalysts for the oxidative and extractive desulfurization (OEDS) of model fuel oils containing heteroaromatic sulfur compounds. The structural properties of the synthesized acidic ionic liquids (ILs) were confirmed by 1H NMR, 13C NMR, and FT-IR spectroscopic analysis. To optimize the performance of the acidic AILs in the desulfurization process, the effects of different parameters, such as H2O2 dosage, reaction time, and temperatures, were investigated. The experimental results showed that AIL1 has exceptionally high desulfurization-extraction rates, with values of 99.8%, 97.8%, and 95.4%, for DBT, BT, and 4,6-DMDBT, respectively, under the optimum conditions established. Under the same conditions, the desulfurization-extraction rates using AIL2 reached 91.6%, 87.3%, and 82.4%, respectively, for DBT, 4, 6-DMDBT, and BT. Both ionic liquids can be recycled up to 9 times without a significant decrease in their sulfur removal efficiencies. Furthermore, density functional theory (DFT) calculations were conducted to evaluate the electronic interaction energies (ΔIE) between the AILs with each of the sulfur-containing compounds and their putative oxidized products. The computational findings strongly supported the experimental outcomes.

Development of a microcantilever-based biosensor for detecting Programmed Death Ligand 1.

The ongoing global concern of cancer worldwide necessitates the development of advanced diagnostic and therapeutic strategies. The majority of recent detection strategies involve the employment of biomarkers. A critical biomarker for cancer immunotherapy efficacy and patient prognosis is Programmed Death Ligand 1 (PD-L1), which is a key immune checkpoint protein. PD-L1 can be particularly linked to cancer progression and therapy response. Current detection methods, such as enzyme-linked immunosorbent assay (ELISA), face limitations like high cost, time consumption, and complexity. This study introduces a microcantilever-based biosensor designed for the detection of soluble PD-L1 (sPD-L1), which has a specific association with PD-L1. The biosensor utilizes anti-PD-L1 as the sensing layer, capitalizing on the specific binding affinity between anti-PD-L1 and sPD-L1. The presence of the sensing layer was confirmed through Atomic Force Microscopy (AFM) and contact angle measurements. Binding between sPD-L1 and anti-PD-L1 induces a shift in the microcantilever's resonance frequency, which is proportional to the PD-L1 concentration. Notably, the resonance frequency shift demonstrates a robust linear relationship with the increasing biomarker concentration, ranging from 0.05 ng/ml to 500 ng/ml. The detection limit of the biosensor was determined to be approximately 10 pg/ml. The biosensor demonstrates excellent performance in detecting PD-L1 with high specificity even in complex biological matrices. This innovative approach not only provides a promising tool for early cancer diagnosis but also holds potential for monitoring immunotherapy efficacy, paving the way for personalized and effective cancer treatments.

Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration.

In this study, we synthesized novel α,ß-unsaturated 2-cyanoacetamide derivatives (1-5) using microwave-assisted Knoevenagel condensation. Characterization of these compounds was carried out using FTIR and 1H NMR spectroscopy. We then evaluated their in vitro antibacterial activity against both gram-positive and gram-negative pathogenic bacteria. Additionally, we employed in silico methods, including ADMET prediction and density functional theory (DFT) calculations of molecular orbital properties, to investigate these cyanoacetamide derivatives (1-5). Molecular docking was used to assess the binding interactions of these derivatives (1-5) with seven target proteins (5MM8, 4NZZ, 7FEQ, 5NIJ, ITM2, 6SE1, and 5GVZ) and compared them to the reference standard tyrphostin AG99. Notably, derivative 5 exhibited the most favorable binding affinity, with a binding energy of -7.7 kcal mol-1 when interacting with the staphylococcus aureus (PDB:5MM8), while also meeting all drug-likeness criteria. Additionally, molecular dynamics simulations were carried out to evaluate the stability of the interaction between the protein and ligand, utilizing parameters such as Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (Rg), and Principal Component Analysis (PCA). A 50 nanosecond molecular dynamics (MD) simulation was performed to investigate stability further, incorporating RMSD and RMSF analyses on compound 5 within the active binding site of the modeled protein across different temperatures (300, 305, 310, and 320 K). Among these temperatures, compound 5 exhibited an RMSD value ranging from approximately 0.2 to 0.3 nm at 310 K (body temperature) with the 5MM8 target, which differed from the other temperature conditions. The in silico results suggest that compound 5 maintained significant conformational stability throughout the 50 ns simulation period. It is consistent with its low docking energy and in vitro findings concerning α,ß-unsaturated cyanoacetamides. Key insights from this study include:•The creation of innovative α,ß-unsaturated 2-cyanoacetamide derivatives (1-5) employing cost-effective, licensed, versatile, and efficient software for both in silico and in vitro assessment of antibacterial activity.•Utilization of FTIR and NMR techniques for characterizing compounds 1-5.

Exploring the anticancer and antibacterial potential of naphthoquinone derivatives: a comprehensive computational investigation.

This study investigates the potential of 2-(4-butylbenzyl)-3-hydroxynaphthalene-1,4-dione (11) and its 12 derivatives as anticancer and biofilm formation inhibitors for methicillin-resistant staphylococcus aureus using in silico methods. The study employed various computational methods, including molecular dynamics simulation molecular docking, density functional theory, and global chemical descriptors, to evaluate the interactions between the compounds and the target proteins. The docking results revealed that compounds 9, 11, 13, and ofloxacin exhibited binding affinities of -7.6, -7.9, -7.5, and -7.8 kcal mol-1, respectively, against peptide methionine sulfoxide reductase msrA/msrB (PDB: 3E0M). Ligand (11) showed better inhibition for methicillin-resistant staphylococcus aureus msrA/msrB enzyme. The complex of the 3E0M-ligand 11 remained highly stable across all tested temperatures (300, 305, 310, and 320 K). Principal Component Analysis (PCA) was employed to evaluate the behavior of the complex at various temperatures (300, 305, 310, and 320 K), demonstrating a total variance of 85%. Convergence was confirmed by the eigenvector's cosine content value of 0.43, consistently displaying low RMSD values, with the minimum observed at 310 K. Furthermore, ligand 11 emerges as the most promising candidate among the compounds examined, showcasing notable potential when considering a combination of in vitro, in vivo, and now in silico data. While the naphthoquinone derivative (11) remains the primary candidate based on comprehensive in silico studies, further analysis using Frontier molecular orbital (FMO) suggests while the Egap value of compound 11 (2.980 eV) and compound 13 (2.975 eV) is lower than ofloxacin (4.369 eV), indicating their potential, so it can be a statement that compound 13 can also be investigated in further research.

The Effect of Femtosecond Laser Surface Patterns on the Effectiveness of Resin Composite to Zirconia Bonding.

This laboratory study aimed to evaluate the effect of different surface patterns using femtosecond laser treatment on the enclosed mold shear bond strength (EM-SBS) of resin composite to zirconia (ZrO2) surfaces and to contrast it with the widely used tribochemical silica coating (TBC) surface conditioning method. A set of fifteen rectangular ZrO2 blocks were randomly divided into five groups according to surface pretreatment: Control G0-no treatment; G1-TBC with silane application; G2-femtosecond laser irradiation with horizontal lines 30 µm apart; G3-femtosecond laser irradiation with horizontal lines 15 µm apart; and G4-femtosecond laser irradiation with cross lines 30 µm apart. The pretreated surfaces were characterized by a surface profilometer, tensiometer and scanning electron microscope. The EM-SBS of resin composite stubs to ZrO2 was measured followed by fractographic analysis. The surface roughness and water contact angle were observed to be statistically higher among the femtosecond laser groups compared to the TBC and control groups. The G4 group exhibited the highest EM-SBS among all the groups, irrespective of the ageing conditions used. At the end of 5000 thermocycles, G4 exhibited EM-SBS of 14.05 ± 4.21 MPa compared to 13.80 ± 3.01 MPa in G1 and 5.47 ± 0.97 MPa in G0. The two-way ANOVA revealed a significant effect of both study groups and ageing conditions on the EM-SBS (p < 0.001). Utilization of femtosecond laser technology holds promise as a potential and alternative mechanical retention approach for enhancing the bonding strength of the resin composite to ZrO2.

Detection of Aromatic Hydrocarbons in Aqueous Solutions Using Quartz Tuning Fork Sensors Modified with Calix[4]arene Methoxy Ester Self-Assembled Monolayers: Experimental and Density Functional Theory Study.

Quartz tuning forks (QTFs), which were coated with gold and with self-assembled monolayers (SAM) of a lower-rim functionalized calix[4]arene methoxy ester (CME), were used for the detection of benzene, toluene, and ethylbenzene in water samples. The QTF device was tested by measuring the respective frequency shifts obtained using small (100 µL) samples of aqueous benzene, toluene, and ethylbenzene at four different concentrations (10-12, 10-10, 10-8, and 10-6 M). The QTFs had lower limits of detection for all three aromatic hydrocarbons in the 10-14 M range, with the highest resonance frequency shifts (±5%) being shown for the corresponding 10-6 M solutions in the following order: benzene (199 Hz) > toluene (191 Hz) > ethylbenzene (149 Hz). The frequency shifts measured with the QTFs relative to that in deionized water were inversely proportional to the concentration/mass of the analytes. Insights into the effects of the alkyl groups of the aromatic hydrocarbons on the electronic interaction energies for their hypothetical 1:1 supramolecular host-guest binding with the CME sensing layer were obtained through density functional theory (DFT) calculations of the electronic interaction energies (ΔIEs) using B3LYP-D3/GenECP with a mixed basis set: LANL2DZ and 6-311++g(d,p), CAM-B3LYP/LANL2DZ, and PBE/LANL2DZ. The magnitudes of the ΔIEs were in the following order: [Au4-CME⊃[benzene] > [Au4-CME]⊃[toluene] > [Au4-CME]⊃[ethylbenzene]. The gas-phase BSSE-uncorrected ΔIE values for these complexes were higher, with values of -96.86, -87.80, and -79.33 kJ mol-1, respectively, and -86.39, -77.23, and -67.63 kJ mol-1, respectively, for the corresponding BSSE-corrected values using B3LYP-D3/GenECP with LANL2dZ and 6-311++g(d,p). The computational findings strongly support the experimental results, revealing the same trend in the ΔIEs for the proposed hypothetical binding modes between the tested analytes with the CME SAMs on the Au-QTF sensing surfaces.

Microelectromechanical system-based biosensor for label-free detection of human cytomegalovirus.

The human cytomegalovirus (HCMV) is an asymptomatic common virus that is typically harmless, but in some cases, it can be life threatening. Thus, there is an urgent need to develop novel diagnostic methods and strengthen the efforts to combat this virus. A microcantilever-based biosensor functionalised with the UL83-antibody of HCMV (UL83-HCMV antibody) has been developed to detect the UL83-antigen of HCMV (UL83-HCMV antigen) at different concentrations ranging from 0.3 to 300 ng/ml. The response of the biosensor to the presence of UL83-HCMV antigen was measured through the shift in resonance frequency before and after antigen-antibody binding. The system shows a low detection limit of 84 pg/ml, which is comparable to traditional sensors, and a detection time of less than 15 min was achieved. The selectivity of the sensor was demonstrated using three different proteins with and without the UL83-HCMV antigen. The biosensor shows high selectivity for the UL83-HCMV antigen. Mass loading by the UL83-HCMV antigen was roughly estimated with a sensitivity of ∼30 fg/Hz. This technique is crucial for the fabrication of portable and low-cost biosensors that can be used in real-time monitoring and enables early medical diagnosis.