Multiple QSAR and molecular modelling for identification of potent human adenovirus inhibitors

Evaluation of diethyl 4-(5-bromo-1H-indol-3-yl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate: synthesis, anti-corrosion potential, and biomedical applications

The pursuit of advanced multifunctional compounds has gained significant momentum in recent scientific endeavours. This study is dedicated to elucidating the synthesis, rigorous characterization, and multifaceted applications-encompassing anti-corrosion, antimicrobial, and antioxidant properties-of Diethyl 4-(5-bromo-1H-indol-3-yl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate. The 1,4-dihydropyridine derivative was meticulously synthesized through a strategic reaction of ethyl acetoacetate, ammonium acetate, and 5-bromoindole-3-carboxaldehydein the ethanol medium at 60  C. Subsequent spectral validations were conducted using sophisticated techniques, namely FTIR, NMR, and Mass spectrometry, resulting in data that perfectly resonated with the hypothesized chemical structure of the compound. Its anti-corrosive potential was assessed on mild steel subjected to an aggressive acidic environment, employing comprehensive methodologies like gravimetric analysis, Tafel polarization, and EIS. Concurrently, its antimicrobial prowess was ascertained against a spectrum of bacterial and fungal pathogens viz., Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas, Candida albicansandAspergillusniger, leveraging the disc diffusion method and using Gentamicin as a reference standard.The empirical results illustrated a substantial decrement in corrosion rates with ascending concentrations of the organic compound, achieving an apex of anti-corrosive efficacy at 81.89% for a concentration of 2 × 103 M. Furthermore, the compound outperformed Gentamicin in antimicrobial screenings, manifesting superior efficacy against all tested pathogens. The antioxidant potential, quantified using the DPPH free radical scavenging assay against ascorbic acid as a benchmark, was found to have an IC50 value of 113.964 ± 0.076 µg/ml.This comprehensive investigation accentuates the paramount potential of the synthesized dihydropyridine derivative in diverse domains-from industrial applications as a corrosion inhibitor to therapeutic avenues given its pronounced antimicrobial and antioxidant capabilities. The compelling results obtained pave the way for expansive research and development initiatives cantered around this multifaceted compound.

Synthesis of the chromone-thiosemicarbazone scaffold as promising α-glucosidase inhibitors: An in vitro and in silico approach toward antidiabetic drug design

Diabetes is a serious metabolic disorder affecting individuals of all age groups and prevails globally due to the failure of previous treatments. This study aims to address the most prevalent form of type 2 diabetes mellitus (T2DM) by reporting on the design, synthesis, and in vitro as well as in silico evaluation of chromone-based thiosemicarbazones as potential α-glucosidase inhibitors. In vitro experiments showed that the tested compounds were significantly more potent than the standard acarbose, with the lead compound 3n exhibiting an IC50 value of 0.40 ± 0.02 μM, ~2183-fold higher than acarbose having an IC50 of 873.34 ± 1.67 μM. A kinetic mechanism analysis demonstrated that compound 3n exhibited reversible inhibition of α-glucosidase. To gain deeper insights, in silico molecular docking, pharmacokinetics, and molecular dynamics simulations were conducted for the investigation of the interactions, orientation, stability, and conformation of the synthesized compounds within the active pocket of α-glucosidase.

Carbonylbis(hydrazine-1-carbothioamide) derivatives as a new class of α-glucosidase inhibitors and their mechanistic insights via molecular docking and dynamic simulations

In the past, efforts have been made to find a cure for diabetes, mainly evaluating new classes of compounds to explore their potency. In this study, we present the synthesis and evaluation of carbonylbis(hydrazine-1-carbothioamide) derivatives as potential α-glucosidase inhibitors, employing both in vivo and in silico investigations. The in vitro experiments revealed that all tested compounds were significantly potent for α-glucosidase inhibition, with the lead compound 3a displaying approximately 80 times higher activity than acarbose. To delve deeper, in silico induced fit docking, pharmacokinetics, and molecular dynamics studies were conducted. Significantly, compound 3a exhibited a docking score of -7.87 kcal/mol, surpassing acarbose, which had a docking score of -6.59 kcal/mol. The in silico ADMET indicated that most of the synthesized compounds have properties conducive to drug development. Molecular dynamics analysis demonstrated that, when the ligand 3a was coupled with the target 3TOP, Cα-RMSD backbone RMSD values below 2.4 Å and "Lig_fit_Prot" values below 2.7 Å were observed. QSAR analysis demonstrates that the "fOC8A" descriptor positively correlates with α-glucosidase inhibition activity, while "lipoplus_AbSA" positively contributes and "notringC_notringO_8B" negatively contributes to this activity.

A Novel Nucleic Acid Sensing-related Genes Signature for Predicting Immunotherapy Efficacy and Prognosis of Lung Adenocarcinoma

BACKGROUND

As a novel pillar for lung adenocarcinoma (LUAD) treatment, immunotherapy has limited efficiency in LUAD patients. The nucleic acid sensing (NAS) pathways are critical in the anti-tumor immune response, but their role in LUAD remains controversial.

OBJECTIVE

The study aims to develop a classification system to identify immune subtypes of LUAD based on nucleic acid sensing-related genes so that it can help screen patients who may respond to immunotherapy.

METHODS

We performed a comprehensive bioinformatics analysis of the NAS molecule expression profiles across multiple public datasets. Using qRT-PCR to verify the NAS genes in multiple lung cancer cell lines. Molecular docking was performed to screen drug candidates.

RESULTS

The NAS-activated subgroup and NAS-suppressed subgroup were validated based on the different patterns of gene expression and pathways enrichment. The NAS-activated subgroup displayed a stronger immune infiltration and better prognosis of patients. Moreover, we constructed a seven nucleic acid sensing-related risk score (NASRS) model for the convenience of clinical application. The predictive values of NASRS in prognosis and immunotherapy were subsequently fully validated in the lung adenocarcinoma dataset and the uroepithelial carcinoma dataset. Additionally, five potential drugs binding to the core target of the NAS signature were predicted through molecular docking.

CONCLUSION

We found a significant correlation between nucleic acid sensing function and the immune treatment efficiency in LUAD. The NASRS can be used as a robust biomarker for the predicting of prognosis and immunotherapy efficiency and may help in clinical decisions for LUAD patients.

Synthesis, Characterization, DFT, and In Silico Investigation of Two Newly Synthesized β-Diketone Derivatives as Potent COX-2 Inhibitors

Despite extensive genetic and biochemical characterization, the molecular genetic basis underlying the biosynthesis of β-diketones remains largely unexplored. β-Diketones and their complexes find broad applications as biologically active compounds. In this study, in silico molecular docking results revealed that two β-diketone derivatives, namely 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione and 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione, exhibit anti-COX-2 activities. However, recent docking results indicated that the relative anti-COX-2 activity of these two studied β-diketones was influenced by the employed docking programs. For improved design of COX-2 inhibitors from β-diketones, we conducted molecular dynamics simulations, density functional theory (DFT) calculations, Hirshfeld surface analysis, energy framework, and ADMET studies. The goal was to understand the interaction mechanisms and evaluate the inhibitory characteristics. The results indicate that 5,5-dimethyl-2-(2-(2-(trifluoromethyl)phenyl)hydrazono)cyclohexane-1,3-dione shows greater anti-COX-2 activity compared to 2-(2-(4-fluorophenyl)hydrazono)-5,5-dimethylcyclohexane-1,3-dione.

Computational insights into pediatric adenovirus inhibitors: in silico strategies for drug repurposing

Human adenovirus (HADV) infection can pose a serious threat to children, leading to a variety of respiratory illnesses and other complications. Particularly, children with weak immune systems are vulnerable to severe adenovirus infections with high mortality. The main focus of this study is to propose new antiviral agents as lead HADV inhibitors for children. So, several antiviral agents used in children were subjected to finding new HADV inhibitors using important computational methods of molecular docking, molecular dynamics (MD) simulation, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding free energy calculations, density functional theory (DFT), and pharmacokinetic analysis. Molecular docking of standard cidofovir along with other ligands, suggested that sofosbuvir has the highest binding energy (-10.8 kcal/mol), followed by baloxavir marboxil (-10.36 kcal/mol). Further, the analysis of molecular interactions using MD simulation (100 ns) and MM-PBSA indicated that baloxavir marboxil has formed the most stable protein-ligand complex with HADV, followed by sofosbuvir. The binding free energies of baloxavir marboxil and sofosbuvir were found to be -61.724 kJ/mol and -48.123 kJ/mol, respectively. The DFT and drug-likeness properties of these compounds were also investigated. Overall, two antiviral agents, such as baloxavir marboxil, and sofosbuvir are suggested as lead repurposed candidates against HADV.Communicated by Ramaswamy H. Sarma.

Theoretical and Anti-Klebsiella pneumoniae Evaluations of Substituted 2,7-dimethylimidazo[1,2-a]pyridine-3-carboxamide and Imidazopyridine Hydrazide Derivatives

A series of multistep synthesis protocols was adopted to synthesize substituted imidazopyridines (IMPs) (SM-IMP-01 to SM-IMP-13, and DA-01-05). All substituted IMPs were then characterized using standard spectroscopic techniques such as ¹H-NMR, ¹³C-NMR, elemental analyses, and mass spectrometry. Our both in vitro qualitative and quantitative results for antibacterial analysis, against Klebsiella pneumoniae ATCC 4352 and Bacillus subtilis ATCC 6051 suggested that all compounds essentially exhibited activity against selected strains of bacteria. Our DFT analyses suggested that the compounds of the SM-IMP-01-SM-IMP-13 series have HOMO/LUMO gaps within 4.43-4.69 eV, whereas the compounds of the DA-01-DA-05 series have smaller values of the HOMO/LUMO gaps, 3.24-4.17 eV. The lowest value of the global hardness and the highest value of the global softness, 2.215 and 0.226 eV, respectively, characterize the compound SM-IMP-02; thus, it is the most reactive compound in the imidazopyridine carboxamide series (except hydrazide series). This compound also depicted lesser MIC values against Klebsiella pneumoniae ATCC 4352 and Bacillus subtilis ATCC 6051 as 4.8 µg/mL, each. In terms of another series, hydrazide DA-05 depicted strong antimicrobial actions (MIC: 4.8 µg/mL against both bacterial strains) and also had the lowest energy gap (3.24 eV), higher softness (0.309 eV), and lesser hardness (1.62 eV). Overall, when we compare qualitative and quantitative antimicrobial results, it is been very clear that compounds with dibromo substitutions on imidazopyridine (IMP) rings would act as better antimicrobial agents than those with -H at the eighth position on the IMP ring. Furthermore, substituents of higher electronegativities would tend to enhance the biological activities of dibromo-IMP compounds. DFT properties were also well comparable to this trend and overall, we can say that the electronic behavior of compounds under investigation has key roles in their bioactivities.

Balanced QSAR and Molecular Modeling to Identify Structural Requirements of Imidazopyridine Analogues as Anti-infective Agents Against Trypanosomiases

Human African trypanosomiasis (HAT), a fatal infection caused by Trypanosoma brucei (T. brucei) is considered as a neglected disease in the tropical areas, and newer agents with unique mechanism of action are urgently needed. In this work, 65 Imidazopyridine analogues from known literature were selected for building statistically robust genetic algorithm (GA) based QSAR models. Furthermore, values for the various cross-validation properties supported its statistical robustness (model 1, [Formula: see text], RMSE[Formula: see text], MAE[Formula: see text], CCC[Formula: see text], and [Formula: see text]). Our in silico ADMET analysis revealed that a designed molecule, S10 may act as potent lead (T. brucei, pEC[Formula: see text] ([Formula: see text]M), [Formula: see text]) with better pharmacokinetics, no carcinogenicity, class III acute oral toxicity, minimal OCT1 and OCT2 inhibitions and no eye corrosion profiles. Our molecular docking analysis (on 42 drug targets) for a dataset and designed molecules demonstrated higher binding affinity of Imidazopyridine analogues with T. brucei farnesyl diphosphate synthase (TbFPPS) (PDB id: 2I19). This observation was further supported by 100[Formula: see text]ns molecular dynamics analysis retaining better stability of complex. Thus, imidazopyridine analogues would provide a promising scaffold for the development of anti-HAT agents.