Structure-based design of new diclofenac: Physicochemical, spectral, molecular docking, dynamics simulation and ADMET studies

Ammonia-Treated Graphene Oxide/ZnIn2S4 Composite for Enhanced Photocatalytic Hydrogen Production under Visible Light Irradiation

In the pursuit of solar-driven photocatalytic energy generation, environmental remediation, and carbon neutrality, the development of semiconductor-based heterojunction photocatalysts presents a promising strategy. However, the photocatalytic efficiency of pristine ZnIn2S4 (ZIS) is hindered by rapid electron-hole recombination and a relatively small surface area. Meanwhile, pure graphene oxide (GO) is not an ideal photocatalyst due to its inappropriate bandgap and the presence of oxygenated functional groups. To overcome these limitations, a surfactant-assisted ZIS synthesis was combined with ammonia-treated GO (NGO) to form an NGO/ZIS composite that enhances light absorption, charge carrier separation and transport, and overall hydrogen production efficiency under visible light illumination. Among the evaluated materials, 0.1NGO/ZIS exhibited the highest hydrogen evolution rate (18.8 mmol·g-1 h-1), demonstrating enhancements of 3-fold and 940-fold increased compared to pristine ZIS (5.8 mmol·g-1 h-1) and NGO (0.02 mmol·g-1 h-1), respectively. This superior photocatalytic performance is attributed to improved interfacial charge transfer between NGO and ZIS, facilitated by the incorporation of amine and amide groups into GO. Furthermore, density functional theory (DFT) calculations were conducted to validate the impact of ammonia treatment on GO and support the experimental findings. The synthesized photocatalysts were characterized by using X-ray diffraction (XRD), Fourier-transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Brunauer-Emmett-Teller (BET), diffuse reflectance sorption spectroscopy (DRS), photoluminescence (PL), electrochemical impedance spectroscopy (EIS), electron spin resonance (ESR), and time-resolved photoluminescence (TRPL) analyses. This study presents a simple yet effective approach to fabricating NGO/ZIS composites, contributing to the advancement of high-performance photocatalysts for sustainable energy applications.

Biochemical and molecular docking-based strategies of Acalypha indica and Boerhavia diffusa extract by targeting bacterial strains and cancer proteins

Antibiotic-resistant microbes have emerged around the world, presenting a risk to health. Plant-derived drugs have become a potential source for the production of antibiotic-resistant drugs and cancer therapies. In this study, we investigated the antibacterial, cytotoxic and antioxidant properties of Acalypha indica and Boerhavia diffusa, and conducted in silico molecular docking experiments against EGFR and VEGFR-2 proteins. The metabolic extract of A. indica inhibited Streptococcus iniae and Staphylococcus sciuri with inhibition zones of 21.66 ± 0.57 mm and 20.33 ± 0.57 mm, respectively. The B. diffusa leaf extract produced inhibition zones of 20.3333 ± 0.5773 mm and 20.33 ± 0.57 mm against Streptococcus iniae and Edwardsiella anguillarum, respectively. A. indica and B. diffusa extracts had toxicities of 162.01 μg/ml and 175.6 μg/ml, respectively. Moreover, B. diffusa (IC50 =154.42 µg/ml) leaf extract exhibited moderately higher antioxidant activity compared with the A. indica (IC50 = 218.97 µg/ml) leaf extract. Multiple interactions were observed at Leu694, Met769 and Leu820 sites for EGFR and at Asp1046 and Cys1045 sites for VEGFR during the molecular docking study. CID-235030, CID-70825 and CID-156619353 had binding energies of -7.6 kJ/mol, -7.5 kJ/mol and -7.6 kJ/mol, respectively, with EGFR protein. VEGFR-2 protein had docking energies of -7.5 kJ/mol, -7.6 kJ/mol and -7.3 kJ/mol, respectively, for CID-6420353, CID-156619353 and CID-70825 compounds. The MD simulation trajectories revealed the hit compound; CID-235030 and EGFR complex, CID-6420353 and VEGFR-2 exhibit stable profile in the root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), hydrogen bond and root mean square fluctuation (RMSF) and the binding free energy by MM-PBSA method. This study indicates that methanol extracts of A. indica and B. diffusa may play a crucial role in developing antibiotic-resistant and cancer drugs.

Isolation, Structure Elucidation, and Bioactivity Evaluation of Two Alkaloids From Piper chaba H. Stem: A Traditional Medicinal Spice and Its Chemico-Pharmacological Aspects

Bangladesh is endowed with an abundance of excellent medicinal plant resources. A well-known traditional medicinal plant Piper chaba H. from the Piperaceae family is rich in bioactive phytochemicals that have antidiarrheal, antimicrobial, analgesic, antioxidant, anticancer, and cytotoxic effects. This plant is locally known as "Chuijhal," and the stem is used as spices. In the current research program, the stems of the P. chaba plant were selected and its chemical and biological investigations such as antidiarrheal, antimicrobial, and analgesic effects were performed. Moreover, docking models were accomplished by exploiting PyRx-Virtual Screening software and implied that isolated compounds of P. chaba exert different pharmacological activity by inhibiting their targeted receptors. Phytochemical investigations revealed the isolation of Chingchengenamide A, a relatively rare alkaloid from the stems of P. chaba. Another alkaloid Chabamide I which is a piperine dimer was also isolated. Their structures were confirmed by comparing these compounds' spectral data (1H and 13C NMR) with their previously published spectral data. Antidiarrheal activity shows a percent reduction of diarrhea by 46.67% and 40%, respectively, for Chabamide I and Chingchengenamide A (at 20 mg/kg b.w.) compared with an 80% reduction by standard loperamide. Similarly, the percent reduction of writhing was 53.06% and 42.86%, respectively, for Chabamide I and Chingchengenamide A at similar doses compared with an 80% reduction by diclofenac sodium considered as standard. Both the alkaloids showed auspicious outcomes against test microorganisms during disk diffusion antimicrobial assay. Molecular docking and ADME/T analysis of the alkaloids also validate a potent pharmacological basis for the traditional utilization of P. chaba in treating diarrhea, pain, and microbial infection. These results emphasize the need to investigate P. chaba as a potential source of natural therapies for common health issues, laying the foundation for future research.

Novel tetraaza macrocyclic Schiff base complexes of bivalent zinc: microwave-assisted green synthesis, spectroscopic characterization, density functional theory calculations, molecular docking studies, in vitro antimicrobial and anticancer activities

In the present manuscript, novel macrocyclic Schiff base complexes [Zn(N4MacL1)Cl2-Zn(N4MacL3)Cl2] were synthesized by the reaction of ZnCl2 and macrocyclic ligands (N4MacL1-N4MacL3) derived from diketone and diamines under microwave irradiation method and conventional method. The structures of the obtained complexes were identified by various spectrometric methods such as Fourier transformation infra-red (FT-IR), nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HR-MS), powder X-ray diffraction, molar conductivity, and UV-vis. The structures of the synthesized compounds were optimized by using the def2-TZV/J and def2-SVP/J Coulomb fitting basis sets at B3LYP level in density functional theory (DFT) calculations. The macrocyclic Schiff base complexes exhibited higher activities against Gram-positive bacteria (Staphylococcus aureus and Bacillus cereus), Gram-negative bacteria (Escherichia coli and Xanthomonas campestris), and fungal strains (Fusarium oxysporum and Candida albicans) in comparison to macrocyclic Schiff base ligands. Furthermore, the newly synthesized macrocyclic compounds were assessed for their anticancer activity against three cell lines: A549 (human alveolar adenocarcinoma epithelial cell line), HT-29 (human colorectal adenocarcinoma cell line), and MCF-7 (human breast adenocarcinoma cell line) using the MTT assay. The obtained results showed that the macrocyclic complex [Zn(N4MacL3)Cl2] displayed the highest cytotoxic activity (2.23 ± 0.25 µM, 6.53 ± 0.28 µM, and 7.40 ± 0.45 µM for A549, HT-29, and MCF-7 cancer cell lines, respectively). Additionally, molecular docking investigations were conducted to elucidate potential molecular interactions between the synthesized macrocyclic compounds and target proteins. The results revealed a consistent agreement between the docking calculations and the experimental data.

An Integrated Framework to Identify Prognostic Biomarkers and Novel Therapeutic Targets in Hepatocellular Carcinoma-Based Disabilities

Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors globally, significantly affecting liver functions, thus necessitating the identification of biomarkers and effective therapeutics to improve HCC-based disabilities. This study aimed to identify prognostic biomarkers, signaling cascades, and candidate drugs for the treatment of HCC through integrated bioinformatics approaches such as functional enrichment analysis, survival analysis, molecular docking, and simulation. Differential expression and functional enrichment analyses revealed 176 common differentially expressed genes from two microarray datasets, GSE29721 and GSE49515, significantly involved in HCC development and progression. Topological analyses revealed 12 hub genes exhibiting elevated expression in patients with higher tumor stages and grades. Survival analyses indicated that 11 hub genes (CCNB1, AURKA, RACGAP1, CEP55, SMC4, RRM2, PRC1, CKAP2, SMC2, UHRF1, and FANCI) and three transcription factors (E2F1, CREB1, and NFYA) are strongly linked to poor patient survival. Finally, molecular docking and simulation identified seven candidate drugs with stable complexes to their target proteins: tozasertib (-9.8 kcal/mol), tamatinib (-9.6 kcal/mol), ilorasertib (-9.5 kcal/mol), hesperidin (-9.5 kcal/mol), PF-562271 (-9.3 kcal/mol), coumestrol (-8.4 kcal/mol), and clofarabine (-7.7 kcal/mol). These findings suggest that the identified hub genes and TFs could serve as valuable prognostic biomarkers and therapeutic targets for HCC-based disabilities.

Modification of ibuprofen to improve the medicinal effect; structural, biological, and toxicological study

Ibuprofen is classified as a non-steroidal anti-inflammatory drug (NSAID) that is employed as an initial treatment option for its non-steroidal anti-inflammatory, pain-relieving, and antipyretic properties. However, Ibuprofen is linked to specific well-known gastrointestinal adverse effects like ulceration and gastrointestinal bleeding. It has been linked to harmful effects on the liver, kidney, and heart. The purpose of the study is to create novel and potential IBU analogue with reduced side effects with the enhancement of their medicinal effects, so as to advance the overall safety profile of the drug. The addition of some novel functional groups including CH3, F, CF3, OCF3, Cl, and OH at various locations in its core structure suggestively boost the chemical as well as biological action. The properties of these newly designed structures were analyzed through chemical, physical, and spectral calculations using Density Functional Theory (DFT) and time-dependent DFT through B3LYP/6-31 g (d,p) basis set for geometry optimization. Molecular docking and non-bonding interaction studies were conducted by means of the human prostaglandin synthase protein (PDB ID: 5F19) to predict binding affinity, interaction patterns, and the stability of the protein-drug complex. Additionally, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) and PASS (Prediction of Activity Spectra for Substances) predictions were employed to evaluate the pharmacokinetic and toxicological properties of these structures. Importantly, most of the analogues displayed reduced hepatotoxicity, nephrotoxicity, and carcinogenicity in comparison to the original drug. Moreover, molecular docking analyses indicated improved medicinal outcomes, which were further supported by pharmacokinetic calculations. Together, these findings suggest that the modified structures have reduced adverse effects along with improved therapeutic action compared to the parent drug.

In silico molecular docking of cyclooxygenase (COX-2), ADME-toxicity and in vitro evaluation of antioxidant and anti-inflammatory activities of marine macro algae

The marine ecosystem harbors unique and diverse bioactive compounds that can offer a vast repertoire of molecules with therapeutic properties. In the present study, four different species of red marine seaweeds were analyzed for its phytoconstituents and the potent antioxidant and anti-inflammatory activity of the methanolic extracts were screened and determined. The results revealed that, among the 4 samples, G. corticata, scored a good antioxidant potential by DPPH (67.61 ± 1.23%, IC50 = 577.7 µg) and metal chelation assay (29.40 ± 0.32%, IC50 = 1684 µg). The anti-inflammatory analysis has shown that, H. dialata was found to exhibit maximum inhibition against the albumin denaturation (83.50 ± 0.24%), whereas G. corticata was observed to measure a maximum inhibition in heat-induced hemolysis (60.40 ± 0.46%) and proteinase inhibition assay (83.30 ± 0.18%). An extensive literature survey was carried out for the bioactive compounds in G.corticata; it was examined for drug likeliness by ADME analysis and toxicological parameters. Further, the best selected bioactive compounds were subjected to in silico molecular docking with pro-inflammatory target, cyclooxygenase (COX-2). Hexadecanal and Neophytadiene were reported to obtain the highest binding affinity (-5.3) for COX-2 enzyme. Hence, in silico molecular docking studies had shown that G. corticata was found to possess potential anti-inflammatory activity that can prevent conversion of arachidonic acid to prostaglandins by inhibiting COX-2. In addition, molecular dynamic simulation studies have shown the stability of Hexadecanal-6 COX complex. To conclude, the outcomes of the present study may shed light on the understanding of the usage of bioactive compounds for therapeutic purpose.

In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori

Helicobacter pylori is the most common cause of gastric ulcers and is associated with gastric cancer. The enzyme HppA of class C nonspecific acid phosphohydrolases (NSAPs) of H. pylori plays a crucial role in the electron transport chain. Herein, we report an in silico homology model of HppA consisting of a monomeric α + β model. A high throughput structure-based virtual screening approach yielded potential inhibitors against HppA with higher binding energies. Further analyses of molecular interaction maps and protein-ligand fingerprints, followed by molecular mechanics-generalized Born surface area (MM-GBSA) end point binding energy calculations of docked complexes, resulted in the detection of top binders/ligands. Our investigations identified potential substrate-competitive small molecule inhibitors of HppA, with admissible pharmacokinetic properties. These molecules may provide a starting point for developing novel therapeutic agents against H. pylori.

DFT Based Comparative Studies of Some Glucofuranose and Glucopyranoside Esters and Ethers

Carbohydrate-based molecular scaffolding received significant interest due to its impact on the drug discovery and development in synthetic carbohydrate chemistry during the last couple of decades. In this respect, four glucose compounds in the furanose and pyranose forms with ester and ether functionality were selected for their structural, thermodynamic and chemical reactivity studies. PASS predication indicated that the glucose in the six-membered pyranose form was more prone to biological properties compared to their five-membered furanose form. Also, in the pyranose form acetate ester (3) had more potentiality than the ethyl ether (4). The HOMO-LUMO energy gaps were almost similar for both monosubstituted furanose and pyranose glucose indicating their almost similar reactivities. It was also inferred that these 6-O-substituted compounds followed Lipinski’s rule with the acceptable range of ADMET levels, and hence, safe from lethal proarrhythmic risks. Hopefully, these results can be used in the near future for their probable pharmaceutical use without any remarkable toxicity.