Computational Insights Research Articles

Understanding the relationship between MCP-1 SNP (rs1024611) and VEGF SNP (rs699947) with aging and lifestyle habits via Computational Insights

Understanding the relationship between <i>MCP-1</i> SNP (rs1024611) and <i>VEGF</i> SNP (rs699947) with aging and lifestyle habits via Computational Insights

Phytogenic Synthesis of Cuprous and Cupric Oxide Nanoparticles Using Black jack Leaf Extract: Antibacterial Effects and Their Computational Docking Insights

Background: Green synthesized nanoparticles (NPs) have gained increasing popularity in recent times due to their broad spectrum of antimicrobial properties. This study aimed to develop a phytofabrication approach for producing cuprous (Cu2O) and cupric oxide (CuO) NPs using a simple, non-hazardous process and to examine their antimicrobial properties. Methods: The synthesis employed Bidens pilosa plant extract as a natural reducing and stabilizing agent, alongside copper chloride dihydrate as the precursor. The biosynthesized NPs were characterized through various techniques, including X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier-transform infrared (FT-IR) spectroscopy, ultraviolet–visible (UV-Vis) spectroscopy, scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDS). Results: XRD analysis confirmed that the synthesized CuO and Cu2O NPs exhibited a high degree of crystallinity, with crystal structures corresponding to monoclinic and face-centered cubic systems. SEM images revealed that the NPs displayed distinct spherical and sponge-like morphologies. EDS analysis further validated the purity of the synthesized CuO NPs. The antimicrobial activity of the CuO and Cu2O NPs was tested against various pathogenic bacterial strains, including Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Bacillus cereus, with the minimum inhibitory concentration (MIC) used to gauge their effectiveness. Conclusions: The results showed that the phytosynthesized NPs had promising antibacterial properties, particularly the Cu2O NPs, which, with a larger crystal size of 68.19 nm, demonstrated significant inhibitory effects across all tested bacterial species. These findings suggest the potential of CuO and Cu2O NPs as effective antimicrobial agents produced via green synthesis.

Computational Insights into Acrylamide Fragment Inhibition of SARS-CoV-2 Main Protease

The pathogen of COVID-19, SARS-CoV-2, has caused a severe global health crisis. So far, while COVID-19 has been suppressed, the continuous evolution of SARS-CoV-2 variants has reduced the effectiveness of vaccines such as mRNA-1273 and drugs such as Remdesivir. To uphold the effectiveness of vaccines and drugs prior to potential coronavirus outbreaks, it is necessary to explore the underlying mechanisms between biomolecules and nanodrugs. The experimental study reported that acrylamide fragments covalently attached to Cys145, the main protease enzyme (Mpro) of SARS-CoV-2, and occupied the substrate binding pocket, thereby disrupting protease dimerization. However, the potential mechanism linking them is unclear. The purpose of this work is to complement and validate experimental results, as well as to facilitate the study of novel antiviral drugs. Based on our experimental studies, we identified two acrylamide fragments and constructed corresponding protein-ligand complex models. Subsequently, we performed molecular dynamics (MD) simulations to unveil the crucial interaction mechanisms between these nanodrugs and SARS-CoV-2 Mpro. This approach allowed the capture of various binding conformations of the fragments on both monomeric and dimeric Mpro, revealing significant conformational dissociation between the catalytic and helix domains, which indicates the presence of allosteric targets. Notably, Compound 5 destabilizes Mpro dimerization and acts as an effective inhibitor by specifically targeting the active site, resulting in enhanced inhibitory effects. Consequently, these fragments can modulate Mpro’s conformational equilibrium among extended monomeric, compact, and dimeric forms, shedding light on the potential of these small molecules as novel inhibitors against coronaviruses. Overall, this research contributes to a broader understanding of drug development and fragment-based approaches in antiviral covalent therapeutics.

Surrogate Modeling for Solving OPF: A Review

The optimal power flow (OPF) problem, characterized by its inherent complexity and strict constraints, has traditionally been approached using analytical techniques. OPF enhances power system sustainability by minimizing operational costs, reducing emissions, and facilitating the integration of renewable energy sources through optimized resource allocation and environmentally aligned constraints. However, the evolving nature of power grids, including the integration of distributed generation (DG), increasing uncertainties, changes in topology, and load variability, demands more frequent OPF solutions from grid operators. While conventional methods remain effective, their efficiency and accuracy degrade as computational demands increase. To address these limitations, there is growing interest in the use of data-driven surrogate models. This paper presents a critical review of such models, discussing their limitations and the solutions proposed in the literature. It introduces both Analytical Surrogate Models (ASMs) and learned surrogate models (LSMs) for OPF, providing a thorough analysis of how they can be applied to solve both DC and AC OPF problems. The review also evaluates the development of LSMs for OPF, from initial implementations addressing specific aspects of the problem to more advanced approaches capable of handling topology changes and contingencies. End-to-end and hybrid LSMs are compared based on their computational efficiency, generalization capabilities, and accuracy, and detailed insights are provided. This study includes an empirical comparison of two ASMs and LSMs applied to the IEEE standard six-bus system, demonstrating the key distinctions between these models for small-scale grids and discussing the scalability of LSMs for more complex systems. This comprehensive review aims to serve as a critical resource for OPF researchers and academics, facilitating progress in energy efficiency and providing guidance on the future direction of OPF solution methodologies.

Computational insights into optimal household portfolio decisions: a stochastic approach with heston model and finite difference scheme

Computational insights into optimal household portfolio decisions: a stochastic approach with heston model and finite difference scheme

Unraveling the Dual Anti-Inflammatory and Antioxidant Mechanisms of Acteoside: Computational Insights and Experimental Validation.

Acteoside (ACT) is one of the primary bioactive ingredients in Cistanche tubulosa (Schenk). Its remarkable efficacy in treating immune-related and inflammatory disorders has garnered significant interest among scientific circles. However, the anti-inflammatory and antioxidant effects of ACT and its underlying molecular mechanisms require further investigation. In this study, pharmacophore-based reverse docking and molecular dynamics simulations identified potential anti-inflammatory targets in silico. Studies conducted in vitro with lipopolysaccharide (LPS)-induced RAW264.7 cells validated the anti-inflammatory properties of ACT. Methyl thiazolyl tetrazolium (MTT) and lactate dehydrogenase (LDH) assays indicated ACT's non-toxic and growth-promoting effects on cells. ACT significantly reduced nitric oxide (NO) and reactive oxygen species (ROS) production and restored levels of antioxidant enzymes. It also decreased pro-inflammatory cytokines. Western blotting assays indicated that ACT inhibited p38, TNF-α, PI3 K/AKT, and NF-κB signaling pathways. These findings underscore ACT's ability to mitigate acute inflammation in RAW264.7 cells by modulating key signaling pathways and provide the scientific basis for enhancing the medicinal value of ACT and future drug development.

Poly(bis(1‐methylpiperazin‐1‐ium‐amide) Nanofilm Composite Membrane with Nanochannel‑Enabled Microporous Structure and Enhanced Steric Hindrance for Magnesium/Lithium Separation

AbstractEfficient lithium/magnesium (Li+/Mg2+) separation attainment is fundamental to the extraction of lithium from brine by nanofiltration membrane separation process, which is essential for resource recovery and a circular water economy. However, for poly(piperazine‐amide) nanofilm composite membranes, the higher electronegativity affects the Mg2+ rejection and consequently Li+/Mg2+ separation performance. Manipulating the positive charge density and pore size regulation of the nanofiltration membranes are determinative of the Li+/Mg2+ separation performance improvement. Here, a new monomer 1,1′‐(hexane‐1,6‐diyl)bis(1‐methylpiperazin‐1‐ium) bromide containing bis‐quaternary ammonium cations is employed as a molecular building block to fabricate polyamide nanofilms via interfacial polymerization. The dual quaternary ammoniums and the rod‐shaped conformation of the monomer confer enhanced electropositivity, steric hindrance, loosely packed microporous network structure (pore diameter∼0.8–1.35 nm), and high free volume. The resultant membrane exhibits high water permeance of 28.34 L m−2 h−1 bar−1 with good Li+/Mg2+ selectivity of up to 76.9. In addition, the membrane also exhibits chlorine stability performance owing to the lack of the chlorine sensitive −NH groups in the formed tertiary amide structures. Computational insights on the structural properties, nanofilm formation, and transmembrane water and ion transport behaviors are provided. This study offers insightful theoretical and technological concepts to design and construct membrane materials for energy‐efficient separations.

Exploring antitumor activity of novel imidazo[2,1-b]thiazole and imidazo[1,2-a]pyridine derivatives on MDA-MB-231 cell line: Targeting VEGFR-2 enzyme with computational insight

Our study explored the anticancer potential of novel heterocyclic compounds, specifically 6a-d, 8a-d, 12a-d, and 13a-d, which are derived from imidazo[2,1-b]thiazole and imidazo[1,2-a]pyridine and linked through a hydrazide moiety. These compounds were assessed for their anticancer activity toward the MDA-MB-231 breast cancer cell line to evaluate their effectiveness in inhibiting cancer cell proliferation. Among the compounds tested, 13c and 13d emerged as the most active, with IC50 values of 4.40 ± 2.87 µM and 4.69 ± 2.55 µM, respectively. These two compounds were further investigated for their effects on VEGFR-2 enzymatic activity, cell cycle progression, and apoptosis, then 13c and 13d were further evaluated for their impact on DNA fragmentation using the comet assay. Both compounds demonstrated a significant increase in DNA fragmentation, with levels of damage being twice as high as those observed in the untreated control cells. Molecular docking studies through VEGFR-2 demonstrated that compounds 13c and 13d bind to VEGFR-2 in a manner comparable to the co-crystallized ligand sunitinib I. Further analysis using density functional theory highlighted their favorable physical properties. Additionally, computational evaluations of ADME and drug-likeness suggest that these derivatives hold promise and merit further investigation. The ultimate goal is to develop effective, safe, and orally bioavailable VEGFR-2 inhibitors for potential use in anticancer therapy.

Computational insights into transition metal-based BaCoX3 (X = Cl, Br, I) halide perovskites for spintronics, photovoltaics, and renewable energy devices

Ab-initio simulations using density functional theory (DFT) were employed to investigate the structural, mechanical, electronic, magnetic, optical, and thermoelectric properties of halide perovskites \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\hbox {BaCoX}_3$$\\end{document} (X = Cl, Br, I). Structural optimization and mechanical stability assessments confirm the reliability of these perovskites in a hexagonal P\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$6_3$$\\end{document}mc symmetry. The stability of the ferromagnetic phase was validated through total crystal energy minimization via Murnaghan’s equation of state. Electronic band structures and density of states, derived from the generalized gradient approximation (GGA), reveal a semiconducting ferromagnetic nature in the spin up channel, spotlighting their potential in semiconductor spintronic applications. Phonon dispersion analysis of \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\hbox {BaCoCl}_3$$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\hbox {BaCoBr}_3$$\\end{document} revealed positive phonon modes throughout the entire Brillouin zone, confirming their dynamical stability. In contrast, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\hbox {BaCoI}_3$$\\end{document} demonstrated dynamical instability. The elastic constants confirm the mechanical stability and ductile nature of the perovskites. Optical and dielectric properties of these perovskites show significant UV absorption and photoconductivity, making them highly suitable for optoelectronic and solar cell applications. Finally, transport properties, such as the Seebeck coefficient, electrical conductivity, thermal conductivity, power factor, and figure of merit (ZT) unveil their exceptional thermoelectric performance. Combining half-metallic ferromagnetic traits with superior thermoelectric and optoelectronic performance positions \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\hbox {BaCoX}_3$$\\end{document} compounds as exceptional candidates for applications in spintronics, optoelectronics, and thermoelectrics. This comprehensive investigation demonstrates their ability to excel across a diverse array of advanced technological applications.

Unlocking the biochemical and computational parameters of Ceropegia foetida: A scientific approach for functional bioactive compounds from a medicinal food plant

Investigating the therapeutic potentials of medicinal plants remains pivotal in the discovery of novel bioactive compounds for food and pharmaceutical applications. This research delves into the phytochemical composition and biological activities of Ceropegia foetida's methanol extract, employing comprehensive UHPLC-MS for secondary metabolites profiling. The study quantifies the extract's substantial phenolic (76.12 mg GAE/g) and flavonoid (21.58 mg QE/g) contents, revealing a promising correlation with robust antioxidant activities, as evidenced by notable ABTS, FRAP, and CUPRAC assay outcomes. Furthermore, the extract demonstrates significant inhibitory effects on key enzymes implicated in neurodegenerative disorders and diabetes, including acetylcholinesterase (3.56 mg GALAE/g), butyrylcholinesterase (2.91 mg GALAE/g), and tyrosinase (128.31 mg KAE/g). UHPLC-MS analysis confirms the presence of 39 distinct phytochemicals across six primary categories, affirming the extract's complex bioactive profile. In complement to experimental assays, computational analyses via molecular docking simulations provided insights into the interaction mechanisms of identified phytochemicals with the target enzymes. These simulations revealed a substantial binding affinity of the plant's constituents towards enzymes compared to standard inhibitors, highlighting the compounds responsible for C. foetida's bioactivity. Such computational insights, alongside empirical data, suggest that C. foetida merits further exploration as a natural source of therapeutic agents. Overall, the efficacious enzyme inhibition, coupled with the identified phytochemical diversity, underscores the potential of C. foetida as a valuable natural resource for developing nutraceuticals and therapeutic agents. These findings support the further investigation of C. foetida for its applicability in enhancing health and treating chronic conditions.

Experimental and Computational Insights into the Effects of -NH2 and -Cl Functional Groups on the Copper Corrosion Inhibition by Benzotriazole

The influences of -NH2 and -Cl groups on the copper corrosion inhibition in 0.5 M H2SO4 solution by benzotriazole were studied using experimental methods and density functional theory calculations. Mass loss tests, potentiodynamic polarization, and surface morphology analyses revealed notable differences: while unmodified benzotriazole showed an inhibition efficiency of 76.6%, the -Cl derivative increased this to 87.6%, whereas the -NH2 derivative dropped it to 61.0% at the concentration of 5 × 10−4 M. Density functional theory calculations indicated these differences are not due to electronic properties or inhibitor-copper interaction energies but rather to the inhibitor’s influence on the oxygen reduction reaction, especially O2 and H2O adsorption. The -NH2 group formed strong hydrogen bonds with O2 and H2O, reducing oxygen reduction inhibition, while the -Cl group repelled O2, resulting in enhanced inhibition. Free energy analysis of the oxygen reduction reaction supported these findings. These new insights into benzotriazole derivatives’ copper corrosion inhibition mechanisms offer valuable guidance for developing next-generation corrosion inhibitors.

Computational Insight into the Optoelectronic and Chemical Reactivity Properties of Metal-Free Phenothiazine Based D-π-A Dye-Sensitizers for Solar Cells Application: DFT and TD-DFT Methods

Computational Insight into the Optoelectronic and Chemical Reactivity Properties of Metal-Free Phenothiazine Based D-π-A Dye-Sensitizers for Solar Cells Application: DFT and TD-DFT Methods

Structural, spectroscopic, and biological properties of an asymmetric Cu (II) Schiff-base complex: Synthesis, DNA/BSA interactions, and antimicrobial potential with experimental and computational insights

A copper (II) complex with the asymmetric bidentate Schiff-base ligand (E)-2-(((4-chlorophenyl) imino) methyl) phenol was synthesized and characterized using FTIR and UV–VIS spectroscopy. Photoluminescence studies were conducted on both the copper (II) complex and the free ligand. XRD analysis revealed the copper (II) complex crystallizes in the monoclinic system, space group P21/c. The complex structure was optimized using DFT calculations with B3LYP/6-31G+(d,p) and Lanl2dz basis sets, with QTAIM and NBO analyses confirming complex formation. The energy gap of the copper (II) complex was determined to be 3.701 eV (alpha state) and 2.764 eV (beta state). MEP analysis of the optimized structure indicated a hydrophobic environment around the nitrogen atom, with the molecule exhibiting overall hydrophobicity. The chlorine atoms were identified as potential nucleophilic sites. The antimicrobial efficacy of a Schiff base copper (II) complex was evaluated against selected pathogenic bacteria (B. subtilis, B. megaterum, K. pneumoniae, E. coli) and the fungus Candida albicans. Among these C. albicans for complex showed larger zones (11–15.5 mm) at higher concentrations such as 2 and 2.5 mg/mL. Molecular docking studies suggested strong binding affinity between the complex and the target protein, this was further supported by obtained root means square deviations, root means square fluctuations, radius of gyration and hydrogen bond values during simulations. The binding free energy between BSA and the copper (II) complex was calculated as −8.7 kcal/mol, indicating significant interaction. However, only weak van der Waals interactions were observed between the complex and DNA. Toxicity studies revealed the copper (II) complex had minimal irritant effects on ocular and cutaneous tissues, with a low lethal dose. In comparison, Tricresyl phosphate showed moderate to severe ocular irritancy and modest cutaneous irritancy.

Intervention mechanism of amphiphilic natural sweeteners on starch chain dynamic behavior: Computational and experimental insights

Amphiphilic natural sweeteners (i.e. steviol glycosides (STE) and glycyrrhizic acid (GA)) have been adopted to improve the quality of various starchy products, which can fundamentally be characterized as the intervention of the former in the chain dynamic behavior of the latter. However, these phenomena and related mechanisms still lack systematic insights. Herein, dual-temperature molecular dynamic simulations combined with experimental analysis were used to tandemly investigate the intervention of sweeteners in six types of chain dynamic behaviors that are strongly correlated with starch properties, including unwinding, movement, long/short-term reassociation, rearrangement, and depolymerization. The results show that STE and GA both promoted the chain unwinding and movement, and also retarded the chain short/long-term reassociation and rearrangement. Besides, GA exhibited a greater role than STE in facilitating chain unwinding and movement. Peculiarly, GA (0 %–40 % w/w) collaborated with starch to form a new microstructure, especially at high content (≥ 20 % w/w), which endowed starch with exceptionally high hardness (15.50 gf→189.36 gf) and hardening rate (2.72 gf/d→17.76 gf/d), and also placed a physical barrier to retard starch depolymerization (slowly digestible starch: 11.26 %→20.62 %). This work contributes data and theoretical support for the development of starch/amphiphilic natural sweetener composite matrices.

First-principle computational insights on Furan- and Thiophene- functionalized zinc-porphyrins as high performance organic cathodes for electrochemical energy storage systems

First-principle computational insights on Furan- and Thiophene- functionalized zinc-porphyrins as high performance organic cathodes for electrochemical energy storage systems

Exploring the interplay between Porphyromonas gingivalis KGP gingipain, herpes virus MicroRNA-6, and Icp4 transcript in periodontitis: Computational and clinical insights.

Porphyromonas gingivalis, a major pathogen in periodontitis, produces KGP (Lys-gingipain), a cysteine protease that enhances bacterial virulence by promoting tissue invasion and immune evasion. Recent studies highlight microRNAs' role in viral latency, potentially affecting lytic replication through host mechanisms. Herpes virus (HSV) establishes latency via interactions between microRNA-6 (miRH-6) and the ICP4 transcription factor in neural ganglia. This suggests a potential link between periodontitis and HSV-induced latency. This study aims to identify and validate the insilico inhibitory interaction of P. gingivalis KGP with ICP4 transcripts and correlate the presence of viral latency-associated transcript micro-RNA-6 with periodontitis. Computational docking analysis was performed to investigate the potential interaction between ICP4 and KGP gingipain. The binding energy and RMSD ligand values were calculated to determine the interaction's strength. Ten patients with recurrent clinical attachment loss despite conventional therapy were included in the clinical study. Subgingival tissue samples were collected post-phase I therapy, and HSV microRNA-6 presence was detected via polymerase chain reaction and confirmed through gel electrophoresis. Computational docking identified the ICP4-KGP gingipain complex with the lowest binding energy (-288.29 kJ mol^1) and an RMSD ligand of 1.5 Angstroms, indicating strong interaction potential. Gel electrophoresis confirmed miRH-6 presence in all samples. The identification of miRNA-6 in periodontitis patients and the strong interaction potential between P. gingivalis KGP gingipain and ICP4 transcripts indicate a possible link between bacterial virulence factors and viral latency dynamics in periodontal tissues. These results highlight the complex interplay between oral pathogens, viral microRNAs, and host immune responses in periodontitis.

Computational and theoretical insights into the cytotoxic prospects of compounds isolated from Elaeodendron buchananii against Leukemia

The present study investigated the cytotoxic prospects of isolated compounds from Elaeodendron buchananii against leukemia, using computational tools. Comprehensive literature searches revealed only buchaninoside, mutangin, methyl 3β-acetoxy-11α, 19α, 28-trihydroxyurs-12-en-23-oic acid, 3β, 11α, 19α-trihydroxyurs-12-en-23, 28-dioic acid, 3β-acetoxy-19α, 24, 28-trihydroxyurs-12-ene, 3-oxo-19α,28-dihydroxyurs-12-en-24-oic acid, and elabunin have been isolated from E. buchananii. The compounds were subjected to Density Functional Theory (DFT) and Molecular Dynamics (MD) analyses, with Fms-like tyrosine kinase (FLT3) and catalytic binding sites of Murine Leukemia Virus (MLV) as the target proteins in lukemia. Following DFT analysis, the structures of the compounds were optimized at the PW6B95D3/Def2-TZVP level of theory; their UV-Visible peaks were in the UV region, with mutangin, 3-oxo-19α,28-dihydroxyurs-12-en-24-oic acid and elabunin exhibiting one single peak. The potent Root-Mean-Square Deviation, Root-Mean-Square Fluctuation, solvent-accessible surface area and radius of gyration values indicated a strong and stable molecular interaction between the compounds and the proteins. These were further supported by high ∆G values, with MLV showing the best interaction. Per-residue decomposition plots also revealed high energy contributions in the interactions’ binding sites residues. These results indicate that the cytotoxic prospects of the isolated compounds against leukemia as indicated by its molecular interactions with FLT3 and MLV.

Corrosion inhibition of steel in acidic media using glycyrrhizic acid: experimental and computational insights

Corrosion inhibition of steel in acidic media using glycyrrhizic acid: experimental and computational insights

Identification of interaction partners of outer inflammatory protein A: Computational and experimental insights into how Helicobacter pylori infects host cells

Outer membrane proteins (OMPs) play a key role in facilitating the survival of Helicobacter pylori within the gastric tissue by mediating adherence. Among these proteins, Outer inflammatory protein A (OipA) is a critical factor in H. pylori colonization of the host gastric epithelial cell surface. While the role of OipA in H. pylori attachment and its association with clinical outcomes have been established, the structural mechanisms underlying OipA’s action in adherence to gastric epithelial cells remain limited. Our study employed experimental and computational approaches to investigate the interaction partners of OipA on the gastric epithelial cell surface. Initially, we conducted a proteomic analysis using a pull-down assay with recombinant OipA and gastric epithelial cell membrane proteins to identify the OipA interactome. This analysis revealed 704 unique proteins that interacted with OipA. We subsequently analyzed 16 of these OipA partners using molecular modeling tools. Among these 16 partners, we highlight three human proteins, namely Hepatocyte growth factor (HGF), Mesenchymal epithelial transition factor receptor (Met), and Adhesion G Protein-Coupled Receptor B1 (AGRB1) that could play a role in H. pylori adherence to the gastric epithelial cell surface with OipA. Collectively, these findings reveal novel host interactions mediated by OipA, suggesting their potential as therapeutic targets for combating H. pylori infection.

Design, Synthesis and Computational Insight of Isolated and Thiophene fused 2H‐Pyran‐2‐ones as PPAR‐γ Agonist

AbstractPeroxisome proliferator‐activated receptor gamma (PPAR‐γ) is a well‐known member of the PPAR family and a potential target for the treatment of various disorders. Herein, we present the design and synthesis of various 6‐aryl‐4‐sec.amino‐2‐oxo‐2H‐pyran‐3‐carbonitrile derivatives and functionalized thieno[3,2‐c]pyran‐2‐ones, derived from ketene dithioacetal. Then all the synthesized compounds were docked for their activity as PPAR‐γ to predict the binding mechanism and affinities regarding rosiglitazone and muraglitazar. Our studies revealed that three compounds 10 e, 10 f, and 10 h showed significant binding affinities, with energy ranges comparable to standard drugs rosiglitazone and muraglitazar. The docking conformation studies revealed that the selected compounds nicely interact with PPAR‐γ in the ligand binding domain with positive predictive values. We also performed molecular dynamics of the most potent compounds to validate the result. Our results indicate that these novel compounds are potential PPAR‐γ ligands, offering new possibilities for therapeutic applications. This study underscores the potential of these synthesized compounds in the development of novel PPAR‐γ agonists.