Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies

Interaction between the antioxidant compound safranal and α-chymotrypsin in spectroscopic fields and molecular modeling approaches

Among various herbal plants, saffron has been the subject of study in various medical and food fields. Among the compounds of saffron, safranal is one of them. Safranal is a monoterpene aldehyde. The precursor of safranal is called picrocrocin, whose hydrolysis leads to the production of safranal. picrocrocin has two sugar components and aglycone. sugar component was separated during the drying process of saffron and safranal is produced. Saffron is the cause of the saffron aroma. Previous studies have shown that safranal offers many benefits such as antioxidants, blood pressure regulation and anti-tumor qualities. On the other hand, α-Chy is an enzyme secreted by the pancreas into the intestine and then acts as an efficient protease. In this study, various methods, such as molecular dynamics (MD) simulation and molecular binding, and different spectroscopic techniques, as well as protein stability techniques, were used to investigate the possible interactions between safranal and α-Chy. UV spectroscopic studies were showing that the existence of safranal decreased α-Chy absorption intensity. safranal caused the intrinsic fluorescence of α-Chy to be quenched too. According to the Stern-Volmer equation, the interaction between safranal and α-Chy was of the static type. In thermodynamic calculations, the interaction between safranal and α-Chy was stabilized by hydrophobic forces. And it was found that this interaction continued spontaneously. These results were, thus, consistent with the Docking data simulation (with the negative ΔG° number and positive changes in enthalpy and entropy). The thermal stability of α-Chy was also measured, showing that its melting point was shifted to a higher threshold as a result of the interaction. also, MD simulation indicated that α-Chy became more stable in the presence of safranal. In this paper, all the results of the laboratory techniques were confirmed by molecular dynamic simulations, so the correctness of the results was confirmed. From this research, we hope to carefully observe the possible changes in the behavior and structure of the enzyme in the presence of safranal.Communicated by Ramaswamy H. Sarma.

Evaluation of the mechanism of Gong Ying San activity on dairy cows mastitis by network pharmacology and metabolomics analysis

OBJECTIVES

The goal of this investigation was to identify the main compounds and the pharmacological mechanism of the traditional Chinese medicine formulation, Gong Ying San (GYS), by infrared spectral absorption characteristics, metabolomics, network pharmacology, and molecular-docking analysis for mastitis. The antibacterial and antioxidant activities were determined in vitro.

METHODS

The chemical constituents of GYS were detected by ultra-high-performance liquid chromatography Q-extractive mass spectrometry (UHPLC-QE-MS). Related compounds were screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP, http://tcmspw.com/tcmsp.php) and the Encyclopedia of Traditional Chinese Medicine (ETCM, http://www.tcmip.cn/ETCM/index.php/Home/) databases; genes associated with mastitis were identified in DisGENT. A protein-protein interaction (PPI) network was generated using STRING. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment screening was conducted using the R module. Molecular-docking analyses were performed with the AutoDockTools V1.5.6.

RESULTS

Fifty-four possible compounds in GYS with forty likely targets were found. The compound-target-network analysis showed that five of the ingredients, quercetin, luteolin, kaempferol, beta-sitosterol, and stigmasterol, had degree values >41.6, and the genes TNF, IL-6, IL-1β, ICAM1, CXCL8, CRP, IFNG, TP53, IL-2, and TGFB1 were core targets in the network. Enrichment analysis revealed that pathways associated with cancer, lipids, atherosclerosis, and PI3K-Akt signaling pathways may be critical in the pharmacology network. Molecular-docking data supported the hypothesis that quercetin and luteolin interacted well with TNF-α and IL-6.

CONCLUSIONS

An integrative investigation based on a bioinformatics-network topology provided new insights into the synergistic, multicomponent mechanisms of GYS's anti-inflammatory, antibacterial, and antioxidant activities. It revealed novel possibilities for developing new combination medications for reducing mastitis and its complications.

Bio synthesis, comprehensive characterization, and multifaceted therapeutic applications of BSA-Resveratrol coated platinum nanoparticles

This study examines the manufacturing, characterization, and biological evaluation of platinum nanoparticles, which were synthesized by Enterobacter cloacae and coated with Bovine Serum Albumin (BSA) and Resveratrol (RSV). The formation of PtNPs was confirmed with the change of color from dark yellow to black, which was due to the bioreduction of platinum chloride by E. cloacae. BSA and RSV functionalization enhanced these nanoparticles' biocompatibility and therapeutic potential. TGA, SEM, XRD, and FTIR were employed for characterization, where PtNPs and drug conjugation-related functional groups were studied by FTIR. XRD confirmed the crystalline nature of PtNPs and Pt-BSA-RSV NPs, while TGA and SEM showed thermal stability and post-drug coating morphological changes. Designed composite was also found to be biocompatible in nature in hemolytic testing, indicating their potential in Biomedical applications. After confirmation of PtNPs based nanocaompsite synthesis, they were examined for anti-bacterial, anti-oxidant, anti-inflammatory, and anti-cancer properties. Pt-BSA-RSV NPs showed higher concentration-dependent DPPH scavenging activity, which measured antioxidant capability. Enzyme inhibition tests demonstrated considerable anti-inflammatory activity against COX-2 and 15-LOX enzymes. In in vitro anticancer studies, Pt-BSA-RSV NPs effectively killed human ovarian cancer cells. This phenomenon was demonstrated to be facilitated by the acidic environment of cancer, as the drug release assay confirmed the release of RSV from the NP formulation in the acidic environment. Finally, Molecular docking also demonstrated that RSV has strong potential as an anti-oxidant, antibacterial, anti-inflammatory, and anticancer agent. Overall, in silico and in vitro investigations in the current study showed good medicinal applications for designed nanocomposites, however, further in-vivo experiments must be conducted to validate our findings.

Design and Fabrication of Environmentally Responsive Nanoparticles for the Diagnosis and Treatment of Atherosclerosis

Cardiovascular disease poses a significant threat to human health in today's society. A major contributor to cardiovascular disease is atherosclerosis (AS). The development of plaque in the affected areas involves a complex pathological environment, and the disease progresses rapidly. Nanotechnology, combined with emerging diagnostic and treatment methods, offers the potential for the management of this condition. This paper presents the latest advancements in environment-intelligent responsive controlled-release nanoparticles designed specifically for the pathological environment of AS, which includes characteristics such as low pH, high reactive oxygen species levels, high shear stress, and multienzymes. Additionally, the paper summarizes the applications and features of nanotechnology in interventional therapy for AS, including percutaneous transluminal coronary angioplasty and drug-eluting stents. Furthermore, the application of nanotechnology in the diagnosis of AS shows promising real-time, accurate, and continuous effects. Lastly, the paper explores the future prospects of nanotechnology, highlighting the tremendous potential in the diagnosis and treatment of atherosclerotic diseases, especially with the ongoing development in nano gas, quantum dots, and Metal-Organic Frameworks materials.

Machine Learning Reinforced Genetic Algorithm for Massive Targeted Discovery of Selectively Cytotoxic Inorganic Nanoparticles

Nanoparticles (NPs) have been employed as drug delivery systems (DDSs) for several decades, primarily as passive carriers, with limited selectivity. However, recent publications have shed light on the emerging phenomenon of NPs exhibiting selective cytotoxicity against cancer cell lines, attributable to distinct metabolic disparities between healthy and pathological cells. This study revisits the concept of NPs selective cytotoxicity, and for the first time proposes a high-throughput in silico screening approach to massive targeted discovery of selectively cytotoxic inorganic NPs. In the first step, this work trains a gradient boosting regression model to predict viability of NP-treated cell lines. The model achieves mean cross-validation (CV) Q2 = 0.80 and root mean square error (RMSE) of 13.6. In the second step, this work develops a machine learning (ML) reinforced genetic algorithm (GA), capable of screening >14 900 candidates/min, to identify the best-performing selectively cytotoxic NPs. As proof-of-concept, DDS candidates for the treatment of liver cancer are screened on HepG2 and hepatocytes cell lines resulting in Ag NPs with selective toxicity score of 42%. This approach opens the door for clinical translation of NPs, expanding their therapeutic application to a wider range of chemical space of NPs and living organisms such as bacteria and fungi.

Characterization, antibacterial, and cytotoxic activities of silver nanoparticles using the whole biofilm layer as a macromolecule in biosynthesis

Recently, multi-drug resistant (MDR) bacteria are responsible for a large number of infectious diseases that can be life-threatening. Globally, new approaches are targeted to solve this essential issue. This study aims to discover novel antibiotic alternatives by using the whole components of the biofilm layer as a macromolecule to synthesize silver nanoparticles (AgNPs) as a promising agent against MDR. In particular, the biosynthesized biofilm-AgNPs were characterized using UV-Vis spectroscopy, electron microscopes, Energy Dispersive X-ray (EDX), zeta sizer and potential while their effect on bacterial strains and normal cell lines was identified. Accordingly, biofilm-AgNPs have a lavender-colored solution, spherical shape, with a size range of 20-60 nm. Notably, they have inhibitory effects when used on various bacterial strains with concentrations ranging between 12.5 and 25 µg/mL. In addition, they have an effective synergistic effect when combined with phage ZCSE9 to inhibit and kill Salmonella enterica with a concentration of 3.1 µg/mL. In conclusion, this work presents a novel biosynthesis preparation of AgNPs using biofilm for antibacterial purposes to reduce the possible toxicity by reducing the MICs using phage ZCSE9.

Alpinia officinarum Hance extract ameliorates diabetic gastroparesis by regulating SCF/c-kit signaling pathway and rebalancing gut microbiota

Diabetic gastroparesis (DGP) is a common complication of type 2 diabetes mellitus (T2DM). Alpinia officinarum Hance (AOH) is one of the most commonly used both as a food and folk medicines, which is rich in diarylheptanoids and flavonoids. The gastroprotection and hypoglycemic effect make AOH has great potential in developing of anti-DGP complementary medicine. However, the molecular mechanisms of AOH that act against DGP are yet to be elucidated. In this study, we evaluated the therapeutic effects, the potential molecular mechanism, and the changes of gut microbiota of AOH in DGP. The 5 components of the AOH were analyzed, and the potential signaling pathway of AOH improving DGP was predicted by molecular docking. Subsequently, DGP rat model was constructed using high-fat-irregular-diet, AOH intervention significantly reduced blood glucose levels, increased gastrointestinal propulsion rate, and improved gastric histological morphology in DGP rats. Meanwhile, AOH has been shown to regulate the SCF/c-kit signaling pathway and rebalance the gut microbiota, which may be closely related to its role in improving DGP. Taken together, AOH may play a protective role on DGP through multiple mechanisms, which might pave the road for development and utilization of AOH.

Assessment of the Binding of Pseudallecin A to Human Serum Albumin with Multi-Spectroscopic Analysis, Molecular Docking and Molecular Dynamic Simulation

The binding of pseudallecin A (PA), a potential antibiotic with strong inhibitory activities against Gram-positive Escherichia coli and Gram-negative Staphylococcus aureus, to human serum albumin (HSA) was explored. The interaction between them was assessed by multi-spectroscopic analysis, binding site competitive analysis, molecular docking and molecular dynamic simulation, showing the results as follows: PA effectively quenched the innate fluorescence of HSA by a static quenching process, formed a complex at a molar ratio of approximately 1 : 1 and performed an effective non-radiative energy transfer; the binding of PA to HSA was a spontaneous exothermic reaction driven by enthalpy with strong affinity and had a slight effect on the conformation of HSA; PA bound at site III of HSA and hydrogen bonds were the major binding forces to maintain the stability of the PA-HSA complex. Molecular dynamic simulation was performed to calculate the root mean square deviation (RMSD), root mean square fluctuation (RMSF) and radius of gyration (Rg) for this complex and effectively supported the spectroscopic outcome. These results meant that the delivery and distribution of PA as a water-insoluble molecule can be efficiently accomplished via HSA in human blood and, it has a good potential for future drug application and pharmacological development.

Network pharmacology combined with molecular docking and experimental verification to elucidate functional mechanism of Fufang Zhenzhu Tiaozhi against type 2 diabetes mellitus

Fufang Zhenzhu Tiaozhi (FTZ) capsules have been prescribed for treating glucose and lipid metabolism disorders such as type 2 diabetes mellitus (T2DM). However, the underlying mechanism remains unknown. In this study, network pharmacology and experimental verification were combined to investigate the mechanisms of FTZ in treating T2DM. A total of 176 active ingredients and 1169 corresponding targets were screened using biological databases. 598 potential targets of T2DM were retrieved from GeneCards, PharmGKB, OMIM, Drugbank, and TTD. The Venn diagram was employed to identify the 194 intersection targets, which were employed to construct the "Herb-Compound-Target" interacting networks. These common targets were also used to prepare a protein-protein interaction (PPI) network to uncover potential targets. The four core targets were docked to their corresponding targets for binding analysis. Additionally, the top-ranked poses of ingredients and the positive compounds from each protein were evaluated for stability using molecular dynamics. Our results suggest that core active ingredients such as kaempferol, luteolin, and baicalein have high binding affinity and stability with AKT1, PTGS2 (also known as COX-2), DPP4, and PAPRG. GO and KEGG analyses indicated that the treatment T2DM by FTZ might be related to different pathway like AMPK and EGFR pathways. The experimental validation results proved that kaempferol, luteolin, and baicalein could significantly inhibit the activity of DPP4 and COX-2, kaempferol and luteolin were also able to activate AKT and AMPK signaling pathway. This study further validated previous findings and enhanced our understanding of the potential effects of FTZ on T2DM.Communicated by Ramaswamy H. Sarma.

Black Phosphorus as a Targeting PPAR-γ Agonist to Reverse Chemoresistance in Patient-derived Organoids, Mice, and Pancreatic Tumor Cells

Black phosphorus (BP) exhibits significant potential for clinical applications. However, further research is necessary to uncover the unknown biological functions of BP and broaden its applications across various fields. This study investigates the potential of BP as a targeting PPAR-γ agonist to overcome chemoresistance in the treatment of pancreatic adenocarcinoma (PAAD) using 2D and 3D cell lines, patient-derived organoids (PDOs), and mouse models. RNA-sequencing analysis shows that BP treatment enriches differentially expressed genes in the PPAR pathway, and molecular modeling predicts the potential docking site between BP and PPAR-γ. Transcriptional activity assays are further to verify the activation of PPAR-γ. BP-activated PPAR-γ inhibits cancer stem cell (CSC) properties and expression of biomarkers such as CD44 and c-Myc, which are involved in chemoresistance. Notably, CD44 overexpression in tumor cells renders them susceptible to BP while insensitive to gemcitabine. This indicates that BP preferentially targets stem-like cells, which exhibit heightened resistance to chemotherapeutic drugs. A combination treatment strategy involving BP and gemcitabine is developed, demonstrating enhanced treatment efficacy of PAAD in both in vitro and in vivo models. Thus, BP serves as a PPAR-γ agonist capable of reversing chemoresistance, establishing it as a potent anti-tumor approach for the treatment of PAAD.

Possible molecular exploration of herbal pair Haizao-Kunbu in the treatment of Graves' disease by network pharmacology, molecular docking, and molecular dynamic analysis

Objective

To promote the development and therapeutic application of new medications, it is crucial to conduct a thorough investigation into the mechanism by which the traditional Chinese herb pair of Haizao-Kunbu (HK) treats Graves' disease (GD).

Materials and methods

Chemical ingredients of HK, putative target genes, and GD-associated genes were retrieved from online public databases. Using Cytoscape 3.9.1, a compound-gene target network was established to explore the association between prosperous ingredients and targets. STRING, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analyses visualized core targets and disease pathways. Additionally, we conducted a refined analysis of the binding interactions between active ingredients and their respective targets. To visualize these findings, we employed precise molecular docking techniques. Furthermore, we carried out molecular dynamics simulations to gain insights into the formation of more tightly bound complexes.

Results

We found that there were nine key active ingredients in HK, which mainly acted on 21 targets. These targets primarily regulated several biological processes such as cell population proliferation, protein phosphorylation, and regulation of kinase activity, and acted on PI3K-AKT and MAPK pathways to treat GD. Analysis of the molecular interaction simulation under computer technology revealed that the key targets exhibited strong binding activity to active ingredients, and Fucosterol-AKT1 and Isofucosterol-AKT1 complexes were highly stable in humans.

Conclusion

This study demonstrates that HK exerts therapeutic effects on GD in a multi-component, multi-target, and multi-pathway manner by regulating cell proliferation, differentiation, inflammation, and immunomodulatory-related targets. This study provides a theoretical foundation for further investigation into GD.

The Anti-Inflammatory Mechanism of Flaxseed Linusorbs on Lipopolysaccharide-Induced RAW 264.7 Macrophages by Modulating TLR4/NF-κB/MAPK Pathway

Flaxseed linusorbs (FLs), cyclic peptides derived from flaxseed oils, have shown multiple activities such as anticancer, antibacterial, and anti-inflammatory effects. However, the anti-inflammatory monomers of FLs and their mechanisms are still unclear. In this study, we have elucidated that FLs suppress the modulation of NF-κB/MAPK signaling pathways by targeting the inhibition of activating TLR4 in LPS-induced RAW 264.7 cells. Therefore, the transcription and expression of inflammatory cytokines (i.e., TNF-α, IL-1β, and IL-6) and inflammatory mediator proteins (i.e., iNos and Cox-2) were significantly suppressed by FLs. In addition, an in silico study discovered that eight monomers of FLs showed high-affinity bindings with TLR4. In silico data combined with HPLC results indicated that FLA and FLE, accounting for 44%, were likely the major anti-inflammatory monomers in FLs. In summary, FLA and FLE were proposed as the main anti-inflammatory active cyclopeptides via hindering TLR4/NF-κB/MAPK signaling pathways, suggesting the potential use of food-derived FLs as natural anti-inflammatory supplements in a daily diet.

Molecular docking in organic, inorganic, and hybrid systems: a tutorial review

Molecular docking simulation is a very popular and well-established computational approach and has been extensively used to understand molecular interactions between a natural organic molecule (ideally taken as a receptor) such as an enzyme, protein, DNA, RNA and a natural or synthetic organic/inorganic molecule (considered as a ligand). But the implementation of docking ideas to synthetic organic, inorganic, or hybrid systems is very limited with respect to their use as a receptor despite their huge popularity in different experimental systems. In this context, molecular docking can be an efficient computational tool for understanding the role of intermolecular interactions in hybrid systems that can help in designing materials on mesoscale for different applications. The current review focuses on the implementation of the docking method in organic, inorganic, and hybrid systems along with examples from different case studies. We describe different resources, including databases and tools required in the docking study and applications. The concept of docking techniques, types of docking models, and the role of different intermolecular interactions involved in the docking process to understand the binding mechanisms are explained. Finally, the challenges and limitations of dockings are also discussed in this review.

Graphical abstract

Colloidal stability and aggregation behavior of CdS colloids in aquatic systems: Effects of macromolecules, cations, and pH

Redox-dynamic environments such as river floodplains and paddy fields have been demonstrated to be important sources of CdS colloids. To date, the aggregation kinetics of CdS colloids had not yet been studied, and the structure and properties of macromolecules on the interaction between different macromolecules and CdS colloids, as well as the aggregation behavior of CdS colloids are unclear. This study investigated the colloidal stability of CdS colloids in model aqueous systems with various solution chemistry and representative of macromolecules. The results showed that increased electrolyte concentration destabilized CdS colloids by charge screening, with the cationic effect following Ca²⁺ > Mg²⁺ > K⁺ > Na⁺; Higher solution pH stabilized CdS colloids by raising the critical coagulation concentration from 33 to 56 mM NaCl. Electron microscopy and spectroscopy verified the strong interaction between macromolecules and CdS colloids, and macromolecule adsorbed on the surface of CdS to form a protective layer called "NOM corona". The interaction between macromolecules and CdS induced distinct aggregation behaviors in NaCl and CaCl₂ solutions. The steric repulsion generated by "NOM corona" significantly stabilized CdS colloids in NaCl solution, and the stabilizing order was consistent with the adsorbing capacity of macromolecules on CdS colloids, namely Bovine serum albumin (BSA) > sodium alginate (SA) > calf thymus DNA (DNA) > Suwannee River humic acid (HA). BSA and DNA also inhibited CdS colloids aggregation in the CaCl₂ solution due to the balance of steric hindrance, cation bridging, and electrostatic repulsion. For HA and SA, Ca²⁺ bridging and EDL compression contributed to their destabilization of CdS colloids in CaCl₂ solution. Macromolecules concentration affect corona formation that alter stability of CdS colloids. There results showed that the complex influences of solution chemistry and macromolecules on fate and transport of CdS colloids in environment. The findings will help to understand the potential risks of CdS colloids in environment.

Application of Molecular Simulation Methods in Food Science: Status and Prospects

Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.

Experimental Methods for the Biological Evaluation of Nanoparticle-Based Drug Delivery Risks

Many novel medical therapies use nanoparticle-based drug delivery systems, including nanomaterials through drug delivery systems, diagnostics, or physiologically active medicinal products. The approval of nanoparticles with advanced therapeutic and diagnostic potentials for applications in medication and immunization depends strongly on their synthesizing procedure, efficiency of functionalization, and biological safety and biocompatibility. Nanoparticle biodistribution, absorption, bioavailability, passage across biological barriers, and biodistribution are frequently assessed using bespoke and biological models. These methods largely rely on in vitro cell-based evaluations that cannot predict the complexity involved in preclinical and clinical studies. Therefore, assessing the nanoparticle risk has to involve pharmacokinetics, organ toxicity, and drug interactions manifested at multiple cellular levels. At the same time, there is a need for novel approaches to examine nanoparticle safety risks due to increased constraints on animal exploitation and the demand for high-throughput testing. We focus here on biological evaluation methodologies that provide access to nanoparticle interactions with the organism (positive or negative via toxicity). This work aimed to provide a perception regarding the risks associated with the utilization of nanoparticle-based formulations with a particular focus on assays applied to assess the cytotoxicity of nanomaterials.

Density functional theory and molecular docking study to lutein molecule for COVID-19 protease inhibitors

Since the beginning of the corona pandemic, numerous scientific projects have been conducted worldwide to investigate how the new virus can be combated. Researchers are developing various vaccines and drugs at full speed - with varying degrees of success. In this work, silico screening (molecular docking analysis) is performed on twenty natural compounds, which are expected to provide valuable lead molecules and medication to treat a new condition SARS-CoV-2. Our results indicate that out of the 20 compounds on the candidate list, lutein and Polydatin, natural components of fruits and vegetables (especially egg yolk and maize) have shown an excellent performance in our docking studies through a minimum binding energy of - 9.8 kcal/mol also - 7.4 kcal/mol, separately. This indicates their potential for the inhibitory molecular interactions against COVID-19. The main intent of the research is to analyse the protein components and investigate the molecules.

Magnetic Iron Nanoparticles: Synthesis, Surface Enhancements, and Biological Challenges

This review focuses on the role of magnetic nanoparticles (MNPs), their physicochemical properties, their potential applications, and their association with the consequent toxicological effects in complex biologic systems. These MNPs have generated an accelerated development and research movement in the last two decades. They are solving a large portion of problems in several industries, including cosmetics, pharmaceuticals, diagnostics, water remediation, photoelectronics, and information storage, to name a few. As a result, more MNPs are put into contact with biological organisms, including humans, via interacting with their cellular structures. This situation will require a deeper understanding of these particles’ full impact in interacting with complex biological systems, and even though extensive studies have been carried out on different biological systems discussing toxicology aspects of MNP systems used in biomedical applications, they give mixed and inconclusive results. Chemical agencies, such as the Registration, Evaluation, Authorization, and Restriction of Chemical substances (REACH) legislation for registration, evaluation, and authorization of substances and materials from the European Chemical Agency (ECHA), have held meetings to discuss the issue. However, nanomaterials (NMs) are being categorized by composition alone, ignoring the physicochemical properties and possible risks that their size, stability, crystallinity, and morphology could bring to health. Although several initiatives are being discussed around the world for the correct management and disposal of these materials, thanks to the extensive work of researchers everywhere addressing the issue of related biological impacts and concerns, and a new nanoethics and nanosafety branch to help clarify and bring together information about the impact of nanoparticles, more questions than answers have arisen regarding the behavior of MNPs with a wide range of effects in the same tissue. The generation of a consolidative framework of these biological behaviors is necessary to allow future applications to be manageable.

Potential Molecular Mechanisms of Ephedra Herb in the Treatment of Nephrotic Syndrome Based on Network Pharmacology and Molecular Docking

Objective

To explore the possible mechanisms of Ephedra herb (EH) in the treatment of nephrotic syndrome (NS) by using network pharmacology and molecular docking in this study.

Methods

Active ingredients and related targets of EH were obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, and the gene names corresponding to the proteins were found through the UniProt database. Then, target genes related to NS were screened out from GeneCards, PharmGKB, and OMIM databases. Next, the intersection targets were obtained successfully through Venn diagram, which were also seen as key target genes of EH and NS. Cytoscape 3.9.0 software was used to construct the effective “active ingredient-target” network diagram, and “drug-ingredient-target-disease (D-I-T-D)” network diagram. After that, the STRING database was used to construct a protein-protein interaction (PPI) network. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment involved in the targets were performed by the DAVID database and ClueGO plugin in Cytoscape. Finally, AutoDockTools software was used for molecular docking to verify the binding strength between main active ingredients and key target proteins.

Results

A total of 22 main active ingredients such as quercetin, kaempferol, luteolin, and naringenin were obtained, which could act on 105 targets related to NS. Through PPI network, 53 core targets such as AKT1, TNF, IL6, VEGFA, and IL1B were found, which might play a crucial role in the treatment of NS. Meanwhile, these targets were significantly involved in PI3K-Akt signaling pathway, TNF signaling pathway, AGE-RAGE signaling pathway, hepatitis B, and pathways in cancer through GO and KEGG enrichment analysis. The docking results indicated that active ingredients such as kaempferol, luteolin, quercetin, and naringenin all had good binding to the target protein AKT1 or TNF. Among them, luteolin and naringenin binding with AKT1 showed the best binding energy (-6.2 kcal/mol).

Conclusion

This study indicated that the potential mechanism of EH in treating NS may be related to PI3K-Akt signaling pathway, TNF signaling pathway, and AGE-RAGE signaling pathway, which provided better approaches for exploring the mechanism in treating NS and new ideas for further in vivo and in vitro experimental verifications.

Influence of protein configuration on aggregation kinetics of nanoplastics in aquatic environment

Aggregation kinetics of nanoplastics in aquatic environment are influenced by their interactions with proteins having different structures and properties. This study employed time-resolved dynamic light scattering (TR-DLS) to investigate the effects of 5 proteins (bovine hemoglobin (BHb), bovine (BSA) and human serum albumin (HSA), collagen type I (Col I), and bovine casein (CS)) on aggregation kinetics of polystyrene nanoplastics (PSNPs) under natural water conditions, which were simulated using various ionic strength (1-1000 mM NaCl and 0.01-100 mM CaCl₂), pH (3-9), and protein concentration (1-5 mg/L of total organic carbon). The results indicated that the interactions between proteins and PSNPs strongly depended on electrostatic properties, protein structures, and solution chemistries, which induced distinct aggregation behaviors in NaCl and CaCl₂ solutions. Electrostatic repulsion and steric hindrance dominated their interactions in NaCl solution by stabilizing PSNPs with the order of spherical BSA and disordered CS > heart-shaped HSA > fibrillar Col I; whereas positively charged BHb destabilized PSNPs with aggregation rate of 1.71 nm/s at 300 mM NaCl. In contrast, at CaCl₂ concentration below 20 mM, proteins destabilized PSNPs following the sequence of HSA > BHb > Col I > BSA depending on counterbalance among double layer compression, cation bridging, and steric hindrance; whereas CS stabilized PSNPs by precipitating Ca²⁺ that inhibited charge screening effect. Both protein concentration and solution pH affected protein corona formation, surface charge, and protein structure that altered stability of PSNPs. Characterizations using fluorescence spectroscopy, circular dichroism, and two-dimensional correlation analysis spectroscopy showed fluorescence quenching and ellipticity reduction of proteins, indicating strong adsorption affinity between PSNPs and proteins. The study provides insight to how protein configuration and water chemistry affect fate and transport of nanoplastics in aquatic environment.

Graphene oxide/gallium nanoderivative as a multifunctional modulator of osteoblastogenesis and osteoclastogenesis for the synergistic therapy of implant-related bone infection

Currently, implant-associated bacterial infections account for most hospital-acquired infections in patients suffering from bone fractures or defects. Poor osseointegration and aggravated osteolysis remain great challenges for the success of implants in infectious scenarios. Consequently, developing an effective surface modification strategy for implants is urgently needed. Here, a novel nanoplatform (GO/Ga) consisting of graphene oxide (GO) and gallium nanoparticles (GaNPs) was reported, followed by investigations of its in vitro antibacterial activity and potential bacterium inactivation mechanisms, cytocompatibility and regulatory actions on osteoblastogenesis and osteoclastogenesis. In addition, the possible molecular mechanisms underlying the regulatory effects of GO/Ga nanocomposites on osteoblast differentiation and osteoclast formation were clarified. Moreover, an in vivo infectious microenvironment was established in a rat model of implant-related femoral osteomyelitis to determine the therapeutic efficacy and biosafety of GO/Ga nanocomposites. Our results indicate that GO/Ga nanocomposites with excellent antibacterial potency have evident osteogenic potential and inhibitory effects on osteoclast differentiation by modulating the BMP/Smad, MAPK and NF-κB signaling pathways. The in vivo experiments revealed that the administration of GO/Ga nanocomposites significantly inhibited bone infections, reduced osteolysis, promoted osseointegration located in implant-bone interfaces, and resulted in satisfactory biocompatibility. In summary, this synergistic therapeutic system could accelerate the bone healing process in implant-associated infections and can significantly guide the future surface modification of implants used in bacteria-infected environments.

An overview on the exploring the interaction of inorganic nanoparticles with microtubules for the advancement of cancer therapeutics

Targeting microtubules (MTs), dynamic and stable proteins in cells, by different ligands have been reported to be a potential strategy to combat cancer cells. Inorganic nanoparticles (NPs) have been widely used as anticancer, antibacterial, and free radical scavenging agents, where the come in contact with biological macromolecules. The interaction between the NPs and biological macromolecules like MTs frequently occurs through different mechanisms. A prerequisite for a detailed exploration of MT structures and functions for biomedical applications like cancer therapy is to investigate profoundly the mechanisms involved in MT-NP interactions, for which the full explanation and characterization of the parameters that are responsible for the formation of a NP-protein complex are crucial. Therefore, in view of the fact that the goal of the rational NP-based future drug design and new therapies is to rely on the information of the structural details and protein-NPs binding mechanisms to manipulate the process of developing new potential drugs, a comprehensive investigation of the essence of the molecular recognition/interaction is also of considerable importance. In the present review, first, the microtubule (MT) structure and its binding sites upon interaction with MT stabilizing agents (MSAs) and MT destabilizing agents (MDAs) are introduced and rationalized. Next, MT targeting in cancer therapy and interaction of NPs with MTs are discussed. Furthermore, interaction of NPs with proteins and the manipulation of protein corona (PC), experimental techniques, and direct interaction of NPs with MTs, are discussed, and finally the challenges and future perspective of the field are introduced. We envision this review can provide useful information on the manipulation of the MT lattice for the progress of cancer nanomedicine.

Experimental and Computational Nanotoxicology-Complementary Approaches for Nanomaterial Hazard Assessment

The growing development and applications of nanomaterials lead to an increasing release of these materials in the environment. The adverse effects they may elicit on ecosystems or human health are not always fully characterized. Such potential toxicity must be carefully assessed with the underlying mechanisms elucidated. To that purpose, different approaches can be used. First, experimental toxicology consisting of conducting in vitro or in vivo experiments (including clinical studies) can be used to evaluate the nanomaterial hazard. It can rely on variable models (more or less complex), allowing the investigation of different biological endpoints. The respective advantages and limitations of in vitro and in vivo models are discussed as well as some issues associated with experimental nanotoxicology. Perspectives of future developments in the field are also proposed. Second, computational nanotoxicology, i.e., in silico approaches, can be used to predict nanomaterial toxicity. In this context, we describe the general principles, advantages, and limitations especially of quantitative structure–activity relationship (QSAR) models and grouping/read-across approaches. The aim of this review is to provide an overview of these different approaches based on examples and highlight their complementarity.

Surface-Decorated Graphene Oxide Sheets with Copper Nanoderivatives for Bone Regeneration: An In Vitro and In Vivo Study Regarding Molecular Mechanisms, Osteogenesis, and Anti-infection Potential

It has been previously reported that graphene oxide/copper nanoderivative (GO/Cu)-incorporated chitosan/hyaluronic acid scaffolds might be promising wound dressings for the management of infected wound healing. The aim of the present research is to deeply explore the potential antimicrobial mechanisms and synergistic osteogenic activity, as well as the in vivo anti-infective behavior of GO/Cu nanocomposites, making them possible candidates for establishing implantable biomaterials for the repair of infected bone defects. The antibacterial mechanisms of the nanocomposites were explored through the examination of membrane integrity, oxidative stress, and metabolic enzyme activities. Then, the cytocompatibility with bone mesenchymal stem cells (rBMSCs) and osteogenic potential were confirmed, and a subcutaneous bacterial infection model in rats was also established to verify the in vivo anti-infective property and biosafety of the nanocomposites. It was found that leakage of adenosine triphosphate, proteins, and reducing sugars from the bacterial cells, indicative of damaged permeability of bacterial membranes, and promoted production of reactive oxygen species and disordered metabolic enzyme activities in response to oxidative stress were possible molecular mechanisms responsible for the synergistic antibacterial effects of the GO/Cu nanocomposites. Additionally, good cytocompatibility with rBMSCs and promoted osteogenic differentiation were found in GO/Cu nanocomposites (mass ratio = 2:1), which also demonstrated satisfactory in vivo anti-infective performance, reduced inflammation, and acceptable biosafety. Based on our results, damaged bacterial membranes, increased ROS production, and disorders of crucial enzyme metabolism were the main antibacterial mechanisms involved in the bacterium-killing events caused by the GO/Cu nanocomposites, which also showed enhanced osteogenic activity, in vivo anti-infective capability, and acceptable cytocompatibility and biosafety. Therefore, GO/Cu (2:1) nanocomposites are a potential strategy for improving the biological performance of current bone substitutes used for combating bacterial-contaminated bone defects.

High affinity protein surface binding through co-engineering of nanoparticles and proteins

Control over supramolecular recognition between proteins and nanoparticles (NPs) is of fundamental importance in therapeutic applications and sensor development. Most NP-protein binding approaches use 'tags' such as biotin or His-tags to provide high affinity; protein surface recognition provides a versatile alternative strategy. Generating high affinity NP-protein interactions is challenging however, due to dielectric screening at physiological ionic strengths. We report here the co-engineering of nanoparticles and protein to provide high affinity binding. In this strategy, 'supercharged' proteins provide enhanced interfacial electrostatic interactions with complementarily charged nanoparticles, generating high affinity complexes. Significantly, the co-engineered protein-nanoparticle assemblies feature high binding affinity even at physiologically relevant ionic strength conditions. Computational studies identify both hydrophobic and electrostatic interactions as drivers for these high affinity NP-protein complexes.

Potential inhibitors of the main protease of SARS-CoV-2 and modulators of arachidonic acid pathway: Non-steroidal anti-inflammatory drugs against COVID-19

The main protease of SARS-CoV-2 is one of the key targets to develop and design antiviral drugs. There is no general agreement on the use of non-steroidal anti-inflammatory drugs (NSAIDs) in COVID-19. In this study, we investigated NSAIDs as potential inhibitors for chymotrypsin-like protease (3CLpro) and the main protease of the SARS-CoV-2 to find out the best candidates, which can act as potent inhibitors against the main protease. We also predicted the effect of NSAIDs on the arachidonic pathway and evaluated the hepatotoxicity of the compounds using systems biology techniques. Molecular docking was conducted via AutoDock Vina to estimate the interactions and binding affinities between selected NSAIDs and the main protease. Molecular docking results showed the presence of 10 NSAIDs based on lower binding energy (kcal/mol) toward the 3CLpro inhibition site compared to the co-crystal native ligand Inhibitor N3 (-6.6 kcal/mol). To validate the docking results, molecular dynamic (MD) simulations on the top inhibitor, Talniflumate, were performed. To obtain differentially-expressed genes under the 27 NSAIDs perturbations, we utilized the L1000 final Z-scores from the NCBI GEO repository (GSE92742). The obtained dataset included gene expression profiling signatures for 27 NSAIDs. The hepatotoxicity of NSAIDs was studied by systems biology modeling of Disturbed Metabolic Pathways. This study highlights the new application of NSAIDs as anti-viral drugs used against COVID-19. NSAIDs may also attenuate the cytokine storm through the downregulation of inflammatory mediators in the arachidonic acid pathway.

Current Strategies in Assessment of Nanotoxicity: Alternatives to In Vivo Animal Testing

Millions of experimental animals are widely used in the assessment of toxicological or biological effects of manufactured nanomaterials in medical technology. However, the animal consciousness has increased and become an issue for debate in recent years. Currently, the principle of the 3Rs (i.e., reduction, refinement, and replacement) is applied to ensure the more ethical application of humane animal research. In order to avoid unethical procedures, the strategy of alternatives to animal testing has been employed to overcome the drawbacks of animal experiments. This article provides current alternative strategies to replace or reduce the use of experimental animals in the assessment of nanotoxicity. The currently available alternative methods include in vitro and in silico approaches, which can be used as cost-effective approaches to meet the principle of the 3Rs. These methods are regarded as non-animal approaches and have been implemented in many countries for scientific purposes. The in vitro experiments related to nanotoxicity assays involve cell culture testing and tissue engineering, while the in silico methods refer to prediction using molecular docking, molecular dynamics simulations, and quantitative structure-activity relationship (QSAR) modeling. The commonly used novel cell-based methods and computational approaches have the potential to help minimize the use of experimental animals for nanomaterial toxicity assessments.

Exploration of the Molecular Mechanism of Polygonati Rhizoma in the Treatment of Osteoporosis Based on Network Pharmacology and Molecular Docking

OBJECTIVE

To explore the effective components and mechanism of Polygonati Rhizoma (PR) in the treatment of osteoporosis (OP) based on network pharmacology and molecular docking methods.

METHODS

The effective components and predicted targets of PR were obtained through the Traditional Chinese Medicine Systems Pharmacology and Analysis Platform (TCMSP) database. The disease database was used to screen the disease targets of OP. The obtained key targets were uploaded to the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database for protein-protein interaction (PPI) network analysis. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of key targets. Analysis and docking verification of chemical effective drug components and key targets were performed with IGEMDOCK software.

RESULTS

A total of 12 chemically active components, 84 drug target proteins and 84 common targets related to drugs and OP were obtained. Key targets such as JUN, TP53, AKT1, ESR1, MAPK14, AR and CASP3 were identified through PPI network analysis. The results of enrichment analysis showed that the potential core drug components regulate the HIF-1 signaling pathway, PI3K-Akt signaling pathway, estrogen signaling pathway and other pathways by intervening in biological processes such as cell proliferation and apoptosis and estrogen response regulation, with an anti-OP pharmacological role. The results of molecular docking showed that the key targets in the regulatory network have high binding activity to related active components.

CONCLUSIONS

PR may regulate OP by regulating core target genes, such as JUN, TP53, AKT1, ESR1, AR and CASP3, and acting on multiple key pathways, such as the HIF-1 signaling pathway, PI3K-Akt signaling pathway, and estrogen signaling pathway.