A Novel Approach to Evaluate Titanium Dioxide Nanoparticle–Protein Interaction Through Docking: An Insight into Mechanism of Action

An insight into in silico strategies used for exploration of medicinal utility and toxicology of nanomaterials

Nanomaterials (NMs) and the exploration of their comprehensive uses is an emerging research area of interest. They have improved physicochemical and biological properties and diverse functionality owing to their unique shape and size and therefore they are being explored for their enormous uses, particularly as medicinal and therapeutic agents. Nanoparticles (NPs) including metal and metal oxide-based NPs have received substantial consideration because of their biological applications. Computer-aided drug design (CADD) involving different strategies like homology modelling, molecular docking, virtual screening (VS), quantitative structure-activity relationship (QSAR) etc. and virtual screening hold significant importance in CADD used for lead identification and target identification. Despite holding importance, there are very few computational studies undertaken so far to explore their binding to the target proteins and macromolecules. Although the structural properties of nanomaterials are well documented, it is worthwhile to know how they interact with the target proteins making it a pragmatic issue for comprehension. This review discusses some important computational strategies like molecular docking and simulation, Nano-QSAR, quantum chemical calculations based on Density functional Theory (DFT) and computational nanotoxicology. Nano-QSAR modelling, based on semiempirical calculations and computational simulation can be useful for biomedical applications, whereas the DFT calculations make it possible to know about the behaviour of the material by calculations based on quantum mechanics, without the requirement of higher-order material properties. Other than the beneficial interactions, it is also important to know the hazardous consequences of engineered nanostructures and NPs can penetrate more deeply into the human body, and computational nanotoxicology has emerged as a potential strategy to predict the delirious effects of NMs. Although computational tools are helpful, yet more studies like in vitro assays are still required to get the complete picture, which is essential in the development of potent and safe drug entities.

Comparative molecular docking and toxicity between carbon-capped metal oxide nanoparticles and standard drugs in cancer and bacterial infections

Introduction

Nanoparticles (NPs) are of great interest in the design of various drugs due to their high surface-to-volume ratio, which result from their unique physicochemical properties. Because of the importance of examining the interactions between newly designed particles with different targets in the case of various diseases, techniques for examining the interactions between these particles with different targets, many of which are proteins, are now very common.

Methods

In this study, the interactions between metal oxide nanoparticles (MONPs) covered with a carbon layer (Ag2O3, CdO, CuO, Fe2O3, FeO, MgO, MnO, and ZnO NPs) and standard drugs related to the targets of Cancer and bacterial infections were investigated using the molecular docking technique with AutoDock 4.2.6 software tool. Finally, the PRO TOX-II online tool was used to compare the toxicity (LD50) and molecular weight of these MONPs to standard drugs.

Results

According to the data obtained from the semi flexible molecular docking process, MgO and Fe2O3 NPs performed better than standard drugs in several cases. MONPs typically have a lower 50% lethal dose (LD50) and a higher molecular weight than standard drugs. MONPs have shown a minor difference in binding energy for different targets in three diseases, which probably can be attributed to the specific physicochemical and pharmacophoric properties of MONPs.

Conclusion

The toxicity of MONPs is one of the major challenges in the development of drugs based on them. According to the results of these molecular docking studies, MgO and Fe2O3 NPs had the highest efficiency among the investigated MONPs.

Emerging Frontiers in Nanotechnology for Precision Agriculture: Advancements, Hurdles and Prospects

This review article provides an extensive overview of the emerging frontiers of nanotechnology in precision agriculture, highlighting recent advancements, hurdles, and prospects. The benefits of nanotechnology in this field include the development of advanced nanomaterials for enhanced seed germination and micronutrient supply, along with the alleviation of biotic and abiotic stress. Further, nanotechnology-based fertilizers and pesticides can be delivered in lower dosages, which reduces environmental impacts and human health hazards. Another significant advantage lies in introducing cutting-edge nanodiagnostic systems and nanobiosensors that monitor soil quality parameters, plant diseases, and stress, all of which are critical for precision agriculture. Additionally, this technology has demonstrated potential in reducing agro-waste, synthesizing high-value products, and using methods and devices for tagging, monitoring, and tracking agroproducts. Alongside these developments, cloud computing and smartphone-based biosensors have emerged as crucial data collection and analysis tools. Finally, this review delves into the economic, legal, social, and risk implications of nanotechnology in agriculture, which must be thoroughly examined for the technology’s widespread adoption.

Mechano-cytoskeleton remodeling mechanism and molecular docking studies on nanosurface technology: Titania nanotube arrays

In biomedical implant technology, nanosurface such as titania nanotube arrays (TNA) could provide better cellular adaptation, especially for long-term tissue acceptance response. Mechanotransduction activities of TNA nanosurface could involve the cytoskeleton remodeling mechanism. However, there is no clear insight into TNA mechano-cytoskeleton remodeling activities, especially computational approaches. Epithelial cells have played critical interface between biomedical implant surface and tissue acceptance, particularly for long-term interaction. Therefore, this study investigates genomic responses that are responsible for cell-TNA mechano-stimulus using epithelial cells model. Findings suggested that cell-TNA interaction may improve structural and extracellular matrix (ECM) support on the cells as an adaptive response toward the nanosurface topography. More specifically, the surface topography of the TNA might improve the cell polarity and adhesion properties via the interaction of the plasma membrane and intracellular matrix responses. TNA nanosurface might engross the cytoskeleton remodeling activities for multidirectional cell movement and cellular protrusions on TNA nanosurface. These observations are supported by the molecular docking profiles that determine proteins' in silico binding mechanism on TNA. This active cell-surface revamping would allow cells to adapt to develop a protective barrier toward TNA nanosurface, thus enhancing biocompatibility properties distinctly for long-term interaction. The findings from this study will be beneficial toward nano-molecular knowledge of designing functional nanosurface technology for advanced medical implant applications.

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

The high frequency of using engineered nanoparticles in various medical applications entails a deep understanding of their interaction with biological macromolecules. Molecular docking simulation is now widely used to study the binding of different types of nanoparticles with proteins and nucleic acids. This helps not only in understanding the mechanism of their biological action but also in predicting any potential toxicity. In this review, the computational techniques used in studying the nanoparticles interaction with biological macromolecules are covered. Then, a comprehensive overview of the docking studies performed on various types of nanoparticles will be offered. The implication of these predicted interactions in the biological activity and/or toxicity is also discussed for each type of nanoparticles.

Tough synthetic spider-silk fibers obtained by titanium dioxide incorporation and formaldehyde cross-linking in a simple wet-spinning process

Due to its unique mechanical properties, spider silk shows great promise as a strong super-thin fiber in many fields. Although progress has been made in the field of synthesizing spider-silk fiber from recombinant spidroin (spider silk protein) in the last few decades, methods to obtain synthetic spider-silk fibers as tough as natural silk from small-sized recombinant protein with a simple spinning process have eluded scientists. In this paper, a recombinant spidroin (MW: 93.4 kDa) was used to spin tough synthetic spider-silk fibers with a simple wet-spinning process. Titanium oxide incorporation and formaldehyde cross-linking were used to improve the mechanical properties of synthetic spider-silk fibers. Fibers treated with incorporation or/and cross-linking varied in microstructure, strength and extensibility while all exhibited enhanced strength and toughness. In particular, one fiber possessed a toughness of 249 ± 22 MJ/m³. This paper presents a new method to successfully spin tough spider-silk fibers in a simple way.

Translocation of intranasal (i.n.) instillation of different-sized cerium dioxide (CeO2) particles: potential adverse effects in mice

Cerium oxide (CeO₂), one of many engineered nanomaterials (ENMs), is composed primarily of metal oxides, such as cerium oxide (CeO₂). CeO₂-containing materials are widely used as a polishing agent for glass mirrors, plate glass, television tubes, ophthalmic lenses, and precision optics. The widespread use of this nanomaterial (NM) resulted in increased environmental contamination levels and consequent human exposure. However, the influence of Ce on humans remains to be determined. The aim of this study was to expose female ICR mice to varying nanoparticle sizes of 35 nm, 300 nm as well as a mixture of 1-5 µM CeO₂ particles through intranasal (i.n.) instillation at 40 mg/kg dose on day 1, 3 and 5, and the experiment terminated on day 7. Histopathology findings demonstrated that hydropic degeneration was prominently associated with hemorrhage in renal cortex and medulla in all CeO₂-administered groups. In liver of CeO₂-exposed mice, hydropic degeneration was also prominent. Serum chemistries also indicated signs of renal and hepatic lesion as evidenced by significantly decreased serum levels of total bilirubin (TBIL) and total phosphate (TP) and activity of alkaline phosphatase (ALP). ICP-MS analysis group demonstrated that Ce levels were not significantly higher in liver and kidneys of mice exposed to 35 nm CeO₂. An increase in Ce content was observed in hepatic and renal tissues of mice exposed to 300 nm or 1-5 µM CeO_2. The levels of Ce were similar in these two groups suggesting a threshold level of Ce was attained regardless of NP size. Data thus demonstrated that i.n. instillation of different-sized CeO₂ particles translocated to liver and kidney and that size difference of CeO₂ particles did not exert significant in the observed histopathology responses.

Insights into the interaction of key biofilm proteins in Pseudomonas aeruginosa PAO1 with TiO2 nanoparticle: An in silico analysis

Pseudomonas aeruginosa is a pathogenic biofilm forming bacteria which exist in wide range of environments such as water, soil and human body. In an earlier study, we used a system biology approach based analysis of biofilm forming genes of P. aeruginosa and their possible role in TiO₂ nanoparticle binding. The major protein of P. aeruginosa targeted by TiO₂ was found to be KatA, a major catalase required for H₂O₂ resistance and acute virulence and the direct interacting protein partners of KatA were found to be DnaK, Hfq, RpoA and RpoS. To understand the protein-protein physical interaction characteristic of these key proteins involved in biofilm related processes, homology modeling, docking and molecular dynamic simulation were performed. For all these proteins, physical and chemical properties, amino acid composition, nest and cleft analysis were performed using online tools. The interactions between TiO₂NPs-KatA and four protein-protein complexes such as KatA-DnaK, KatA-Hfq, KatA-RpoA and KatA-RpoS were studied. Our results indicate that all four key proteins and TiO₂NPs can have stable complexation with KatA. The study has given enough clues to understand the interaction of TiO₂NPs with P. aeruginosa biofilm in natural environment. Further investigations could lead to development of TiO₂NPs based therapeutic and sanitary interventions to combat this pathogenic bacterium.

CASTp 3.0: computed atlas of surface topography of proteins

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

Bovine serum albumin interacts with silver nanoparticles with a "side-on" or "end on" conformation

As the nanoparticles (NPs) enter into the biological interface, they have to encounter immediate and first exposure to many proteins of different concentrations. The physicochemical interaction of NPs and proteins is greatly influenced not only by the number and type of proteins; but also the surface chemistry of NPs. To analyze the effects of NPs on proteins, the interaction between bovine serum albumin (BSA) and silver nanoparticles (AgNPs) at different concentrations were investigated. The interaction, BSA conformations, kinetics and adsorption were analyzed by UV-Visible spectrophotometer, dynamic light scattering (DLS), FT-IR spectroscopy and fluorescence quenching. DLS, FTIR and UV-visible spectrophotometric analysis confirms the interaction with minor alterations in size of the protein. Fluorescence quenching analysis confirms the side-on or end-on interaction of 1.5 molecules of BSA to AgNP. Further, pseudo-second order kinetics was determined with equilibrium contact-time of 30 min. The data of the present study determines the detailed evaluation of BSA adsorption on AgNP along with mechanism, kinetics and isotherm of the adsorption.

Assessment on the antibacterial activity of nanosized silica derived from hypercoordinated silicon(iv) precursors

Silica nanoparticles were synthesized through a versatile sol–gel combustion method from hydrazide based hypercoordinated silicon complexes derived from the reaction of silicon tetrachloride with O-silylated hydrazide derivatives.