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.

Radiation induced DNA damage and its protection by a gadolinium(III) complex: Spectroscopic, molecular docking and gel electrophoretic studies

The current work describes the efficacy of an artificially synthesized Gd(III) complex as a potential radioprotecting molecule. The work involves utilization of spectroscopic and electrophoretic techniques to investigate the radioprotecting behavior of the Gd(III) complex. Spectroscopic studies revealed that the complex interacted strongly with DNA while molecular docking studies suggested groove binding through H-bond formation and other non-covalent interactions. The Gd(III) complex was found to impart 94% and 91% protection to irradiatively damaged DNA at radiation doses of 20 and 25 Gy respectively. The protection is believed to occur via radical scavenging mechanism and the antioxidant behavior of the complex suggested a strong radical scavenging property.

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.

Studies on the interaction of a synthetic nitro-flavone derivative with DNA: A multi-spectroscopic and molecular docking approach

Interaction of a ligand with DNA is often the basis of drug action of many molecules. Flavones are important in this regard as their structural features confer them the ability to bind to DNA. 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO) is an important biologically active synthetic flavone derivative. We are therefore interested in studying its interaction with DNA. Absorption spectroscopy studies included standard and reverse titration, effect of ionic strength on titration, determination of stoichiometry of binding and thermal denaturation. Spectrofluorimetry techniques included fluorimetric titration, quenching studies and fluorescence displacement assay. Assessment of relative viscosity and estimation of thermodynamic parameters from CD spectral studies were also undertaken. Furthermore, molecular docking analyses were also done with different short DNA sequences. The fluorescent flavone 4NCO reversibly interacted with DNA through partial intercalation as well as minor-groove binding. The binding constant and the number of binding sites were of the order 10⁴ M^-1 and 1 respectively. The binding stoichiometry with DNA was found to be 1:1. The nature of the interaction of 4NCO with DNA was hydrophobic in nature and the process of binding was spontaneous, endothermic and entropy-driven. The flavone also showed a preference for binding to GC rich sequences. The study presents a profile for structural and thermodynamic parameters, for the binding of 4NCO with DNA. DNA is an important target for ligands that are effective against cell proliferative disorders. In this regard, the molecule 4NCO is important since it can exert its biological activity through its DNA binding ability and can be a potential drug candidate.

Silica nanoparticles induce conformational changes of tau protein and oxidative stress and apoptosis in neuroblastoma cell line

The adverse effects of SiO₂ NPs on the biological systems like nervous system have not been well explored. This study aimed to evaluate the toxicity of SiO₂ NPs on the nervous system in vitro. Therefore, human tau protein and neuroblastoma cell line (SH-SY5Y) were used as targets. In this study we examined the side effects of SiO₂ NPs on tau protein structure using several techniques including CD, ANS fluorescence, UV-vis (360 nm), Congo red absorbance, TEM, and molecular dynamic. Also, the cytotoxicity effects of SiO₂ NPs against SH-SY5Y cell line were evaluated using MTT, ROS and apoptotic assays. Spectroscopic and molecular dynamic investigations indicated that natively unfolded structure of tau in the presence of SiO₂ NPs experienced a partially folded and amorphous aggregated structure. Cellular assay demonstrated that SiO₂ NPs exerted cytotoxic effect on SH-SY5Y cells through ROS accumulation and induction of apoptosis. Overall, these findings proved that SiO₂ NPs could induce adverse effects on tau structure and SH-SY5Y cell integrity. Moreover, further studies are required to elucidate the molecular mechanism of SiO₂ NPs-induced side effects in vivo.

Biocompatible properties of nano-drug carriers using TiO2-Au embedded on multiwall carbon nanotubes for targeted drug delivery

Nanomaterial-based drug carriers have become a hot spot of research at the interface of nanotechnology and biomedicine because they allow efficient loading, targeted delivery, controlled release of drugs, and therefore are promising for biomedical applications. The current study made an attempt to decorate the multiwalled carbon nanotubes (MWCNT) with titanium dioxide‑gold nanoparticles in order to enhance the biocompatibility for doxorubicin (DOX) delivery. The successful synthesis of nano drug carrier (NDC) was confirmed by XRD, XPS and UV-Visible spectroscopy. FESEM and TEM revealed that the morphology of NDC can be controlled by manipulating the reaction duration, MWCNT concentration and TiO₂-Au source concentration. Results showed that TiO₂ and Au nanoparticles were well coated on MWCNT. NDC had finely tuned biocompatible properties, as elucidated by hemolytic and antimicrobial assays. NDC also showed a high antioxidant potential, 80.7% expressed as ascorbic acid equivalents. Commercial DOX drug was utilized to treat A549 and MCF7 cancer cell lines showing improved efficiency by formulating it with NDC, which selectively delivered at the pH 5.5 with drug loading capacity of 0.45 mg/mL. The drug releasing capacity achieved by NDC was 90.66% for 10 h, a performance that far encompasses a wide number of current literature reports.

Optimal conditions for producing bactericidal sodium hyaluronate-TiO2 bionanocomposite and its characterization

In this research, the creation of optimum conditions for the formation of sodium hyaluronate-TiO₂ bionanocomposite and its antibacterial effect on gram positive and gram negative bacteria was evaluated. The Fourier transform infrared spectroscopy spectra, scanning electron microscopy images and energy dispersive X-ray spectroscopy pattern confirmed the formation of the bionanocomposite. Thermogravimetric analysis and differential thermal analysis indicated that the thermal stability rate had significantly improved with formation of the bionanocomposite. Nine experiments were designed based on the Taguchi method by applying different proportions of sodium hyaluronate biopolymer and TiO₂ nanoparticles at different stirring times. Bionanocomposite produced under conditions of experiment 5 (TiO₂ 4mg/ml, sodium hyaluronate 1mg/ml and stirring time of 90min) and experiment 9 (TiO₂ 8mg/ml, sodium hyaluronate 2mg/ml and stirring time of 60min) completely prevented the growth of Staphylococcus aureus and Escherichia coli. It can be concluded that sodium hyaluronate-TiO₂ bionanocomposite can be used as an effective antimicrobial compound in food, pharmaceutical, medical and environmental sectors.

Pharmacological evaluation of poly(3-methylthiophene) and its titanium(IV)phosphate nanocomposite: DNA interaction, molecular docking, and cytotoxic activity

Cancer and pathogenic microbial diseases have terribly affected human health over a longer period of time. In response to the increasing casualties due to cancer and microbial diseases, unique poly(3-methylthiophene) and poly(3-methylthiophene)-titanium(IV)phosphate composite were prepared via in-situ oxidative chemical polymerization in this work. The poly(3-methylthiophene) and poly(3-methylthiophene)-titanium(IV)phosphate composite were well characterized by Fourier transform infrared spectroscopy and field emission scanning electron microscopy. DNA binding studies by UV-Visible and fluorescence spectroscopic investigations indicated strong binding affinities of poly(3-methylthiophene) and poly(3-methylthiophene)-titanium(IV)phosphate nanocomposite; leading to structural damage of DNA. Poly(3-methylthiophene)-titanium(IV)phosphate nanocomposite showed stronger interactions with DNA as compared to poly(3-methylthiophene) and from dye displacement assay it was confirmed that mode of binding of both the formulations was intercalative. The antimicrobial screening revealed that polymer and its composite displayed stronger antibacterial effects than ampicillin against Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa and Salmonella typhimurium. Besides, the poly(3-methylthiophene) and poly(3-methylthiophene)-titanium(IV)phosphate nanocomposite showed dose dependent effects towards estrogen receptor positive breast cancer (MCF-7) and estrogen receptor negative breast cancer (MDA-MB-231) cell lines; with poly(3-methylthiophene)-titanium(IV)phosphate nanocomposite showing better activities against both cell lines. In all in-vitro biological investigations, poly(3-methylthiophene)-titanium(IV)phosphate composite showed superior properties to that of the pure poly(3-methylthiophene), which encouraged us to suggest its potential as future therapeutic gear in drug delivery and other allied fields.

Nano-hydroxyapatite/β-CD/chitosan nanocomposite for potential applications in bone tissue engineering

Herein, we report the synthesis of a novel tri-component nanocomposite system incorporating β-cyclodextrin (β-CD) with nano-hydroxyapatite (n-HA) and chitosan (CS), (n-HA/β-CD/CS) at three different temperatures via co-precipitation method. The chemical interactions and surface morphology have been evaluated by TEM, SEM and AFM techniques revealing the agglomerated nanoparticles in CS/n-HA-HA binary system whereas the ternary systems produced needle shaped nanoparticles dispersed homogeneously at low temperature with more porous and rougher surface. The addition of β-CD in CS/n-HA at low temperature decreased the particle size and raised the thermal stability as compared to CS/n-HA. The comparative hemolytic, protein adsorption and platelet adhesion studies confirmed the better hemocompatibility of n-HA/β-CD/CS-(RT,HT,LT) nanocomposites relative to CS/n-HA. The cell viability has been evaluated in vitro using MG-63 cell line which revealed superior non toxicity of n-HA/β-CD/CS-LT nanocomposite in comparison to n-HA/β-CD/CS-(RT,HT) and CS/n-HA nanocomposites. Thus it may be concluded that the orchestrated organic/inorganic n-HA/β-CD/CS-(RT,HT,LT) nanocomposites exhibited relatively higher cell viability of human osteoblast cells, stimulated greater osteogenesis, controlled biodegradation, enhanced antibacterial activity with excellent in-vitro biomineralization and remarkable mechanical parameters as compared to CS/n-HA nanocomposite and thus may provide opportunities for potential use as an alternative biomaterial for Bone tissue engineering applications.

Nano-hydroxyapatite/chitosan-starch nanocomposite as a novel bone construct: Synthesis and in vitro studies

A novel ternary nanocomposite system incorporating hydroxyapatite, chitosan and starch (n-HA/CS-ST) has been synthesized by co-precipitation method at room temperature, addressing the issues of biocompatibility, mechanical strength and cytotoxicity required for bone tissue engineering. The interactions, crystallite size, surface morphology and thermal stability against n-HA/CS nanocomposite have been obtained by comparing the results of FTIR, SEM, TEM, DLS, XRD and TGA/DTA. A comparative study of bioactivity and thermal stability of n-HA/CS and n-HA/CS-ST nanocomposites revealed that the incorporation of starch as templating agent enhanced these properties in n-HA/CS-ST nanocomposite. A lower swelling rate of n-HA/CS-ST relative to n-HA/CS indicates a higher mechanical strength supportive of bone tissue ingrowths. The MTT assay on murine fibroblast L929 and human osteoblasts-like MG-63 cells and in vitro bioactivity of n-HA/CS-ST matrix referred superior non-toxic nature of n-HA/CS-ST nanocomposite and greater possibility of osteointegration in vivo respectively. Furthermore n-HA/CS-ST exhibited improved antibacterial property against both Gram-positive and Gram-negative bacteria relative to n-HA/CS.

Ag@TiO2 nanocomposite; synthesis, characterization and its application as a novel and recyclable catalyst for the one-pot synthesis of benzoxazole derivatives in aqueous media

A Ag@TiO₂ nanocomposite/water as a novel catalytic system is used for the synthesis of benzoxazole derivatives. A shorter reaction time along with high product yield, catalyst stability and recyclability are the merits of this novel protocol.

Novel hybrid PVA–InZnO transparent thin films and sandwich capacitor structure by dip coating method: preparation and characterizations

In this paper, a very simple and cost effective dip coating method to obtain novel hybrid PVA–InZnO transparent thin films and sandwich capacitor structures for future transparent device applications.