Molecular dynamics study on DNA nanotubes as drug delivery vehicle for anticancer drugs

Conformational dynamics and mechanical properties of biomimetic RNA, DNA, and RNA-DNA hybrid nanotubes: an atomistic molecular dynamics study

With the nanotechnology boom, artificially designed nucleic acid nanotubes have aroused interest due to their practical applications in nanorobotics, vaccine design, membrane channels, drug delivery, and force sensing. In this paper, computational study was performed to investigate the structural dynamics and mechanical properties of RNA nanotubes (RNTs), DNA nanotubes (DNTs), and RNA-DNA hybrid nanotubes (RDHNTs). So far, the structural and mechanical properties of RDHNTs have not been examined in experiments or theoretical calculations, and there is limited knowledge regarding these properties for RNTs. Here, the simulations were carried out using the equilibrium molecular dynamics (MD) and steered molecular dynamics (SMD) approaches. Using in-house scripting, we modeled hexagonal nanotubes composed of six double-stranded molecules connected by four-way Holliday junctions. Classical MD analyses were performed on the collected trajectory data to investigate structural properties. Analyses of the microscopic structural parameters of RDHNT indicated a structural transition from the A-form to a conformation between the A- and B-forms, which may be attributable to the increased rigidity of RNA scaffolds compared to DNA staples. Comprehensive research on the elastic mechanical properties was also conducted based on spontaneous thermal fluctuations of nanotubes and employing the equipartition theorem. The Young's modulus of RDHNT (E = 165 MPa) and RNT (E = 144 MPa) was found to be almost the same and nearly half of that found for DNT (E = 325 MPa). Furthermore, the results showed that RNT was more resistant to bending, torsional, and volumetric deformations than DNT and RDHNT. We also used non-equilibrium SMD simulations to acquire comprehensive knowledge of the mechanical response of nanotubes to tensile stress.

Exploring the benefits of functionally graded carbon nanotubes (FG-CNTs) as a platform for targeted drug delivery systems

BACKGROUND AND OBJECTIVE

Modern therapeutic systems have benefited from the use of functionally graded carbon nanotubes (FG-CNTs) to enhance their efficiency. Various studies have shown that the study of dynamic response and stability of fluid-conveying FG-nanotubes can be improved by considering a Multiphysics framework for the modeling of such a complex biological environment. However, despite noticing important aspects in modeling, the previous studies have drawbacks such as underrepresenting the effect of varying composition of the nanotube on magnetic drug release in drug delivery systems. The present work has the novelty of studying the combined effects of fluid flow, magnetic field, small-scale parameters, and functionally graded material on the performance of FG-CNTs for drug delivery applications. Additionally, the lack of an inclusive parametric study is resolved in the present study by evaluating the significance of different geometrical and physical parameters. As such, the achievements support the development of an efficient drug delivery treatment.

METHODS

The Euler-Bernoulli beam theory is implemented to model the nanotube and Hamilton's principle based on Eringen's nonlocal elasticity theory is used to derive the constitutive equations of motion. To add the effect of slip velocity on the CNT's wall, a correction factor is applied to velocity based on the Beskok-Karniadakis model.

RESULTS

demonstrate that the dimensionless critical flow velocity increases by 227% as the magnetic field intensity increases from 0 to 20 T, and improves the system stability. On the contrary, drug loading on the CNT has the opposite effect, as the critical velocity decreases from 10.1 to 8.38 using a linear function for drug loading, and it decreases to 7.95 using an exponential function. By employing a hybrid load distribution, an optimum material distribution can be achieved.

CONCLUSIONS

To benefit from the potential of CNTs in drug delivery systems while minimizing the instability problems, a suitable design for the drug loading is required prior to the clinical implementation of the nanotube.

The effect of initial temperature on the mechanical interaction of 3DN5/5OTF protein-based structures using molecular dynamics simulation

Nowadays, advances in science and technology in biological macromolecules have led to the early detection and treatment of cancer-based cells. In this study, molecular dynamics (MD) simulation examines atomic interactions between 3DN5 and 5OTF structures. Technically, the effect of the initial temperature on the atomic behavior (AB) of the simulated samples is investigated. The stability of simulated structures is examined with changes in temperature and kinetic energy (KE) quantities. The biomechanical interaction is examined by the radius of gyration (RoG), interaction energy (IE), and interaction force (IF). The results show that the RoG changes from a numerical value of 40.25 to 41.33 Å, and the IE and IF converge to -552.38 kcal/mol and - 207.10 kcal/mol.Å after 10 ns, respectively. Due to the temperature effect on the AB of the structures, the RoG increases by increasing the initial temperature from 41.33 to 58.91 Å. By increasing the initial temperature to 350 K, the IE increases from -551.38 to -500.11 kcal/mol, and the IF increases from -207.10 to -183.39 kcal/mol.Å. Finally, the results of these studies are expected to lead to early detection and treatment of cancer cells.

Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations

In this study, the interaction of 5-fluorouracil (5FU) drug with adenine (A), guanine(G), cytosine(C), uracil (U), and thymine (T) nucleobases of DNA and RNA are surveyed at the ωB97XD/LANL2DZ, M06-2X/6-31G (d, p), MPW1PWQ1/6-31G(d, p), PBEPBE/6-31(d, p) and ωB97XD/6-31G(d, p) levels of density functional theory (DFT). The considered complexes of 5FU drug with nucleobases are optimized at the above level of theories. Max Force and RMS of optimization criteria are 0.00035 (Ha), and 0.0003 respectively. From optimized structures, the adsorption energy, thermodynamic parameters in gas and solvent media, quantum theory atom in molecule (QTAIM), electron localized function (ELF), and reduced density gradient (RDG) are calculated at ωB97XD/LANL2DZ and M06-2X/6-31G (d, p) level of DFT theory. The QTAIM, ELF, and RDG results confirm that the nature of bonding between 5FU drug with A, C, G, U, and T nucleobases is electrostatic or hydrogen bond type. The adsorption and thermodynamic energy results demonstrate that the interaction of the 5FU drug with C and G nucleobases is stronger than other nucleobases. The results of this study can be suggested the mechanism of interaction of the 5FU drug with nucleobases of DNA and RNA.Communicated by Ramaswamy H. Sarma.

Computational Indicator Approach for Assessment of Nanotoxicity of Two-Dimensional Nanomaterials

The increasing growth in the development of various novel nanomaterials and their biomedical applications has drawn increasing attention to their biological safety and potential health impact. The most commonly used methods for nanomaterial toxicity assessment are based on laboratory experiments. In recent years, with the aid of computer modeling and data science, several in silico methods for the cytotoxicity prediction of nanomaterials have been developed. An affordable, cost-effective numerical modeling approach thus can reduce the need for in vitro and in vivo testing and predict the properties of designed or developed nanomaterials. We propose here a new in silico method for rapid cytotoxicity assessment of two-dimensional nanomaterials of arbitrary chemical composition by using free energy analysis and molecular dynamics simulations, which can be expressed by a computational indicator of nanotoxicity (CIN_2D). We applied this approach to five well-known two-dimensional nanomaterials promising for biomedical applications: graphene, graphene oxide, layered double hydroxide, aloohene, and hexagonal boron nitride nanosheets. The results corroborate the available laboratory biosafety data for these nanomaterials, supporting the applicability of the developed method for predictive nanotoxicity assessment of two-dimensional nanomaterials.

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology

The mechanical properties of DNA have enabled it to be a structural and sensory element in many nanotechnology applications. While specific base-pairing interactions and secondary structure formation have been the most widely utilized mechanism in designing DNA nanodevices and biosensors, the intrinsic mechanical rigidity and flexibility are often overlooked. In this article, we will discuss the biochemical and biophysical origin of double-stranded DNA rigidity and how environmental and intrinsic factors such as salt, temperature, sequence, and small molecules influence it. We will then take a critical look at three areas of applications of DNA bending rigidity. First, we will discuss how DNA's bending rigidity has been utilized to create molecular springs that regulate the activities of biomolecules and cellular processes. Second, we will discuss how the nanomechanical response induced by DNA rigidity has been used to create conformational changes as sensors for molecular force, pH, metal ions, small molecules, and protein interactions. Lastly, we will discuss how DNA's rigidity enabled its application in creating DNA-based nanostructures from DNA origami to nanomachines.

Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

Bent DNA Bows as Sensing Amplifiers for Detecting DNA-Interacting Salts and Molecules

Due to the central role of DNA, its interactions with inorganic salts and small organic molecules are important. For example, such interactions play important roles in various fundamental cellular processes in living systems and are involved in many DNA-damage related diseases. Strategies to improve the sensitivity of existing techniques for studying DNA interactions with other molecules would be appreciated in situations where the interactions are too weak. Here we report our development and demonstration of bent DNA bows for amplifying, sensing, and detecting the interactions of 14 inorganic salts and small organic molecules with DNA. With the bent DNA bows, these interactions were easily visualized and quantified in gel electrophoresis, which were difficult to measure without bending. In addition, the strength of the interactions of DNA with the various salts/molecules were quantified using the modified Hill equation. This work highlights the amplification effects of the bending elastic energy stored in the DNA bows and the potential use of the DNA bows for quantitatively measuring DNA interactions with small molecules as simple economic methods; it may also pave the way for exploiting the bent DNA bows for other applications such as screening DNA-interacting molecules and drugs.

pH-sensitive loading/releasing of doxorubicin using single-walled carbon nanotube and multi-walled carbon nanotube: A molecular dynamics study

BACKGROUND AND OBJECTIVE

Doxorubicin is one of the drugs used to treat cancer, and many studies have been conducted to control its release. In this study, carbon nanotubes have been proposed as a doxorubicin carrier, and the effect of carboxyl functional group on the controlled release of doxorubicin has been studied.

METHODS

This study has been done by molecular dynamics simulation and was based on changing the pH as a mechanism controller.

RESULTS

This work is intended to test the efficacy of this drug carrier for the release of doxorubicin. A comparison was also made between single-walled and double-walled carbon nanotubes to answer the question of which one can be a better carrier for doxorubicin. The study of DOXORUBICIN adsorption and release showed that the DOXORUBICIN adsorption on single-walled carbon nanotube and multi-walled carbon nanotube in neutral pH was stronger than it was in acidic pH, which could be due to the electrostatic interactions between the carboxyl group of nanotubes and DOXORUBICIN. Based on this and according to the investigation of hydrogen bonds, diffusion coefficients, and other results it was clear that the drug release in acidic pH was appropriate for body conditions. Since cancer tissues pH is acidic, this shows the suitability of carbon nanotube in drug delivery and DOXORUBICIN release in cancer tissues. In addition, it was shown that the blood pH (pH = 7) is suitable for DOXORUBICIN loading on the carbon nanotube and carbon nanotube-DOXORUBICIN linkage remained stable at this pH; accordingly, the carbon nanotube could deliver DOXORUBICIN in blood quite well and release it in cancerous tissues. This suggests the carbon nanotubes as a promising drug carrier in the cancer therapy which can be also investigated in experiments.

CONCLUSION

It was revealed that the bonds between multi-walled carbon nanotube and DOXORUBICIN was stronger and this complex had a slower release in the cancer tissues compared to the single-walled carbon nanotube; this can be regarded as an advantage over the single-walled carbon nanotube in the DOXORUBICIN delivery and release.

Potential of graphene oxide as a drug delivery system for Sumatriptan: a detailed density functional theory study

The adsorption property of Sumatriptan drug onto graphene oxide (GO) was studied using density functional theory (DFT) calculations. All possible initial positions of drug adsorption were considered to find out which one is energetically favorable. According to the achieved findings, the stronger interactions occurred between the positively polarized parts of the Sumatriptan (i.e. hydrogen atoms of the-OH and -NH parts) and negatively polarized oxygen atoms of the GO. The presence of non-covalent interactions of GO and Sumatriptan was confirmed based on the determined geometrical parameters, electronic structure analysis results, and adsorption energies. Different parameters such as frontier molecular orbital (FMO), natural bond orbital (NBO), dipole moment, and solation energy were investigated. Global indices such as hardness, softness, chemical potential, and electrophilicity of all systems were calculated and compared. The adsorption energy values were determined within the range of -8.39 to -10.59 kcal/mol (-1.87 to -5.67 BSSE corrected) in the water solvent for different adsorption geometries. The obtained results show that GO can act as a promising carrier/sensor for Sumatriptan drug in practical application.Communicated by Ramaswamy H. Sarma.

Electrospun nanofibers: a promising horizon toward the detection and treatment of cancer

Due to the increase in the number of cancer patients, because of environmental parameters, high stress, low immunity, etc., there is an urgent need to develop cost-effective sensors for early targeted detection of cancerous cells with adequate selectivity and efficiency. Early disease diagnosis is important, as it is necessary to start treatments before disease progression. On the other hand, we need new, more efficient cancer treatment approaches with minimized side effects, more biocompatibility, and easy disposal. Nanobiotechnology is a field that can assist in developing new diagnostic and treatment approaches, specifically in fatal cancers. Herein, a study on the different applications of nanofibers in cancer detection as well as its treatment has been done. Here, a very brief survey on the main structure of biosensors and their different categories has been conducted and will precede the discussion of the study to serve as a reference and guide the reader's understanding.

Advances in mathematical models of the active targeting of tumor cells by functional nanoparticles

BACKGROUND AND OBJECTIVE

The process of nanoparticles (NPs) entering blood circulation to actively target tumor cells involves four stages-the transport of NPs in blood vessels, transvascular transport of NPs, transport of NPs in the tumor interstitial matrix and entry of NPs into tumor cells. These four stages are a complex process involving mechanical, physical, biochemical, and biophysical factors, the tumor microenvironment (TME) and properties of NPs play important roles in this process. Because this process involves a large number of factors and is very complex, it is difficult to study with conventional methods.

METHODS

Using mathematical models for simulation is suitable for addressing this complex situation and can describe the complexity well.

RESULTS

This work focuses on the theoretical simulation of NPs that target tumor cells to illustrate the effects of the abnormal microenvironment of tumors and properties of NPs on the transport process. Mathematical models constructed by different methods are enumerated. Through studying these mathematical models, different methods to overcome nanoparticle (NP) transport obstacles are illustrated.

CONCLUSIONS

It is necessary to construct a theoretical model of active targeting nanodrug delivery under the coupling of micro-flow field and specific binding force field, and to simulate and analyze the delivery process at mesoscopic scale using computational fluid dynamics (CFD) method, so as to reveal the law and characteristics of drug delivery and cell uptake in the micro-environment of tumors in vivo. The methods and techniques discussed can serve as the basis for systematic studies of active targeting of functional nanoparticles to tumor cells.

Hierarchical nanomaterials via biomolecular self-assembly and bioinspiration for energy and environmental applications

Bioinspired synthesis offers potential green strategies to build highly complex nanomaterials by utilizing the unique nanostructures, functions, and properties of biomolecules, in which the biomolecular recognition and self-assembly processes play important roles in tailoring the structures and functions of bioinspired materials. Further understanding of biomolecular self-assembly for inspiring the formation and assembly of nanoparticles would promote the design and fabrication of functional nanomaterials for various applications. In this review, we focus on recent advances in bioinspired synthesis and applications of hierarchical nanomaterials based on biomolecular self-assembly. We first discuss biomolecular self-assembly towards biological nanomaterials, in which the mechanisms and ways of biomolecular self-assembly as well as various self-assembled biomolecular nanostructures are demonstrated. Secondly, the bioinspired synthesis strategies including molecule-molecule interaction, molecule-material recognition, molecule-mediated nucleation and growth, and molecule-mediated reduction/oxidation are introduced and discussed. Meanwhile, typical examples and discussions on how biomolecular self-assembly inspires the formation of hierarchical hybrid nanomaterials are presented. Finally, the applications of bioinspired nanomaterials in biofuel cells, light-harvesting systems, batteries, supercapacitors, catalysis, water/air purification, and environmental monitoring are presented and discussed. We believe that this review will be very helpful for readers to understand the self-assembly of biomolecules and the biomimetic/bioinspired strategies for synthesizing hierarchical nanomaterials on the one hand, and on the other hand to design novel materials for extended applications in nanotechnology, materials science, analytical science, and biomedical engineering.

Fibrous polymer nanomaterials for biomedical applications and their transport by fluids: an overview

Over the past few decades, there has been strong interest in the development of new micro- and nanomaterials for biomedical applications. Their use in the form of capsules, particles or filaments suspended in body fluids is associated with conformational changes and hydrodynamic interactions responsible for their transport. The dynamics of fibres or other long objects in Poiseuille flow is one of the fundamental problems in a variety of biomedical contexts, such as mobility of proteins, dynamics of DNA or other biological polymers, cell movement, tissue engineering, and drug delivery. In this review, we discuss several important applications of micro and nanoobjects in this field and try to understand the problems of their transport in flow resulting from material-environment interactions in typical, crowded, and complex biological fluids. Our aim is to elucidate the relationship between the nano- and microscopic structures of elongated polymer particles and their flow properties, thus opening the possibility to design nanoobjects that can be efficiently transported by body fluids for targeted drug release or local tissue regeneration.

pH-Sensitive Co-Adsorption/Release of Doxorubicin and Paclitaxel by Carbon Nanotube, Fullerene, and Graphene Oxide in Combination with N-isopropylacrylamide: A Molecular Dynamics Study

Nanotechnology based drug delivery systems for cancer therapy have been the topic of interest for many researchers and scientists. In this research, we have studied the pH sensitive co-adsorption and release of doxorubicin (DOX) and paclitaxel (PAX) by carbon nanotube (CNT), fullerene, and graphene oxide (GO) in combination with N-isopropylacrylamide (PIN). This simulation study has been performed by use of molecular dynamics. Interaction energies, hydrogen bond, and gyration radius were investigated. Results reveal that, compared with fullerene and GO, CNT is a better carrier for the co-adsorption and co-release of DOX and PAX. It can adsorb the drugs in plasma pH and release it in vicinity of cancerous tissues which have acidic pH. Investigating the number of hydrogen bonds revealed that PIN created many hydrogen bonds with water resulting in high hydrophilicity of PIN, hence making it more stable in the bloodstream while preventing from its accumulation. It is also concluded from this study that CNT and PIN would make a suitable combination for the delivery of DOX and PAX, because PIN makes abundant hydrogen bonds and CNT makes stable interactions with these drugs.

Programmable and Multifunctional DNA-Based Materials for Biomedical Applications

DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg²⁺ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.

Cellulose-based film modified by succinic anhydride for the controlled release of domperidone

Succinic anhydride (SAD) modified microcrystalline cellulose (MCC) films was prepared and used for the controlled release of the drug domperidone (dom). The morphology and chemical structure of the modified materials were characterized by SEM, FTIR, XRD and TG/DSC techniques. The physical properties, such as water uptake and swelling, light barrier properties, mechanical testing, in vitro degradation behavior, have been investigated. Results showed that the modified cellulose membranes exhibited good anti-UV properties, higher water uptake values, improved mechanical capacity and anti-biodegradability. In addition, the modified MCC films (MS) as the drug carrier indicated the controlled release of domperidone and the release mechanism was proposed using Korsmeyer-Peppas equation at pH 7.4. The developed drug delivery system possessed the profound significance in improving pharmacodynamics and bioavailability of drugs.

Noncalssical multiscale modeling of ssDNA manipulation using a CNT-nanocarrier based on AFM

Nanocarriers are useful tools in biological and medical research fields. In nanomanipulation, a nondestructive and successful process can be achieved by using nanocarriers. In this paper, a nonclassical multiscale approach has been presented for modeling a single strand DNA (ssDNA) manipulation based on AFM. To achieve a nondestructive nanomanipulation process, carbon nanotube (CNT) has been used as a nanocarrier. AFM setup has been separated into a Micro field (MF) and a Nano field (NF). The governing equations of the MF have been derived based on Kirchhoff plate model and a modified couple stress theory. The NF has been modeled by molecular dynamics (MD) method. A set of nanomanipulations has been performed for the free ssDNA and the ssDNA inside the nanocarrier (shielded ssDNA) on three types of substrates. The exerted forces on the free ssDNA and the shielded ssDNA have been compared for manipulation on various substrates. The results show that using the nanocarrier reduces the manipulation force considerably. The results of RMSD as a general geometrical criterion have illustrated that the maximum damage occurs on the golden substrate for free ssDNA. Elongation and curvature criteria have been presented to investigate the ssDNA deformation in detail. The elongation and curvature criteria have been shown that using a nanocarrier is a good approach for a successful and nondestructive nanomanipulation. Finally it can be concluded that the manipulation process of free ssDNA on silicon substrate is successful as well as the manipulation process of the shielded ssDNA on all three types of substrates.

Gemcitabine–camptothecin conjugates: a hybrid prodrug for controlled drug release and synergistic therapeutics

Self-assembled small molecule prodrug loaded with gemcitabine and camptothecin and responsive to reductive tumour microenvironment for combination cancer chemotherapy.