Cytosine-Rich DNA Fragments Covalently Bound to Carbon Nanotube as Factors Triggering Doxorubicin Release at Acidic pH. A Molecular Dynamics Study

Insights into the Molecular Structure, Stability, and Biological Significance of Non-Canonical DNA Forms, with a Focus on G-Quadruplexes and i-Motifs

This article provides a comprehensive examination of non-canonical DNA structures, particularly focusing on G-quadruplexes (G4s) and i-motifs. G-quadruplexes, four-stranded structures formed by guanine-rich sequences, are stabilized by Hoogsteen hydrogen bonds and monovalent cations like potassium. These structures exhibit diverse topologies and are implicated in critical genomic regions such as telomeres and promoter regions of oncogenes, playing significant roles in gene expression regulation, genome stability, and cellular aging. I-motifs, formed by cytosine-rich sequences under acidic conditions and stabilized by hemiprotonated cytosine-cytosine (C:C+) base pairs, also contribute to gene regulation despite being less prevalent than G4s. This review highlights the factors influencing the stability and dynamics of these structures, including sequence composition, ionic conditions, and environmental pH. Molecular dynamics simulations and high-resolution structural techniques have been pivotal in advancing our understanding of their folding and unfolding mechanisms. Additionally, the article discusses the therapeutic potential of small molecules designed to selectively bind and stabilize G4s and i-motifs, with promising implications for cancer treatment. Furthermore, the structural properties of these DNA forms are explored for applications in nanotechnology and molecular devices. Despite significant progress, challenges remain in observing these structures in vivo and fully elucidating their biological functions. The review underscores the importance of continued research to uncover new insights into the genomic roles of G4s and i-motifs and their potential applications in medicine and technology. This ongoing research promises exciting developments in both basic science and applied fields, emphasizing the relevance and future prospects of these intriguing DNA structures.

In Silico Investigation on the Molecular Behavior and Structural Stability of the Rosette Nanotubes as the Drug Vehicles for Paclitaxel, an Anti-Cancer Drug

Most anticancer drugs affect healthy cells in addition to cancer cells, causing severe side effects. Targeted delivery by nano-based drug delivery systems (NDDS) can reduce these severe side effects while maintaining therapeutic efficacy. This work introduced rosette nanotube (RNT) as a potential drug vehicle for paclitaxel (PTX) due to its self-assembling property, biocompatibility, amphiphilicity, and low toxicity. Molecular dynamics (MD) simulations aided with molecular mechanics Poisson Boltzmann surface area (MMPBSA) analysis are used here to investigate the molecular behavior and the loading energetics of each type of RNT (K1, xK1, and iEt-xK1) with PTX. Analysis showed that the most probable configuration of PTX is on either end of each RNT. The binding free energies (-117.74 to -69.29 kJ/mol) when PTX is closer to one end were stronger than when it is in the inner channel (-53.51 to -40.88 kJ/mol). The latter alludes to the encapsulation of the PTX by each RNT. Thus, loading is possible by encapsulation during the self-assembly process given the favorable estimated binding free energies. Based on the results, RNT has potential as a drug vehicle for PTX, which warrants further investigation.

Recent Development of Nano-Carbon Material in Pharmaceutical Application: A Review

Carbon nanomaterials have attracted researchers in pharmaceutical applications due to their outstanding properties and flexible dimensional structures. Carbon nanomaterials (CNMs) have electrical properties, high thermal surface area, and high cellular internalization, making them suitable for drug and gene delivery, antioxidants, bioimaging, biosensing, and tissue engineering applications. There are various types of carbon nanomaterials including graphene, carbon nanotubes, fullerenes, nanodiamond, quantum dots and many more that have interesting applications in the future. The functionalization of the carbon nanomaterial surface could modify its chemical and physical properties, as well as improve drug loading capacity, biocompatibility, suppress immune response and have the ability to direct drug delivery to the targeted site. Carbon nanomaterials could also be fabricated into composites with proteins and drugs to reduce toxicity and increase effectiveness in the pharmaceutical field. Thus, carbon nanomaterials are very effective for applications in pharmaceutical or biomedical systems. This review will demonstrate the extraordinary properties of nanocarbon materials that can be used in pharmaceutical applications.

Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields

Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems.

Nanomaterial-Based Drug Delivery System Targeting Lymph Nodes

The lymphatic system plays an indispensable role in humoral balance, lipid metabolism, and immune regulation. The lymph nodes (LNs) are known as the primary sites of tumor metastasis and the metastatic LNs largely affected the prognosis of the patiens. A well-designed lymphatic-targeted system favors disease treatment as well as vaccination efficacy. In recent years, development of nanotechnologies and emerging biomaterials have gained increasing attention in developing lymph-node-targeted drug-delivery systems. By mimicking the endogenous macromolecules or lipid conjugates, lymph-node-targeted nanocarries hold potential for disease diagnosis and tumor therapy. This review gives an introduction to the physiological functions of LNs and the roles of LNs in diseases, followed by a review of typical lymph-node-targeted nanomaterial-based drug-delivery systems (e.g., liposomes, micelles, inorganic nanomaterials, hydrogel, and nanocapsules). Future perspectives and conclusions concerned with lymph-node-targeted drug-delivery systems are also provided.

Regulation of water access, storage, separation and release of drugs from the carbon nanotube functionalized by cytosine rich DNA fragments

We found that carmustine can be stored in the carbon nanotube (CNT) interior for a long time due to hydrophobic interactions. The access of water to carmustine phase in the CNT interior can be controlled by the state of cytosine rich DNA fragments covalently bound to the CNT tips and to the presence of doxorubicin molecules intercalated within bundles of DNA fragments. More effective control of water access and subsequent decomposition of carmustine due to the contact with water was observed when some small amount of doxorubicin molecules cork the CNT ends. Our analysis shows that carmustine decomposition products naturally separate when decomposition occurs within the CNT. The alkylating agent, chloroethyl carbonium cation, spontaneously escapes from the CNT but the carbamylation agent, chloroethyl isocyanate, is still kept within the nanotube interior. The separation process and release of the alkylating agent needs uncorking the nanotube by doxorubicin molecules. The latter process is likely to occur spontaneously at acidic pH when intercalation of doxorubicin within the DNA fragments becomes ineffective. The features of the proposed molecular model, obtained from molecular dynamics simulations, can be beneficial in design of novel smart drugs carriers to a tumor microenvironment revealing the reduced extracellular pH.

Stimuli-responsive nanomaterials for cancer treatment: boundaries, opportunities and applications

Small molecule drugs, including most chemotherapies, are rapidly degraded and/or eliminated from the body, which is why high doses of these drugs are necessary, potentially producing toxic effects. Several types of nanoparticles loaded with anti-cancer drugs have been designed to overcome the disadvantages of conventional therapies. Modified nanoparticles can circulate for a long time, thus improving the solubility and biodistribution of drugs. Furthermore, they also allow the controlled release of the payload once its target tissue has been reached. These mechanisms can reduce the exposure of healthy tissues to chemotherapeutics, since the drugs are only released in the presence of specific tumour stimuli. Overall, these properties can improve the effectiveness of treatments while reducing undesirable side effects. In this article, we review the recent advances in stimuli-responsive albumin, gold and magnetic nanostructures for controlled anti-cancer drug delivery. These nanostructures were designed to release drugs in response to different internal and external stimuli of the cellular environment, including pH, redox, light and magnetic fields. We also describe various examples of applications of these nanomaterials. Overall, we shed light on the properties, potential clinical translation and limitations of stimuli-responsive nanoparticles for cancer treatment.