Molecular dynamics study on the mechanism of polynucleotide encapsulation by chitosan

Physicochemical characteristics of chitosan molecules: Modeling and experiments

Chitosan, a biocompatible polysaccharide, finds a wide range of applications, inter alia as an antimicrobial agent, stabilizer of food products, cosmetics, and in the targeted delivery of drugs and stem cells. This work represents a comprehensive review of the properties of chitosan molecule and its aqueous solutions uniquely combining theoretical modeling and experimental results. The emphasis is on physicochemical aspects which were sparsely considered in previous reviews. Accordingly, in the first part, the explicit solvent molecular dynamics (MD) modeling results characterizing the conformations of chitosan molecule, the contour length, the chain diameter and the density are discussed. These MD data are used to calculate several parameters for larger chitosan molecules using a hybrid approach based on continuous hydrodynamics. The dependencies of hydrodynamic diameter, frictional ratio, radius of gyration, and intrinsic viscosity on the molar mass of molecules are presented and discussed. These theoretical predictions, comprising useful analytical solutions, are used to interpret and rationalize the extensive experimental data acquired by advanced experimental techniques. In the final part, the molecule charge, acid-base, and electrokinetic properties, comprising the electrophoretic mobility and the zeta potential, are reviewed. Future research directions are defined and discussed.

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. The relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein-Frenkel Hamiltonian model.

Development, Evaluation, and Molecular Dynamics Study of Ampicillin-Loaded Chitosan-Hyaluronic Acid Films as a Drug Delivery System

Periodontitis is an inflammatory periodontal disease defined by the progressive loss of tissues surrounding the tooth. Ampicillin is an antibiotic for managing and treating specific bacterial infections, including periodontitis. Periodontal pockets occur due to periodontal disease progression and act as a natural reservoir that is easily reachable for the insertion of a delivery system, and the amount of drug to be released has a major role in the efficiency of treatment of the disease. Polyelectrolyte complexes (PECs), particularly those based on chitosan and hyaluronic acid combinations, offer a promising avenue to overcome the challenges associated with drug delivery. These complexes are both biodegradable and biocompatible, making them an optimal choice for enabling targeted drug delivery. This study centers on developing and assessing the structure and dynamic attributes of a drug-PEC system encompassing ampicillin and chitosan-hyaluronic acid components, which represents a targeted drug delivery system to better alleviate the periodontitis. To achieve this goal, we conducted experiments including weight and drug content uniformity, swelling ındex, drug release %, FT-IR and SEM analyses, and atomistic molecular dynamics simulations on the drug PECs loaded with ampicillin with varying amounts of hyaluronic acid. All simulations and the experimental analysis suggested that increased HA amount resulted in an increase in drug release % and swelling index. The simulation outcomes provide insights into the nature of the drug and PEC interactions alongside transport properties such as drug diffusion coefficients. These coefficients offer valuable insights into the molecular behavior of ampicillin-PEC drug delivery systems, particularly in the context of their application in periodontitis treatment.

Effect of Fragment 1 on the Binding of Epigallocatechin Gallate to the PD-L1 Dimer Explored by Molecular Dynamics

Blocking the interaction between programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) by directly targeting the PD-L1 dimer has emerged as a hot topic in the field of cancer immunotherapy. Epigallocatechin gallate (EGCG), a natural product, has been demonstrated binding to the PD-L1 dimer in our previous study, but has a weaker binding capacity, moreover, EGCG is located at the end of the binding pocket of the PD-L1 dimer. The inhibitor fragment 1 (FRA) lies at the other end. So, we proposed that the introduction of FRA might be able to improve the binding ability. To illuminate this issue, molecular dynamics (MD) simulation was performed in the present study. Binding free energy calculations show that the binding affinity is significantly increased by 17 kcal/mol upon the introduction of FRA. It may be due to the energy contributions of emerging key residues ATyr56, AMet115, BTyr123, AIle54 and the enhanced contributions of initial key residues ATyr123 and BVal68. Binding mode and non-bonded interaction results indicate that FRA_EGCG (EGCG in combination with FRA) binds to the C-, F- and G-sheet of the PD-L1 dimer. Importantly, the introduction of FRA mainly strengthened the nonpolar interactions. The free energy landscape and secondary structure results further show that FRA_EGCG can interact with the PD-L1 dimer more stably. These data demonstrated here provide the theoretical basis for screening two or more natural products with additive inhibitory effect on this pathway and therefore exerting more effective anticancer immunity.

Chitosan Polysaccharides from a Polarizable Multiscale Approach

We report simulations of chitosan polysaccharides in the aqueous phase, at infinite dilute conditions and zero ionic strength. Those simulations are performed by means of a polarizable multiscale modeling scheme that relies on a polarizable all atom force field to model solutes and on a polarizable solvent coarse grained approach. Force field parameters are assigned only from quantum chemistry ab initio data. We simulate chitosan monomer units, dimers and 50-long chains. Regarding the 50-long chains we simulate three sets of ten randomly built chain replica at three different pH conditions (corresponding to different chain protonation states, the chain degree of deacetylation is 85%). Our simulations show the persistence length of 50-long chitosan chains at strong acidic conditions (pH <5) to be 24 ± 2 nm (at weak/negligible ionic strength conditions), and to be 1 order of magnitude shorter at usual pH conditions. Our simulation data support the most recent simulation and experimental studies devoted to chitosan polysaccharides in the aqueous phase.

Multifunctional nanoparticles for the treatment and diagnosis of osteosarcoma

Osteosarcoma (OS) is a common primary malignant bone tumor in adolescents. Currently, the commonly used treatment strategies for OS include surgery, chemotherapy and radiotherapy. However, these methods have some problems that cannot be ignored, such as postoperative sequelae and severe side effects. Therefore, in recent years, researchers have been looking for other means to improve the treatment or diagnosis effect of OS and increase the overall survival rate of patients. With the development of nanotechnology, nanoparticles (NPs) have presented excellent properties in improving the therapeutic efficacy of drugs for OS. Nanotechnology makes it possible for NPs to combine various functional molecules and drugs to achieve multiple therapeutic effects. This review presents the important properties of multifunctional NPs for the treatment and diagnosis of OS and focuses on the research progress of common NPs applied for drug or gene delivery, phototherapy and diagnosis of OS, such as carbon-based quantum dots, metal, chitosan and liposome NPs. Finally, the promising prospects and challenges of developing multifunctional NPs with enhanced efficacy are discussed, which lays the foundation and direction for improving the future therapeutic and diagnostic methods of OS.

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck-Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck-Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck-Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

Polymorphism of chitosan-based networks stabilized by phytate investigated by molecular dynamics simulations

Chitosan can associate in the presence of polyphosphates into insoluble hydrogels capable of drug encapsulation and safe and efficient release. On the one hand, chitosan hydrogels were synthesized using the phytate anion as a crosslinking agent and were characterized by employing dynamic light scattering (DLS) and Fourier transform infrared spectroscopy (FTIR). On the other hand, an effective chitosan-phytate model with atomistic details was created to examine the underlying physical crosslinking pattern, and the structure and dynamics of the chitosan-phytate complex were systematically investigated by using molecular dynamics (MD) simulations. To harbor the crosslinker potential for obtaining chitosan-based hydrogels, the impact of the phytate concentration and the functional groups of the chitosan on the reticulation process was addressed. The phytate association was determined by the phosphates' capacity for H-bonding to the amine and hydroxyl groups belonging to two consecutive glucosidic units. The physical crosslinking pattern was determined by the number of chitosan chains bound by one phytate anion and the phytate orientation relative to the glucopyranose neighbors. Cross-linking of two up to six chitosan chains mediated by a phytate anion represented favorable states, and the number distribution of cross-linked chains depended on the phytate concentration. The circular distribution of the cross-linkable phosphates regulated the nearly isotropic orientation of the chitosan chains and phytate at the junction, and the variety of topological crosslinking demonstrated the phytate ion's potential for developing chitosan-based hydrogels with improved structural attributes.

The interactions of folate with the enzyme furin: a computational study

Entrance of coronavirus into cells happens through the spike proteins on the virus surface, for which the spike protein should be cleaved into S1 and S2 domains. This cleavage is mediated by furin, a member of the proprotein convertases family, which can specifically cleave Arg-X-X-Arg↓ sites of the substrates. Here, folate (folic acid), a water-soluble B vitamin, is introduced for the inhibition of furin activity. Therefore, molecular insight into the prevention of furin activity in the presence of folic acid derivatives is presented. To this aim, molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations were performed to clarify the inhibitory mechanism of these compounds. In this regard, molecular docking studies were conducted to probe the furin binding sites of folic acid derivatives. The MD simulation results indicated that these drugs can efficiently bind to the furin active site. While the folic acid molecule tended to be positioned slightly towards the Glu271, Tyr313, Ala532, Gln488, and Asp530 amino acids of furin at short and long ranges, the folinic acid molecule interacted with Glu271, Ser311, Arg490, Gln488, and Lys499 amino acids. Consequently, binding free energy calculations illustrated that folic acid (−27.90 kcal mol⁻¹) has better binding in comparison with folinic acid (−12.84 kcal mol⁻¹).

The present study introduces the ability of folic acid to interact and inhibit furin proprotein.

Chitosan-based smart hybrid materials: a physico-chemical perspective

Chitosan is one of the most studied cationic polysaccharides. Due to its unique characteristics of being water soluble, biocompatible, biodegradable, and non-toxic, this macromolecule is highly attractive for a broad range of applications. In addition, its complex behavior and the number of ways it interacts with different components in a system result in an astonishing variety of chitosan-based materials. Herein, we present recent advances in the field of chitosan-based materials from a physico-chemical perspective, with focus on aqueous mixtures with oppositely charged colloids, chitosan-based thin films, and nanocomposite systems. In this review, we focus our attention on the physico-chemical properties of chitosan-based materials, including solubility, mechanical resistance, barrier properties, and thermal behaviour, and provide a link to the chemical peculiarities of chitosan, such as its intrinsic low solubility, high rigidity, large charge separation, and strong tendency to form intra- and inter-molecular hydrogen bonds.

Nucleotide Interaction with a Chitosan Layer on a Silica Surface: Establishing the Mechanism at the Molecular Level

The growing interest in gene therapy is coupled with the strong need for the development of safe and efficient gene transfection vectors. A composite based on chitosan and fumed silica has been found to be a prospective gene delivery carrier. This study presents an investigation of the nature of the bonds between a series of nucleotides with a chitosan layer deposited on a fumed silica surface. Experimentally measured surface complex formation constants (logK) of the nucleotides were found to be in the range of 2.69-4.02, which is higher than that for the orthophosphate (2.39). Theoretically calculated nucleotide complexation energies for chitosan deposited on the surface range from 11.5 to 23.0 kcal·mol^-1, in agreement with experimental data. The adsorption of nucleotides was interpreted using their calculated speciation in an aqueous solution. Based on the structures of all optimized complexes determined from quantum-chemical PM6 calculations, electrostatic interactions between the surface-located NH₃⁺ groups and -PO₃H^--/-PO₃^2- fragments of the nucleotides were identified to play the decisive role in the adsorption mechanism. The saccharide fragment of monophosphates also plays an important role in the binding of the nucleotides to chitosan through the creation of hydrogen bonds.

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.

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.

Molecular dynamics study on the encapsulation and release of anti-cancer drug doxorubicin by chitosan

Doxorubicin (DOX) is a broad-spectrum anti-tumor drug, but it has certain limitations in its therapeutic effects due to poor tumor selectivity. Chitosan-based pH-sensitive polymers drug delivery systems could improve DOX's activity and selectivity against tumor cells. Understanding the atomic interaction mechanism between chitosan and DOX at different pH levels is important in the design and application of chitosan-based drug delivery systems. In this study, molecular dynamics simulations were performed to investigate the encapsulation and release of DOX by chitosan at different pH levels. Our results show that the protonation state of amine groups of chitosan and the π-π stacking interaction between the conjugated anthraquinone ring of DOX regulate the interaction behavior between chitosan and DOX. Moreover, DOX could gradually release from chitosan at acidic pH environment in tumor tissue. These results revealed the underlying atomic interaction mechanism between DOX and chitosan at various pH levels and may provide novel ideas for the design and application of chitosan-based drug delivery system.

Chitosan as a Natural Copolymer with Unique Properties for the Development of Hydrogels

Hydrogel-based polymers are represented by those hydrophilic polymers having functional groups in their chain such as amine (NH2), hydroxyl [-OH], amide (-CONH-, -CONH2), and carboxyl [COOH]. These hydrophilic groups raise their potential to absorb fluids or aqueous solution more than their weights. This physicochemical mechanism leads to increased hydrogel expansion and occupation of larger volume, the process which shows in swelling behavior. With these unique properties, their use for biomedical application has been potentially raised owing also to their biodegradability and biocompatibility. Chitosan as a natural copolymer, presents a subject for hydrogel structures and function. This review aimed to study the structure as well as the function of chitosan and its hydrogel properties.

A multifunctional polymeric gene delivery system for circumventing biological barriers

Crucial light-controlled-ROS and pH-stimulus-responsive functionalities are tailored into a triblock copolymer for manufacture of gene delivery vehicles.

Chitosan-Based Nanomaterials for Drug Delivery

This review discusses different forms of nanomaterials generated from chitosan and its derivatives for controlled drug delivery. Nanomaterials are drug carriers with multiple features, including target delivery triggered by environmental, pH, thermal responses, enhanced biocompatibility, and the ability to cross the blood-brain barrier. Chitosan (CS), a natural polysaccharide largely obtained from marine crustaceans, is a promising drug delivery vector for therapeutics and diagnostics, owing to its biocompatibility, biodegradability, low toxicity, and structural variability. This review describes various approaches to obtain novel CS derivatives, including their distinct advantages, as well as different forms of nanomaterials recently developed from CS. The advanced applications of CS-based nanomaterials are presented here in terms of their specific functions. Recent studies have proven that nanotechnology combined with CS and its derivatives could potentially circumvent obstacles in the transport of drugs thereby improving the drug efficacy. CS-based nanomaterials have been shown to be highly effective in targeted drug therapy.

Protein moiety in oligochitosan modified vector regulates internalization mechanism and gene delivery: Polyplex characterization, intracellular trafficking and transfection

Oligochitosan-modified proteins have gained attention as efficient non-viral vectors for gene delivery. However, little information exists if protein moieties can serve as an important role for internalization and endosome escape ability of the genetic material. To explore this issue, we designed two cationic oligochitosan-modified vectors that consist of different proteins, namely a hydrophobic plant protein (zein) and a hydrophilic animal protein (ovalbumin (OVA)) to deliver pDNA to epithelial cell line CHO-K1 and HEK 293 T. These cationic vectors were systematically characterized by molecular weight, infrared (IR) structural analysis, transmission electron microscopy (TEM) morphology, and surface charge. A remarkable impact of protein moieties was observed on physiochemical properties of the developed vectors. Oligochitosan-modified zein containing hydrophobic protein exhibited high buffering capacity and excellent DNA binding ability compared to the oligochitosan-modified OVA. The data on transfection in the presence of endocytic inhibitors indicated that the caveolae-mediated pathway (CvME) played a key role in the internalization of the zein-based polyplex. However, the OVA-based polyplex was internalized in CHO-K1 cells via CvME and in HEK 293 T cells via the lipid-mediated pathway. Moreover, oligochitosan-modified zein exhibited lower cytotoxicity, greater lysosomal escape ability, better plasmid stability, and better transfection efficiency than the oligochitosan-modified OVA. This study offers a facile procedure for the synthesis of cationic vectors and elucidates the relationship that exists between protein moieties and transfection activity, thus providing an alternative, non-viral platform for the gene delivery.