An accurate coarse-grained model for chitosan polysaccharides in aqueous solution

The multi-scale polarizable pseudo-particle solvent coarse-grained approach: From NaCl salt solutions to polyelectrolyte hydration

We discuss key parameters that affect the reliability of hybrid simulations in the aqueous phase based on an efficient multi-scale coarse-grained polarizable pseudo-particle approach, denoted as pppl, to model the solvent water, whereas solutes are modeled using an all atom polarizable force field. Among those parameters, the extension of the solvent domain (SD) at the solute vicinity (domain in which each solvent particle corresponds to a single water molecule) and the magnitude of solute/solvent short range polarization damping effects are shown to be pivotal to model NaCl salty aqueous solutions and the hydration of charged systems, such as the hydrophobic polyelectrolyte polymer that we have recently investigated [Masella et al., J. Chem. Phys. 155, 114903 (2021)]. Strong short range damping is pivotal to simulate aqueous salt NaCl solutions at moderate concentration (up to 1.0M). The SD extension (as well as short range damping) has a weak effect on the polymer conformation; however, it plays a pivotal role in computing accurate polymer/solvent interaction energies. As the pppl approach is up to two orders of magnitude computationally more efficient than all atom polarizable force field methods, our results show it to be an efficient alternative route to investigate the equilibrium properties of complex charged molecular systems in extended chemical environments.

Effect of Acetylation on the Nanofibril Formation of Chitosan from All-Atom De Novo Self-Assembly Simulations

Chitosan-based materials have broad applications, from biotechnology to pharmaceutics. Recent experiments showed that the degree and pattern of acetylation along the chitosan chain modulate its biological and physicochemical properties; however, the molecular mechanism remains unknown. Here, we report, to the best of our knowledge, the first de novo all-atom molecular dynamics (MD) simulations to investigate chitosan's self-assembly process at different degrees and patterns of acetylation. Simulations revealed that 10 mer chitosan chains with 50% acetylation in either block or alternating patterns associate to form ordered nanofibrils comprised of mainly antiparallel chains in agreement with the fiber diffraction data of deacetylated chitosan. Surprisingly, regardless of the acetylation pattern, the same intermolecular hydrogen bonds mediate fibril sheet formation while water-mediated interactions stabilize sheet-sheet stacking. Moreover, acetylated units are involved in forming strong intermolecular hydrogen bonds (NH-O6 and O6H-O7), which offers an explanation for the experimental observation that increased acetylation lowers chitosan's solubility. Taken together, the present study provides atomic-level understanding the role of acetylation plays in modulating chitosan's physiochemical properties, contributing to the rational design of chitosan-based materials with the ability to tune by its degree and pattern of acetylation. Additionally, we disseminate the improved molecular mechanics parameters that can be applied in MD studies to further understand chitosan-based materials.

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.

Biocompatible Macroion/Growth Factor Assemblies for Medical Applications

Growth factors are a class of proteins that play a role in the proliferation (the increase in the number of cells resulting from cell division) and differentiation (when a cell undergoes changes in gene expression becoming a more specific type of cell) of cells. They can have both positive (accelerating the normal healing process) and negative effects (causing cancer) on disease progression and have potential applications in gene therapy and wound healing. However, their short half-life, low stability, and susceptibility to degradation by enzymes at body temperature make them easily degradable in vivo. To improve their effectiveness and stability, growth factors require carriers for delivery that protect them from heat, pH changes, and proteolysis. These carriers should also be able to deliver the growth factors to their intended destination. This review focuses on the current scientific literature concerning the physicochemical properties (such as biocompatibility, high affinity for binding growth factors, improved bioactivity and stability of the growth factors, protection from heat, pH changes or appropriate electric charge for growth factor attachment via electrostatic interactions) of macroions, growth factors, and macroion-growth factor assemblies, as well as their potential uses in medicine (e.g., diabetic wound healing, tissue regeneration, and cancer therapy). Specific attention is given to three types of growth factors: vascular endothelial growth factors, human fibroblast growth factors, and neurotrophins, as well as selected biocompatible synthetic macroions (obtained through standard polymerization techniques) and polysaccharides (natural macroions composed of repeating monomeric units of monosaccharides). Understanding the mechanisms by which growth factors bind to potential carriers could lead to more effective delivery methods for these proteins, which are of significant interest in the diagnosis and treatment of neurodegenerative and civilization diseases, as well as in the healing of chronic wounds.

Chitosan characteristics in electrolyte solutions: Combined molecular dynamics modeling and slender body hydrodynamics

Molecular dynamics modeling was applied to predict chitosan molecule conformations, the contour length, the gyration radius, the effective cross-section and the density in electrolyte solutions. Using various experimental techniques the diffusion coefficient, the hydrodynamic diameter and the electrophoretic mobility of molecules were determined. This allowed to calculate the zeta potential, the electrokinetic charge and the effective ionization degree of the chitosan molecule as a function of pH and the temperature. The chitosan solution density and zero shear dynamic viscosity were also measured, which enabled to determine the intrinsic viscosity increment. The experimental results were quantitatively interpreted in terms of the slender body hydrodynamics exploiting molecule characteristics derived from the modeling. It is also confirmed that this approach can be successfully used for a proper interpretation of previous literature data obtained under various physicochemical conditions.

Multifaceted Computational Modeling in Glycoscience

Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.

Highly Efficient Synthesis of Type B Gelatin and Low Molecular Weight Chitosan Nanoparticles: Potential Applications as Bioactive Molecule Carriers and Cell-Penetrating Agents

Gelatin and chitosan nanoparticles have been widely used in pharmaceutical, biomedical, and nanofood applications due to their high biocompatibility and biodegradability. This study proposed a highly efficient synthesis method for type B gelatin and low-molecular-weight (LMW) chitosan nanoparticles. Gelatin nanoparticles (GNPs) were synthesized by the double desolvation method and the chitosan nanoparticles (CNPs) by the ionic gelation method. The sizes of the obtained CNPs and GNPs (373 ± 71 nm and 244 ± 67 nm, respectively) and zeta potential (+36.60 ± 3.25 mV and −13.42 ± 1.16 mV, respectively) were determined via dynamic light scattering. Morphology and size were verified utilizing SEM and TEM images. Finally, their biocompatibility was tested to assure their potential applicability as bioactive molecule carriers and cell-penetrating agents.

Conformation and persistence length of chitosan in aqueous solutions of different ionic strengths via asymmetric flow field-flow fractionation

Conformation of chitosan in acidic aqueous solutions is strongly influenced by ionic strength, but the conventional employed size exclusion chromatography is limited to high ionic strength. Here we show that conformation of chitosan in acetate buffer down to millimolar ionic strength can be studied via asymmetric flow field-flow fractionation (AF4), where the separation is governed by the diffusion properties of the chitosan molecules and assisted by the electrostatic repulsion of the polyelectrolyte from the channel membrane. The size of chitosan decreases with ionic strength due to increasing screening of the polyelectrolyte effect. The persistence length of chitosan in the solutions, obtained by fitting the conformation plot by the wormlike chain model, decreases linearly with the Debye screening length from 44.5 nm at a salt concentration of 1.25 mM dominated by the electrostatic contribution to 8.6 nm in 800 mM acetate buffer close to its intrinsic persistence length of 7.7 nm.

Fe-chitosan complexes for oxidative degradation of emerging contaminants in water: Structure, activity, and reaction mechanism

Versatile and ecofriendly methods to perform oxidations at near-neutral pH are of crucial importance for processes aimed at purifying water. Chitosan, a deacetylated form of chitin, is a promising starting material owing to its biocompatibility and ability to form stable films and complexes with metals. Here, we report a novel chitosan-based organometallic complex that was tested both as homogeneous and heterogeneous catalyst in the degradation of contaminants of emerging concern in water. The stoichiometry of the complex was experimentally verified with different metals, namely, Cu(II), Fe(III), Fe(II), Co(II), Pd(II), and Mn(II), and we identified the chitosan-Fe(III) complex as the most efficient catalyst. This complex effectively degraded phenol, triclosan, and 3-chlorophenol in the presence of hydrogen peroxide. A putative ferryl-mediated reaction mechanism is proposed based on experimental data, density functional theory calculations, and kinetic modeling. Finally, a film of the chitosan-Fe(III) complex was synthesized and proven a promising supported heterogeneous catalyst for water purification.

Systematic Structural Characterization of Chitooligosaccharides Enabled by Automated Glycan Assembly

Chitin, a polymer composed of β(1-4)-linked N-acetyl-glucosamine monomers, and its partially deacetylated analogue chitosan, are abundant biopolymers with outstanding mechanical as well as elastic properties. Their degradation products, chitooligosaccharides (COS), can trigger the innate immune response in humans and plants. Both material and biological properties are dependent on polymer length, acetylation, as well as the pH. Without well-defined samples, a complete molecular description of these factors is still missing. Automated glycan assembly (AGA) enabled rapid access to synthetic well-defined COS. Chitin-cellulose hybrid oligomers were prepared as important tools for a systematic structural analysis. Intramolecular interactions, identified by molecular dynamics simulations and NMR analysis, underscore the importance of the chitosan amino group for the stabilization of specific geometries.

A multiscale coarse-grained model to predict the molecular architecture and drug transport properties of modified chitosan hydrogels

Hydrogels constructed with functionalized polysaccharides are of interest in a multitude of applications, chiefly the design of therapeutic and regenerative formulations. Tailoring the chemical modification of polysaccharide-based hydrogels to achieve specific drug release properties involves the optimization of many tunable parameters, including (i) the type, degree (χ), and pattern of the functional groups, (ii) the water-polymer ratio, and (iii) the drug payload. To guide the design of modified polysaccharide hydrogels for drug release, we have developed a computational toolbox that predicts the structure and physicochemical properties of acylated chitosan chains, and their impact on the transport of drug molecules. Herein, we present a multiscale coarse-grained model to investigate the structure of networks of chitosan chains modified with acetyl, butanoyl, or heptanoyl moieties, as well as the diffusion of drugs doxorubicin (Dox) and gemcitabine (Gem) through the resulting networks. The model predicts the formation of different network structures, in particular the hydrophobically-driven transition from a uniform to a cluster/channel morphology and the formation of fibers of chitin chains. The model also describes the impact of structural and physicochemical properties on drug transport, which was confirmed experimentally by measuring Dox and Gem diffusion through an ensemble of modified chitosan hydrogels.

Extending the Martini Coarse-Grained Force Field to N-Glycans

Glycans play a vital role in a large number of cellular processes. Their complex and flexible nature hampers structure-function studies using experimental techniques. Molecular dynamics (MD) simulations can help in understanding dynamic aspects of glycans if the force field parameters used can reproduce key experimentally observed properties. Here, we present optimized coarse-grained (CG) Martini force field parameters for N-glycans, calibrated against experimentally derived binding affinities for lectins. The CG bonded parameters were obtained from atomistic (ATM) simulations for different glycan topologies including high mannose and complex glycans with various branching patterns. In the CG model, additional elastic networks are shown to improve maintenance of the overall conformational distribution. Solvation free energies and octanol-water partition coefficients were also calculated for various N-glycan disaccharide combinations. When using standard Martini nonbonded parameters, we observed that glycans spontaneously aggregated in the solution and required down-scaling of their interactions for reproduction of ATM model radial distribution functions. We also optimized the nonbonded interactions for glycans interacting with seven lectin candidates and show that a relatively modest scaling down of the glycan-protein interactions can reproduce free energies obtained from experimental studies. These parameters should be of use in studying the role of glycans in various glycoproteins and carbohydrate binding proteins as well as their complexes, while benefiting from the efficiency of CG sampling.

Preparation, in vitro and in vivo evaluation of PLGA/Chitosan based nano-complex as a novel insulin delivery formulation

The smart self-regulated drug delivery systems for insulin administration are desirable to achieve glycemic control, and decrease the long-term micro- and macro vascular complications. In this study, we developed an injectable nano-complex formulation for closed-loop insulin delivery after subcutaneous administration and release of insulin in response to increased blood glucose levels. The nano-complex was prepared by mixing oppositely charged chitosan and PLGA nanoparticles. PLGA nanoparticles were prepared using double-emulsion solvent diffusion method, and were loaded with glucose oxidase (GOx) and catalase (CAT) enzymes. These negatively charged particles decrease micro-environmental pH, by gluconic acid production in the glucose molecules presence. Positively charged chitosan nanoparticles were prepared using ionic gelation method, and were loaded with insulin. These nanoparticles (NPs) released insulin by dissociation in acidic pH caused by the GOx activity. Following in vitro studies, in vivo evaluation of nano-complex formulations in streptozocin induced diabetic rats showed significant glycemic regulation up to 98 h after subcutaneous administration.

Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications

Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.