Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides

Synthesis of Amphiphilic Amino Poly-Amido-Saccharide and Poly(lactic) Acid Block Copolymers and Fabrication of Paclitaxel-Loaded Mucoadhesive Nanoparticles

Drug delivery to the esophagus through systemic administration remains challenging, as minimal drug reaches the desired target. Local delivery offers the potential for improved efficacy while minimizing off-target toxicities but necessitates bioadhesive properties for mucosal delivery. Herein, we describe the synthesis of two new mucoadhesive amphiphilic copolymers prepared by sequential ring-opening copolymerization or postpolymerization click conjugation. Both strategies yield block copolymers containing a hydrophilic amine-functionalized poly-amido-saccharide and either a hydrophobic alkyl derivatized poly-amido-saccharide or poly(lactic acid), respectively. The latter resulting copolymers readily self-assemble into spherical, ≈200 nm diameter, positively charged mucoadhesive nanoparticles. The NPs entrap ultrahigh levels of paclitaxel via encapsulation of free paclitaxel and paclitaxel conjugated to a biodegradable, biocompatible poly(1,2-glycerol carbonate). Paclitaxel-loaded NPs rapidly enter cells, release paclitaxel, are cytotoxic to esophageal OE33 and OE19 tumor cells in vitro, and, importantly, demonstrate improved mucoadhesion compared to conventional poly(ethylene glycol)-poly(lactic acid) nanoparticles to ex vivo esophageal tissue.

Current Advancement and Future Prospects: Biomedical Nanoengineering

Recent advancements in biomedicine have seen a significant reliance on nanoengineering, as traditional methods often fall short in harnessing the unique attributes of biomaterials. Nanoengineering has emerged as a valuable approach to enhance and enrich the performance and functionalities of biomaterials, driving research and development in the field. This review emphasizes the most prevalent biomaterials used in biomedicine, including polymers, nanocomposites, and metallic materials, and explores the pivotal role of nanoengineering in developing biomedical treatments and processes. Particularly, the review highlights research focused on gaining an in-depth understanding of material properties and effectively enhancing material performance through molecular dynamics simulations, all from a nanoengineering perspective.

Computational biophysics approach towards the discovery of multi-kinase blockers for the management of MAPK pathway dysregulation

The MAPK pathway is important in human lung cancer and is improperly activated in a substantial proportion through number of ways. Strategies on dual-targeting RAF and MEK are an alternative option to diminish the limitations in this pathway inhibition. Hence, we implemented parallel pharmacophore screening of 11,808 DrugBank compounds against RAF and MEK. ADHRR and DHHRR were modeled as a pharmacophore hypothesis for RAF and MEK respectively. Importantly, these hypotheses resulted an AUC value of > 0.90 with the external data set. As a result of phase screening, glide docking, and prime-MM/GBSA scoring, it is determined that DB08424 and DB08907 have the best chances of acting as multi-kinase inhibitors. The pi-cation interaction with key amino acid residues of both target receptors may responsible for the stronger binding with these kinases. Cumulative 600 ns MD simulation studies validate the binding ability of these compounds. Significantly, the hit compounds resulted higher number of stable conformational state with less atomic movements than the reference compound against both targets. The anti-cancer efficacy of the lead compounds was validated through machine learning-based approaches. These findings suggest that DB08424 and DB08907 might be novel molecules to be explored further experimentally to block the MAPK signaling in lung cancer patients.

Therapeutic phosphorodiamidate morpholino oligonucleotides: Physical properties, solution structures, and folding thermodynamics

Elucidating the structure-function relationships for therapeutic RNA mimicking phosphorodiamidate morpholino oligonucleotides (PMOs) is challenging due to the lack of information about their structures. While PMOs have been approved by the US Food and Drug Administration for treatment of Duchenne muscular dystrophy, no structural information on these unique, charge-neutral, and stable molecules is available. We performed circular dichroism and solution viscosity measurements combined with molecular dynamics simulations and machine learning to resolve solution structures of 22-mer, 25-mer, and 30-mer length PMOs. The PMO conformational dynamics are defined by the competition between non-polar nucleobases and uncharged phosphorodiamidate groups for shielding from solvent exposure. PMO molecules form non-canonical, partially helical, stable folded structures with a small 1.4- to 1.7-nm radius of gyration, low count of three to six base pairs and six to nine base stacks, characterized by -34 to -51 kcal/mol free energy, -57 to -103 kcal/mol enthalpy, and -23 to -53 kcal/mol entropy for folding. The 4.5- to 6.2-cm³/g intrinsic viscosity and Huggins constant of 4.5-9.9 are indicative of extended and aggregating systems. The results obtained highlight the importance of the conformational ensemble view of PMO solution structures, thermodynamic stability of their non-canonical structures, and concentration-dependent viscosity properties. These principles form a paradigm to understand the structure-properties-function relationship for therapeutic PMOs to advance the design of new RNA-mimic-based drugs.

Synthesis of bioactive (1→6)-β-glucose branched poly-amido-saccharides that stimulate and induce M1 polarization in macrophages

β-Glucans are of significant interest due to their potent antitumor and immunomodulatory activities. Nevertheless, the difficulty in purification, structural heterogenicity, and limited solubility impede the development of structure-property relationships and translation to therapeutic applications. Here, we report the synthesis of a new class of (1→6)-β-glucose-branched poly-amido-saccharides (PASs) as β-glucan mimetics by ring-opening polymerization of a gentiobiose-based disaccharide β-lactam and its copolymerization with a glucose-based β-lactam, followed by post-polymerization deprotection. The molecular weight (Mn) and frequency of branching (FB) of PASs is readily tuned by adjusting monomer-to-initiator ratio and mole fraction of gentiobiose-lactam in copolymerization. Branched PASs stimulate mouse macrophages, and enhance production of pro-inflammatory cytokines in a FB-, dose-, and Mn-dependent manner. The stimulation proceeds via the activation of NF-κB/AP-1 pathway in a Dectin-1-dependent manner, similar to natural β-glucans. The lead PAS significantly polarizes primary human macrophages towards M1 phenotype compared to other β-glucans such as lentinan, laminarin, and curdlan.

Sulfated poly-amido-saccharides (sulPASs) are anticoagulants in vitro and in vivo

Anticoagulant therapeutics are a mainstay of modern surgery and of clotting disorder management such as venous thrombosis, yet performance and supply limitations exist for the most widely used agent - heparin. Herein we report the first synthesis, characterization, and performance of sulfated poly-amido-saccharides (sulPASs) as heparin mimetics. sulPASs inhibit the intrinsic pathway of coagulation, specifically FXa and FXIa, as revealed by ex vivo human plasma clotting assays and serine protease inhibition assays. sulPASs activity positively correlates with molecular weight and degree of sulfation. Importantly, sulPASs are not degraded by heparanases and are non-hemolytic. In addition, their activity is reversed by protamine sulfate, unlike small molecule anticoagulants. In an in vivo murine model, sulPASs extend clotting time in a dose dependent manner with bleeding risk comparable to heparin. These findings support continued development of synthetic anticoagulants to address the clinical risks and shortages associated with heparin.

Immune Effect Regulated by the Chain Length: Interaction between Immune Cell Surface Receptors and Synthetic Glycopolymers

Glycopolymer-based drugs for immunotherapy have attracted increasing attention because the affinity between glycans and proteins plays an important role in immune responses. Previous studies indicate that the polymer chain length influences the affinity. In the studies on enhancing the immune response by glycans, it is found that both oligosaccharides and long-chain glycopolymers work well. However, there is a lack of systematic studies on the immune enhancement effect and the binding ability of oligomers and polymers to immune-related proteins. In this paper, to study the influence of the chain length, glycopolymers based on N-acetylglucosamine with different chain lengths were synthesized, and their interaction with immune-related proteins and their effect on dendritic cell maturation were evaluated. It was proved that compared with l-glycopolymers (degree of polymerization (DP) > 20), s-glycopolymers (DP < 20) showed better binding ability to the dendritic cell-specific ICAM-3-grabbing nonintegrin protein and the toll-like receptor 4 and myeloid differentiation factor 2 complex protein by quartz crystal microbalance and molecular docking simulation. When the total sugar unit amounts are equal, s-glycopolymers are proved to be superior in promoting dendritic cell maturation by detecting the expression level of CD80 and CD86 on the surface of dendritic cells. Through the combination of experimental characterization and theoretical simulation, a deep look into the interaction between immune-related proteins and glycopolymers with different chain lengths is helpful to improve the understanding of the immune-related interactions and provides a good theoretical basis for the design of new glycopolymer-based immune drugs.

Molecular simulation study of 3,4-dihydroxyphenylalanine in the context of underwater adhesive design

Adhesives that can stick to multiple surface types in underwater and high moisture conditions are critical for various applications such as marine coatings, sealants, and medical devices. The analysis of natural underwater adhesives shows that L-3,4-dihydroxyphenylalanine (DOPA) and functional amyloid nanostructures are key components that contribute to the adhesive powers of these natural glues. The combination of DOPA and amyloid-forming peptides into DOPA-amyloid(-forming peptide) conjugates provides a new approach to design generic underwater adhesives. However, it remains unclear how the DOPA monomers may interact with amyloid-forming peptides and how these interactions may influence the adhesive ability of the conjugates. In this paper, we investigate the behavior of DOPA monomers, (glycine-DOPA)₃ chains, and a KLVFFAE and DOPA-glycine chain conjugate in aqueous environments using molecular simulations. The DOPA monomers do not aggregate significantly at concentrations lower than 1.0M. Simulations of (glycine-DOPA)₃ chains in water were done to examine the intra-molecular interactions of the chain, wherein we found that there were unlikely to be interactions detrimental to the adhesion process. After combining the alternating DOPA-glycine chain with the amyloid-forming peptide KLVFFAE into a single chain conjugate, we then simulated the conjugate in water and saw the possibility of both intra-chain folding and no chain folding in the conjugate.

Beyond Amphiphilic Balance: Changing Subunit Stereochemistry Alters the Pore-Forming Activity of Nylon-3 Polymers

Amphiphilic nylon-3 polymers have been reported to mimic the biological activities of natural antimicrobial peptides, with high potency against bacteria and minimal toxicity toward eukaryotic cells. Amphiphilic balance, determined by the proportions of hydrophilic and lipophilic subunits, is considered one of the most important features for achieving this activity profile for nylon-3 polymers and many other antimicrobial polymers. Insufficient hydrophobicity often correlates with weak activities against bacteria, whereas excessive hydrophobicity correlates with high toxicity toward eukaryotic cells. To ask whether factors beyond amphiphilic balance influence polymer activities, we synthesized and evaluated new nylon-3 polymers with two stereoisomeric subunits, each bearing an ethyl side chain and an aminomethyl side chain. Subunits that differ only in stereochemistry are predicted to contribute equally to amphiphilic balance, but we observed that the stereochemical difference correlates with significant changes in biological activity profile. Antibacterial activities were not strongly affected by subunit stereochemistry, but the ability to disrupt eukaryotic cell membranes varied considerably. Experiments with planar lipid bilayers and synthetic liposomes suggested that eukaryotic membrane disruption results from polymer-mediated formation of large pores. Collectively, our results suggest that factors other than amphiphilic balance influence the membrane activity profile of synthetic polymers. Subunits that differ in stereochemistry are likely to have distinct conformational propensities, which could potentially lead to differences in the average shapes of polymer chains, even when the subunits are heterochiral. These findings highlight a dimension of polymer design that should be considered more broadly in efforts to improve specificity and efficacy of antimicrobial polymers.

Synthesis and Biopharmaceutical Applications of Sugar-Based Polymers: New Advances and Future Prospects

The rapid rise in research interest in carbohydrate-based polymers is undoubtedly due to the nontoxic nature of such materials in an in vivo environment and the versatile roles that the polymers can play in cellular functions. Such polymers have served as therapeutic tools for drug delivery, including antigens, proteins, and genes, as well as diagnostic devices. Our focus in the first half of this Review is on synthetic methods based on ring-opening polymerization and enzyme-catalyzed polymerization, along with controlled radical polymerization. In the second half of this Review, sugar-based polymers are discussed on the basis of their remarkable success in competitive receptor binding, as multifunctional nanocarriers of targeting inhibitors for cancer treatment, in genome-editing delivery, in immunotherapy based on endogenous antibody recruitment, and in treatment of respiratory diseases, including influenza A. Particular emphasis is put on the synthesis and biopharmaceutical applications of sugar-based polymers published in the most recent 5 years. A noticeable attribute of carbohydrate-based polymers is that the sugar-receptor interactions can be facilitated by the cooperative effect of multiple sugar units. Their diversified topology and structures will drive the development of new synthetic strategies and bring about important applications, including coronavirus-related drug therapy.

Poly-Amido-Saccharides (PASs): Functional Synthetic Carbohydrate Polymers Inspired by Nature

Carbohydrates are ubiquitous in nature, playing vital roles in all organisms ranging from metabolism to intercellular signaling. Polysaccharides, repeating units of small molecule carbohydrates, are hydrophilic, densely functionalized, stereoregular, and rigid macromolecules, and these characteristics are simultaneously advantageous in biomedical applications while presenting major hurdles for synthetic methodology and development of structure property relationships. While naturally obtained polysaccharides are widely utilized in the biochemical and medical literature, their poor physicochemical definition and the potential for contaminated samples hinders the clinical translation of this work. To address the need for new methods to synthesize carbohydrate polymers, we reported a novel class of biomaterials (Poly-Amido-Saccharides; PAS) in 2012. PASs share many properties with natural polysaccharides, such as hydrophilicity, dense hydroxyl functionality, stereoregularity, and a rigid backbone. PASs are connected by an α-1,2-amide linkage, instead of an ether linkage, that confers resistance to enzymatic and hydrolytic degradation and leads to a unique helical conformation. Importantly, our synthetic methodology affords control over molecular weight distribution resulting in pure, well-defined polymers. This Account provides an overview of the development of PAS, from the factors that initially motivated our research to current efforts to translate functional PAS to biomedical applications. We detail the synthesis of glucose- and galactose-based PAS and their biophysical properties including conformation analysis, lectin interactions, cell internalization, and water solubility. Additionally, we describe postpolymerization modification strategies to afford PASs that act as protein stabilizers. We also highlight our recent efforts toward a mechanistic understanding of monomer synthesis via [2 + 2] cycloaddition reactions in order to develop novel monomers with different stereochemistry and amine or alkyl functionality, thereby accessing functional carbohydrate polymers. Throughout our work, we apply computational and theoretical analysis to explain how properties at the monomer level (e.g., stereochemistry, functionality) significantly impact polymer properties, helical conformation, and bioactivities. Collectively, the results from the theoretical, synthetic, and applied aspects of this research advance us toward our goal of utilizing PASs in key biomedical applications as alternatives to natural polysaccharides. The importance of carbohydrates in nature and the versatility of their functions continue to inspire our investigation of new monomers, polymers, and copolymers, leveraging the advantageous properties of PAS to develop potential therapies.

A Synthetic Bioinspired Carbohydrate Polymer with Mucoadhesive Properties

Mucoadhesive polymers are of significant interest to the pharmaceutical, medical device, and cosmetic industries. Polysaccharides possessing charged functional groups, such as chitosan, are known for mucoadhesive properties but suffer from poor chemical definition and solubility, while the chemical synthesis of polysaccharides is challenging with few reported examples of synthetic carbohydrate polymers with engineered-in ionic functionality. We report the design, synthesis, and evaluation of a synthetic, cationic, enantiopure carbohydrate polymer inspired by the structure of chitosan. These water-soluble, cytocompatible polymers are prepared via an anionic ring-opening polymerization of a bicyclic β-lactam sugar monomer. The synthetic method provides control over the site of amine functionalization and the length of the polymer while providing narrow dispersities. These well-defined polymers are mucoadhesive as documented in single-molecule scale (AFM), bulk solution phase (FRAP), and ex vivo tissue experiments. Polymer length and functionality affects bioactivity as long, charged polymers display higher mucoadhesivity than long, neutral polymers or short, charged polymers.

Polymers from sugars and unsaturated fatty acids: ADMET polymerisation of monomers derived from d-xylose, d-mannose and castor oil

High molecular weight renewable polyesters are synthesised from an unsaturated fatty acid and structurally unmodified, hemicellulosic sugars, with post-polymerisation modification inducing semicrystallinity and allowing casting of transparent films.

Cationic poly-amido-saccharides: stereochemically-defined, enantiopure polymers from anionic ring-opening polymerization of an amino-sugar monomer

We expand the scope of the PAS methodology and evaluate multiple synthetic routes to generate a regioselectively-functionalized 6-amino carbohydrate polymer sharing key properties with natural polysaccharides, including high water-solubility.

Enantiomeric glycosylated cationic block co-beta-peptides eradicate Staphylococcus aureus biofilms and antibiotic-tolerant persisters

The treatment of bacterial infections is hindered by the presence of biofilms and metabolically inactive persisters. Here, we report the synthesis of an enantiomeric block co-beta-peptide, poly(amido-D-glucose)-block-poly(beta-L-lysine), with high yield and purity by one-shot one-pot anionic-ring opening (co)polymerization. The co-beta-peptide is bactericidal against methicillin-resistant Staphylococcus aureus (MRSA), including replicating, biofilm and persister bacterial cells, and also disperses biofilm biomass. It is active towards community-acquired and hospital-associated MRSA strains which are resistant to multiple drugs including vancomycin and daptomycin. Its antibacterial activity is superior to that of vancomycin in MRSA mouse and human ex vivo skin infection models, with no acute in vivo toxicity in repeated dosing in mice at above therapeutic levels. The copolymer displays bacteria-activated surfactant-like properties, resulting from contact with the bacterial envelope. Our results indicate that this class of non-toxic molecule, effective against different bacterial sub-populations, has promising potential for the treatment of S. aureus infections.

The authors report the synthesis of an enantiomeric block co-beta-peptide that kills methicillin-resistant Staphylococcus aureus, including biofilm and persister bacterial cells, and disperses biofilms. The copolymer displays antibacterial activity in human ex vivo and mouse in vivo infection models without toxicity.

Sequence isomerism-dependent self-assembly of glycopeptide mimetics with switchable antibiofilm properties

In biological systems, diverse amino acid sequences and functional decorations endow proteins with specific functions. Functionally modified oligopeptides are attractive building blocks to assemble stimuli-responsive biomimetic superstructures for mimicking soft structures in nature and biomaterial applications. In this work, we selectively synthesized the structurally simplest isomeric tripeptides (i.e., Ala-Gly-Gly-OH, Gly-Ala-Gly-OH and Gly-Gly-Ala-OH) to demonstrate how the subtlest change in sequence isomerism influences the self-assembly of glycopeptides. To impart self-assembly capability and stimuli-responsiveness, the isomeric tripeptides were modified with a hydrophobic n-butylazobenzene tail at the N-terminal. We observed three different self-assembled 1-D morphologies (i.e., nanotwists, nanoribbons and nanofibers) from the azobenzene-glycopeptides (AGPs) under the same conditions when the position of the Ala residue was switched. Experimental methods including transmission electron microscopy (TEM), atomic force microscopy (AFM), X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy and circular dichroism (CD) spectroscopy were used to characterize the structural details of glycopeptide mimetic assemblies. Martini coarse-grained molecular dynamics (MD) simulations confirmed such structural observations and investigated the differences in assembly mechanisms. Furthermore, the glycopeptide mimetic assemblies showed a reversible disassembly-assembly process in response to temperature, light or host-guest chemistry, and can be used as switchable antibiofilm nanoagents.

Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach

The NF1 gene encodes for neurofibromin protein, which is ubiquitously expressed, but most highly in the central nervous system. Non-synonymous SNPs (nsSNPs) in the NF1 gene were found to be associated with Neurofibromatosis Type 1 disease, which is characterized by the growth of tumors along nerves in the skin, brain, and other parts of the body. In this study, we used several in silico predictions tools to analyze 16 nsSNPs in the RAS-GAP domain of neurofibromin, the K1444N (K1423N) mutation was predicted as the most pathogenic. The comparative molecular dynamic simulation (MDS; 50 ns) between the wild type and the K1444N (K1423N) mutant suggested a significant change in the electrostatic potential. In addition, the RMSD, RMSF, Rg, hydrogen bonds, and PCA analysis confirmed the loss of flexibility and increase in compactness of the mutant protein. Further, SASA analysis revealed exchange between hydrophobic and hydrophilic residues from the core of the RAS-GAP domain to the surface of the mutant domain, consistent with the secondary structure analysis that showed significant alteration in the mutant protein conformation. Our data concludes that the K1444N (K1423N) mutant lead to increasing the rigidity and compactness of the protein. This study provides evidence of the benefits of the computational tools in predicting the pathogenicity of genetic mutations and suggests the application of MDS and different in silico prediction tools for variant assessment and classification in genetic clinics.

Interplay of structure and diffusion in ternary liquid mixtures of benzene + acetone + varying alcohols

The Fick diffusion coefficient matrix of ternary mixtures containing benzene + acetone + three different alcohols, i.e., methanol, ethanol, and 2-propanol, is studied by molecular dynamics simulation and Taylor dispersion experiments. Aiming to identify common features of these mixtures, it is found that one of the main diffusion coefficients and the smaller eigenvalue do not depend on the type of alcohol along the studied composition path. Two mechanisms that are responsible for this invariant behavior are discussed in detail, i.e., the interplay between kinetic and thermodynamic contributions to Fick diffusion coefficients and the presence of microscopic heterogeneities caused by hydrogen bonding. Experimental work alone cannot explain these mechanisms, while present simulations on the molecular level indicate structural changes and uniform intermolecular interactions between benzene and acetone molecules in the three ternary mixtures. The main diffusion coefficients of these ternary mixtures exhibit similarities with their binary subsystems. Analyses of radial distribution functions and hydrogen bonding statistics quantitatively evidence alcohol self-association and cluster formation, as well as component segregation. Furthermore, the excess volume of the mixtures is analyzed in the light of intermolecular interactions, further demonstrating the benefits of the simultaneous use of experiment and simulation. The proposed framework for studying diffusion coefficients of a set of ternary mixtures, where only one component varies, opens the way for further investigations and a better understanding of multicomponent diffusion. The presented numerical results may also give an impulse to the development of predictive approaches for multicomponent diffusion.

Biologically Active Branched Polysaccharide Mimetics: Synthesis via Ring-Opening Polymerization of a Maltose-Based β-Lactam

Stereoregular poly-amido-saccharides bearing α-glucopyranose branches (Mal-PASs) are synthesized by anionic ring-opening polymerization of a maltose-based β-lactam monomer followed by debenzylation. The polymerization affords high molecular weight polymers (up to 31500 g/mol) with narrow dispersities (Đ < 1.1). Deprotected Mal-PASs are highly soluble in water and adopt a left-handed helical conformation in solution. Turbidimetric assay shows that Mal-PASs are multivalent ligands to lectin Concanavalin A.

Polymers from sugars and CS2: synthesis and ring-opening polymerisation of sulfur-containing monomers derived from 2-deoxy-d-ribose and d-xylose

Cyclic thionocarbonate and xanthate monomers were synthesised directly from ribose- and xylose-derived diols and CS₂, and yielded novel sugar-based polymers with regioregular sulfur-containing linkages.

Polymers from sugars: cyclic monomer synthesis, ring-opening polymerisation, material properties and applications

This feature article gives an overview of sugar-based polymers that can be made by ring-opening-polymerisation and their applications.