Molecular dynamics studies of PEGylated α-helical coiled coils and their self-assembled micelles

Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities

The covalent modification of proteins with polymers is a well-established method for improving the pharmacokinetic properties of therapeutically valuable biologics. The conjugated polymer chains of the resulting hybrid represent highly flexible macromolecular structures. As the dynamics of such systems remain rather elusive for established experimental techniques from the field of protein structure elucidation, molecular dynamics simulations have proven as a valuable tool for studying such conjugates at an atomistic level, thereby complementing experimental studies. With a focus on new developments, this review aims to provide researchers from the polymer bioconjugation field with a concise and up to date overview of such approaches. After introducing basic principles of molecular dynamics simulations, as well as methods for and potential pitfalls in modeling bioconjugates, the review illustrates how these computational techniques have contributed to the understanding of bioconjugates and bioconjugation strategies in the recent past and how they may lead to a more rational design of novel bioconjugates in the future.

PEGylation of Insulin and Lysozyme To Stabilize against Thermal Denaturation: A Molecular Dynamics Simulation Study

Biologic drugs or "biologics" (proteins derived from living organisms) are one of the fastest-growing classes of FDA-approved therapeutics. These compounds are often fragile and require conjugation to polymers for stabilization, with many proteins too ephemeral for therapeutic use. During storage or administration, proteins tend to unravel and lose their secondary structure due to changes in solution temperature, pH, and other external stressors. To enhance their lifetime, protein drugs currently in the market are conjugated with polyethylene glycol (PEG), owing to its ability to increase the stability, solubility, and pharmacokinetics of protein drugs. Here, we perform all-atom molecular dynamics simulations to study the unfolding process of egg-white lysozyme and insulin at elevated temperatures. We test the validity of two force fields─CHARMM36 and Amber ff99SB-ILDN─in the unfolding process. By calculating global and local properties, we capture residues that deteriorate first─these are the "weak links" in the proteins. Next, we conjugate both proteins with PEG and find that PEG preserves the native structure of the proteins at elevated temperatures by blocking water molecules from entering the hydrophobic core, thereby causing the secondary structure to stabilize.

Solutions and Condensed Phases of PEG2000 from All-Atom Molecular Dynamics

Extensive all-atom molecular dynamics studies of polyethylene glycol (PEG₂₀₀₀) when solvated and in the polymer bulk condensed phases were performed across a wide temperature range. We proposed two modified all-atom force field and observed the fate of the PEG₂₀₀₀ macromolecule when solvated in water, water with 4% ethanol, and ethyl acetate. In aqueous solutions, the macromolecule collapsed into a prolate spheroidal ball-like structure while adopting a rather elongated coiled structure in ethyl acetate. Inspection of the polymer-condensed phases across the 150-340 K temperature range enabled the atomistic view of the solid glass below the glass transition temperature of 230 K < T_g < 250 K and the rubber behavior above T_g. Predicted properties include the enthalpy, density, and cohesive energy temperature behavior, the specific heat, thermal expansivity, thermal compressibility, bulk modulus, and Hildebrand solubility parameter both below and above T_g. Within the polymer matrix, the PEG₂₀₀₀ macromolecules were entangled displaying a wide distribution of sizes that persisted when transitioning from the glass to the rubbery phases. Calculated properties agree very well with experiments when available or stand as crucial predictions while awaiting experimental measurement. Understanding the thermodynamics and structure of this useful polymer enables the efficient prediction of its behavior when building novel composite materials for nanomedicine and nanotherapeutics.

Protocol for Simulations of PEGylated Proteins with Martini 3

Enhancement of proteins by PEGylation is an active area of research. However, the interactions between polymer and protein are far from fully understood. To gain a better insight into these interactions or even make predictions, molecular dynamics (MD) simulations can be applied to study specific protein-polymer systems at molecular level detail. Here we present instructions on how to simulate PEGylated proteins using the latest iteration of the Martini coarse-grained (CG) force-field. CG MD simulations offer near atomistic information and at the same time allow to study complex biological systems over longer time and length scales than fully atomistic-level simulations.

Design of 18 nm Doxorubicin-Loaded 3-Helix Micelles: Cellular Uptake and Cytotoxicity in Patient-Derived GBM6 Cells

The fate of nanocarrier materials at the cellular level constitutes a critical checkpoint in the development of effective nanomedicines, determining whether tissue level accumulation results in therapeutic benefit. The cytotoxicity and cell internalization of ∼18 nm 3-helix micelle (3HM) loaded with doxorubicin (DOX) were analyzed in patient-derived glioblastoma (GBM) cells in vitro. The half-maximal inhibitory concentration (IC₅₀) of 3HM-DOX increased to 6.2 μg/mL from <0.5 μg/mL for free DOX in patient-derived GBM6 cells, to 15.0 μg/mL from 6.5 μg/mL in U87MG cells, and to 21.5 μg/mL from ∼0.5 μg/mL in LN229 cells. Modeling analysis of previous 3HM biodistribution results predicts that these cytotoxic concentrations are achievable with intravenous injection in rodent GBM models. 3HM-DOX formulations were internalized intact and underwent intracellular trafficking distinct from free DOX. 3HM was quantified to have an internalization half-life of 12.6 h in GBM6 cells, significantly longer than that reported for some liposome and polymer systems. 3HM was found to traffic through active endocytic processes, with clathrin-mediated endocytosis being the most involved of the pathways studied. Inhibition studies suggest substantial involvement of receptor recognition in 3HM uptake. As the 3HM surface is PEG-ylated with no targeting functionalities, protein corona-cell surface interactions, such as the apolipoprotein-low-density lipoprotein receptor, are expected to initiate internalization. The present work gives insights into the cytotoxicity, pharmacodynamics, and cellular interactions of 3HM and 3HM-DOX relevant for ongoing preclinical studies. This work also contributes to efforts to develop predictive mathematical models tracking the accumulation and biodistribution kinetics at a systemic level.

A self-assembled polymer therapeutic for simultaneously enhancing solubility and antimicrobial activity and lowering serum albumin binding of fusidic acid

The global antimicrobial resistance crisis has prompted worldwide efforts to develop new and more efficient antimicrobial compounds, as well as to develop new drug delivery strategies and targeting mechanisms. This study aimed to synthesize a novel polyethylene glycol-fusidic acid (PEG-FA) conjugate for self-assembly into nano-sized structures and explore its potential for simultaneously enhancing aqueous solubility and antibacterial activity of FA. In addition, the ability of PEG-FA to bind to HSA with lower affinity than FA is also investigated. Haemolysis and in vitro cytotoxicity studies confirmed superior biosafety of the novel PEG-FA compared to FA. The water solubility of FA after PEG conjugation was increased by 25-fold compared to the bare drug. PEG-FA nanoparticles displayed particle size, polydispersity index and zeta potential of 149.3 ± 0.21 nm, 0.267 ± 0.01 and 5.97 ± 1.03 mV, respectively. Morphology studies using high-resolution transmission electron microscope revealed a homogenous spherical shape of the PEG-FA nanoparticles. In silico studies showed that Van der Waals forces facilitated PEG-FA self-assembly. HSA binding studies showed that PEG-FA had very weak or no interaction with HSA using in silico molecular docking (-2.93 kcal/mol) and microscale thermophoresis (K_d=14999 ± 1.36 µM), which may prevent bilirubin displacement. Conjugation with PEG did not inhibit the antibacterial activity of FA but rather enhanced it by 2.5-fold against Staphylococcus aureus and methicillin-resistant Staphylococcus aureus, compared to the bare FA. These results show that PEG-FA can simultaneously enhance solubility and antibacterial activity of FA, whilst also reducing binding of HSA to decrease its side effects.

Molecular Simulations of PEGylated Biomolecules, Liposomes, and Nanoparticles for Drug Delivery Applications

Since the first polyethylene glycol (PEG)ylated protein was approved by the FDA in 1990, PEGylation has been successfully applied to develop drug delivery systems through experiments, but these experimental results are not always easy to interpret at the atomic level because of the limited resolution of experimental techniques. To determine the optimal size, structure, and density of PEG for drug delivery, the structure and dynamics of PEGylated drug carriers need to be understood close to the atomic scale, as can be done using molecular dynamics simulations, assuming that these simulations can be validated by successful comparisons to experiments. Starting with the development of all-atom and coarse-grained PEG models in 1990s, PEGylated drug carriers have been widely simulated. In particular, recent advances in computer performance and simulation methodologies have allowed for molecular simulations of large complexes of PEGylated drug carriers interacting with other molecules such as anticancer drugs, plasma proteins, membranes, and receptors, which makes it possible to interpret experimental observations at a nearly atomistic resolution, as well as help in the rational design of drug delivery systems for applications in nanomedicine. Here, simulation studies on the following PEGylated drug topics will be reviewed: proteins and peptides, liposomes, and nanoparticles such as dendrimers and carbon nanotubes.

Adsorption of plasma proteins onto PEGylated single-walled carbon nanotubes: The effects of protein shape, PEG size and grafting density

Single-walled carbon nanotubes (SWCNTs) covalently functionalized or noncovalently coated with polyethylene glycol (PEG) of different sizes (M_w=2000 and 5000) and grafting densities (5-16 PEGs per SWCNT) are simulated with human fibrinogen (HFG) and serum albumin (HSA). Proteins migrate toward the SWCNT, but their adsorption extents differ. The extent of the HFG-SWCNT binding decreases with increasing PEG size and grafting density because PEGs more completely cover SWCNTs and thus block hydrophobic interactions between HFGs and SWCNTs, which occurs on PEG-functionalized SWCNTs but not on PEG-coated ones. In particular, the HFG-SWCNT binding significantly decreases in the transition region of PEG conformation from mushroom to brush, where PEGs extend like brushes as described in the Alexander-de Gennes theory. While the HFG adsorption is modulated by PEG conformation, the HSA adsorption is much weaker and less influenced by PEG, because spherical HSAs can bind to the restricted area of the SWCNT and thus cannot bind to the SWCNT as tightly as do linear HFGs. These findings agree with experiments showing less adsorption of proteins on the SWCNT functionalized with larger and more PEGs, and support experimental suggestions regarding the dependence of protein adsorption on protein shape and the mushroom-brush transition of PEG conformation.

Self-assembling peptide-based building blocks in medical applications

Peptides and peptide-conjugates, comprising natural and synthetic building blocks, are an increasingly popular class of biomaterials. Self-assembled nanostructures based on peptides and peptide-conjugates offer advantages such as precise selectivity and multifunctionality that can address challenges and limitations in the clinic. In this review article, we discuss recent developments in the design and self-assembly of various nanomaterials based on peptides and peptide-conjugates for medical applications, and categorize them into two themes based on the driving forces of molecular self-assembly. First, we present the self-assembled nanostructures driven by the supramolecular interactions between the peptides, with or without the presence of conjugates. The studies where nanoassembly is driven by the interactions between the conjugates of peptide-conjugates are then presented. Particular emphasis is given to in vivo studies focusing on therapeutics, diagnostics, immune modulation and regenerative medicine. Finally, challenges and future perspectives are presented.

Non-covalent modification of granulocyte-colony stimulating factor (G-CSF) by coiled-coil technology

We present here an approach to non-covalently combine an engineered model protein with a PEGylated peptide via coiled-coil binding. To this end a fusion protein of G-CSF and the peptide sequence (JunB) was created-one sequence of JunB was expressed at the N-terminal of GCSF. JunB is able to bind to the peptide sequence cFos, which was in turn covalently linked to a chain of poly(ethylene glycol) (PEG). The selected peptide sequences are leucine zipper motives from transcription factors and are known to bind to each other specifically by formation of a super secondary structure called coiled-coil. The binding between PEGylated peptides of various molecular weights and the modified protein was assessed by isothermal calorimetry (ITC), dynamic light scattering (DLS), circular dichroism (CD), and fluorescence anisotropy. Our findings show that the attachment of 2 and 5kDa PEG does not interfere with coiled-coil formation and thus binding of peptide to fusion protein. With this work we successfully demonstrate the non-covalent binding of a model moiety (PEG) to a protein through coiled-coil interaction.

The binding and insertion of imidazolium-based ionic surfactants into lipid bilayers: the effects of the surfactant size and salt concentration

Imidazolium-based ionic surfactants with hydrocarbon tails of different sizes were simulated with lipid bilayers at different salt concentrations.