Optimizing Protein–Polymer Interactions in a Poly(ethylene glycol) Coarse-Grained Model

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.

Biomolecular engineering of drugs loading in Riboflavin-targeted polymeric devices: simulation and experimental

The synthesis of polymeric nanoparticles (NPs) with efficient drug loading content and targeting moieties is an attractive field and remains a challenge in drug delivery systems. Atomistic investigations can provide an in-depth understanding of delivery devices and reduce the number of expensive experiments. In this paper, we studied the self-assembly of poly (lactic-co-glycolic acid)-b-poly (ethylene glycol) with different molecular weights and surface compositions. The innovation of this molecular study is the loading of an antitumor drug (docetaxel) on a targeting ligand (riboflavin). According to this work, a novel, biocompatible and targeted system for cancer treatment has been developed. The obtained results revealed a correlation between polymer molecular weight and the stability of particles. In this line, samples including 20 and 10 w/w% moiety NPs formed from polymers with 3 and 4.5 kDa backbone sizes, respectively, are the stable models with the highest drug loading and entrapment efficiencies. Next, we evaluated NP morphology and found that NPs have a core/shell structure consisting of a hydrophobic core with a shell of poly (ethylene glycol) and riboflavin. Interestingly, morphology assessments confirmed that the targeting moiety located on the surface can improve drug delivery to receptors and cancerous cells. The developed models provided significant insight into the structure and morphology of NPs before the synthesis and further analysis of NPs in biological environments. However, in the best cases of this system, Dynamic Light Scattering (DLS) tests were also taken and the results were consistent with the results obtained from All Atom and Coarse Grained simulations.

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.

Martini Coarse-Grained Model of Hyaluronic Acid for the Structural Change of Its Gel in the Presence of Monovalent and Divalent Salts

Hyaluronic acid (HA) has a wide range of biomedical applications including the formation of hydrogels, microspheres, sponges, and films. The modeling of HA to understand its behavior and interaction with other biomolecules at the atomic level is of considerable interest. The atomistic representation of long HA polymers for the study of the macroscopic structural formation and its interactions with other polyelectrolytes is computationally demanding. To overcome this limitation, we developed a coarse grained (CG) model for HA adapting the Martini scheme. A very good agreement was observed between the CG model and all-atom simulations for both local (bonded interactions) and global properties (end-to-end distance, a radius of gyration, RMSD). Our CG model successfully demonstrated the formation of HA gel and its structural changes at high salt concentrations. We found that the main role of CaCl₂ is screening the electrostatic repulsion between chains. HA gel did not collapse even at high CaCl₂ concentrations, and the osmotic pressure decreased, which agrees well with the experimental results. This is a distinct property of HA from other proteins or polynucleic acids which ensures the validity of our CG model. Our HA CG model is compatible with other CG biomolecular models developed under the Martini scheme, which allows for large-scale simulations of various HA-based complex systems.

An insight into the role of riboflavin ligand in the self-assembly of poly(lactic-co-glycolic acid)-based nanoparticles - a molecular simulation and experimental approach

Nanoparticles (NPs) used for targeted delivery purposes are rapidly gaining importance in diagnostic and therapeutic fields. These agents have been studied extensively so far to reveal their optimal physicochemical properties including the effects of ligands and their density on the surface of NPs. This article was conducted through a computational approach (all-atom molecular dynamics simulations) to predict the stability of NPs based on a poly-lactic-co-glycolic acid (PLGA) hydrophobic core with a poly-ethylene glycol (PEG) hydrophilic shell and varying numbers of riboflavin (RF) molecules as ligands. Depending on the molecular weight of the polymers, the most stable composition of NPs was achieved at 20 wt% and 10 wt% PLGA-PEG-RF for PLGA3kDa-PEG2kDa and PLGA4.5kDa-PEG2kDa polymers, respectively. According to the simulations, riboflavin molecules were located on the surface of the NPs, which would indicate that riboflavin-bound PLGA-PEG NPs could be efficiently utilized for active targeting purposes. To scrutinize the simulation results, NPs with riboflavin ligands were synthesized and put into in vitro experiments. Outstandingly, the empirical outcomes revealed that the hydrodynamic sizes of NPs also met minimum points at 20 and 10 wt% for PLGA3kDa-PEG2kDa and PLGA4.5kDa-PEG2kDa, respectively. Moreover, similar trends in the gyration radius as a function of riboflavin content were observed in the simulation analysis and the experimental results, which would indicate that the method of molecular dynamics (MD) simulation is a reliable mathematical technique and could be applied for predicting the physicochemical properties of NPs.

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.

Molecular Modeling and Simulations of Peptide–Polymer Conjugates

Peptide–polymer conjugates are a class of soft materials composed of covalently linked blocks of protein/polypeptides and synthetic/natural polymers. These materials are practically useful in biological applications, such as drug delivery, DNA/gene delivery, and antimicrobial coatings, as well as nonbiological applications, such as electronics, separations, optics, and sensing. Given their broad applicability, there is motivation to understand the molecular and macroscale structure, dynamics, and thermodynamic behavior exhibited by such materials. We focus on the past and ongoing molecular simulation studies aimed at obtaining such fundamental understanding and predicting molecular design rules for the target function. We describe briefly the experimental work in this field that validates or motivates these computational studies. We also describe the various models (e.g., atomistic, coarse-grained, or hybrid) and simulation methods (e.g., stochastic versus deterministic, enhanced sampling) that have been used and the types of questions that have been answered using these computational approaches.

Structure-function-dynamics of α-chymotrypsin based conjugates as a function of polymer charge

The field of protein-polymer conjugates has suffered from a lack of predictive tools and design guidelines to synthesize highly active and stable conjugates. In order to develop this type of information, structure-function-dynamics relationships must be understood. These relationships depend strongly on protein-polymer interactions and how these influence protein dynamics and conformations. Probing nanoscale interactions is experimentally difficult, but computational tools, such as molecular dynamics simulations, can easily obtain atomic resolution. Atomistic molecular dynamics simulations were used to study α-chymotrypsin (CT) densely conjugated with either zwitterionic, positively charged, or negatively charged polymers. Charged polymers interacted with the protein surface to varying degrees and in different regions of the polymer, depending on their flexibilities. Specific interactions of the negatively charged polymer with CT caused structural deformations in CT's substrate binding pocket and active site while no deformations were observed for zwitterionic and positively charged polymers. Attachment of polymers displaced water molecules from CT's surface into the polymer phase and polymer hydration correlated with the Hofmeister series.

PEGylation within a confined hydrophobic cavity of a protein

The conjugation of polyethylene glycol (PEG) to proteins, known as PEGylation, has increasingly been employed to expand the efficacy of therapeutic drugs. Recently, research has emphasized the effect of the conjugation site on protein-polymer interactions. In this study, we performed atomistic molecular dynamics (MD) simulations of lysine 116 PEGylated bovine serum albumin (BSA) to illustrate how conjugation near a hydrophobic pocket affects the conjugate's dynamics and observed altered low mode vibrations in the protein. MD simulations were performed for a total of 1.5 μs for each PEG chain molecular mass from 2 to 20 kDa. Analysis of preferential PEG-BSA interactions showed that polymer behavior was also affected as proximity to the attractive protein surface patches promoted interactions in small (2 kDa) PEG chains, while the confined environment of the conjugation site reduced the expected BSA surface coverage when the polymer molecular mass increased to 10 kDa. This thorough analysis of PEG-BSA interactions and polymer dynamics increases the molecular understanding of site-specific PEGylation and enhances the use of protein-polymer conjugates as therapeutics.

Atom Transfer Radical Polymerization for Biorelated Hybrid Materials

Proteins, nucleic acids, lipid vesicles, and carbohydrates are the major classes of biomacromolecules that function to sustain life. Biology also uses post-translation modification to increase the diversity and functionality of these materials, which has inspired attaching various other types of polymers to biomacromolecules. These polymers can be naturally (carbohydrates and biomimetic polymers) or synthetically derived and have unique properties with tunable architectures. Polymers are either grafted-to or grown-from the biomacromolecule's surface, and characteristics including polymer molar mass, grafting density, and degree of branching can be controlled by changing reaction stoichiometries. The resultant conjugated products display a chimerism of properties such as polymer-induced enhancement in stability with maintained bioactivity, and while polymers are most often conjugated to proteins, they are starting to be attached to nucleic acids and lipid membranes (cells) as well. The fundamental studies with protein-polymer conjugates have improved our synthetic approaches, characterization techniques, and understanding of structure-function relationships that will lay the groundwork for creating new conjugated biomacromolecular products which could lead to breakthroughs in genetic and tissue engineering.