Internal Structure of 15 nm 3-Helix Micelle Revealed by Small-Angle Neutron Scattering and Coarse-Grained MD Simulation

Role of Triggers on the Structural and Functional Facets of TAR DNA-binding Protein 43

Nuclear TAR DNA-binding protein 43 (TDP-43) mitigates cellular function, but the dynamic nucleus-cytoplasm shuttling of TDP-43 is disrupted in diseases, such as Amyotrophic Lateral Sclerosis (ALS). The polymorphic nature of the TDP-43 structures in vitro and in vivo is a result of environmental factors leading to the protein pathogenesis. Once the triggers which mitigate TDP-43 biochemistry are identified, new therapies can be developed. This review aims to illustrate recent discoveries in the diversity of TDP-43 structures (amyloidogenic and non-amyloidogenic) and highlight the triggers which result in their formation.

Recent advances in coiled-coil peptide materials and their biomedical applications

Extensive research has gone into deciphering the sequence requirements for peptides to fold into coiled-coils of varying oligomeric states. More recently, additional signals have been introduced within coiled-coils to promote higher order assembly into biomaterials with a rich distribution of morphologies. Herein we describe these strategies for association of coiled-coil building blocks and biomedical applications. With many of the systems described herein having proven use in protein storage, cargo binding and delivery, three dimensional cell culturing and vaccine development, the future potential of coiled-coil materials to have significant biomedical impact is highly promising.

Blood-brain barrier models: Rationale for selection

Brain delivery is a broad research area, the outcomes of which are far hindered by the limited permeability of the blood-brain barrier (BBB). Over the last century, research has been revealing the BBB complexity and the crosstalk between its cellular and molecular components. Pathologically, BBB alterations may precede as well as be concomitant or lead to brain diseases. To simulate the BBB and investigate options for drug delivery, several in vitro, in vivo, ex vivo, in situ and in silico models are used. Hundreds of drug delivery vehicles successfully pass preclinical trials but fail in clinical settings. Inadequate selection of BBB models is believed to remarkably impact the data reliability leading to unsatisfactory results in clinical trials. In this review, we suggest a rationale for BBB model selection with respect to the addressed research question and downstream applications. The essential considerations of an optimal BBB model are discussed.

Designing sub-20 nm self-assembled nanocarriers for small molecule delivery: Interplay among structural geometry, assembly energetics, and cargo release kinetics

Biological constraints in diseased tissues have motivated the need for small nanocarriers (10-30 nm) to achieve sufficient vascular extravasation and pervasive tumor penetration. This particle size limit is only an order of magnitude larger than small molecules, such that cargo loading is better described by co-assembly processes rather than simple encapsulation. Understanding the structural, kinetic, and energetic contributions of carrier-cargo co-assembly is thus critical to achieve molecular-level control towards predictable in vivo behavior. These interconnected set of properties were systematically examined using sub-20 nm self-assembled nanocarriers known as three-helix micelles (3HM). Both hydrophobicity and the "geometric packing parameter" dictate small molecule compatibility with 3HM's alkyl tail core. Planar obelisk-like apomorphine and doxorubicin (DOX) molecules intercalated well within the 3HM core and near the core-shell interface, forming an integral component to the co-assembly, as corroborated by small-angle X-ray and neutron-scattering structural studies. DOX promoted crystalline alkyl tail ordering, which significantly increased (+63%) the activation energy of 3HM subunit exchange. Subsequently, 3HM-DOX displayed slow-release kinetics (t_1/2 = 40 h) at physiological temperatures, with ~50× greater cargo preference for the micelle core as described by two drug partitioning coefficients (micellar core/shell K_p1 ~ 24, and shell/bulk solvent K_p2 ~ 2). The geometric and energetic insights between nanocarrier and their small molecule cargos developed here will aid in broader efforts to deconvolute the interconnected properties of carrier-drug co-assemblies. Adding this knowledge to pharmacological and immunological explorations will expand our understanding of nanomedicine behavior throughout all the physical and in vivo processes they are intended to encounter.

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.

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.

Multicomponent peptide assemblies

Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.

Stable micelles based on a mixture of coiled-coils: the role of different oligomeric states

Homomeric micelles with tunable size, shape and stability have been extensively studied for biomedical applications such as drug carriers. However, designing the local valency and self-assembled morphology of nanophase-separated multicomponent micelles with varied ligand binding possibilities remains challenging. Here, we present micelles self-assembled from amphiphilic peptide-PEG-lipid hybrid conjugates, where the peptides can be either a 3-helix or 4-helix coiled-coil. We demonstrate that the micelle size and sphericity can be controlled based on the coiled-coil oligomeric state. Using theory and coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent simulation, we studied the distribution of 3-helix and 4-helix conjugates within the mixed micelles and observed self-organization into nanodomains within the mixed micelle. We discovered that the phase separation behavior is dictated by the geometry mismatch in the alkyl chain length from different coiled-coil oligomeric states. Our analyses of the self-assembly tendency and drug delivery potency of mixed micelles with controlled multivalency provide important insights into the assembly and formation of nanophase-separated micelles.

Phase to Phase with TDP-43

TDP-43 is a dimeric nuclear protein that plays a central role in RNA metabolism. In recent years, this protein has become a focal point of research in the amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD) disease spectrum, as pathognomonic inclusions within affected neurons contain post-translationally modified TDP-43. A key question in TDP-43 research involves determining the mechanisms and triggers that cause TDP-43 to form pathological aggregates. This review gives a brief overview of the physiological and pathological roles of TDP-43 and focuses on the structural features of its protein domains and how they may contribute to normal protein function and to disease. A special emphasis is placed on the C-terminal prion-like region thought to be implicated in pathology, as it is where nearly all ALS/FTD-associated mutations reside. Recent structural studies of this domain revealed its crucial role in the formation of phase-separated liquid droplets through a partially populated α-helix. This new discovery provides further support for the theory that liquid droplets such as stress granules may be precursors to pathological aggregates, linking environmental effects such as stress to the potential etiology of the disease. The transition of TDP-43 among soluble, droplet, and aggregate phases and the implications of these transitions for pathological aggregation are summarized and discussed.

Design of polymer conjugated 3-helix micelles as nanocarriers with tunable shapes

Amphiphilic peptide-polymer conjugates have the ability to form stable nanoscale micelles, which show great promise for drug delivery and other applications. A recent design has utilized the end-conjugation of alkyl chains to 3-helix coiled coils to achieve amphiphilicity, combined with the side-chain conjugation of polyethylene glycol (PEG) to tune micelle size through entropic confinement forces. Here we investigate this phenomenon in depth, using coarse-grained dissipative particle dynamics (DPD) simulations in an explicit solvent and micelle theory. We analyze the conformations of PEG chains conjugated to three different positions on 3-helix bundle peptides to ascertain the degree of confinement upon assembly, as well as the ordering of the subunits making up the micelle. We discover that the micelle size and stability is dictated by a competition between the entropy of PEG chain conformations in the assembled state, as well as intermolecular cross-interactions among PEG chains that promote cohesion between neighboring conjugates. Our analyses build on the role of PEG molecular weight and conjugation site and lead to computational phase diagrams that can be used to design 3-helix micelles. This work opens pathways for the design of multifunctional micelles with tunable size, shape and stability.

Understanding Peptide Oligomeric State in Langmuir Monolayers of Amphiphilic 3-Helix Bundle-Forming Peptide-PEG Conjugates

Coiled-coil peptide-polymer conjugates are an emerging class of biomaterials. Fundamental understanding of the coiled-coil oligomeric state and assembly process of these hybrid building blocks is necessary to exert control over their assembly into well-defined structures. Here, we studied the effect of peptide structure and PEGylation on the self-assembly process and oligomeric state of a Langmuir monolayer of amphiphilic coiled-coil peptide-polymer conjugates using X-ray reflectivity (XR) and grazing-incidence X-ray diffraction (GIXD). Our results show that the oligomeric state of PEGylated amphiphiles based on 3-helix bundle-forming peptide is surface pressure dependent, a mixture of dimers and trimers was formed at intermediate surface pressure but transitions into trimers completely upon increasing surface pressure. Moreover, the interhelical distance within the coiled-coil bundle of 3-helix peptide-PEG conjugate amphiphiles was not perturbed under high surface pressure. Present studies provide valuable insights into the self-assembly process of hybrid peptide-polymer conjugates and guidance to develop biomaterials with controlled multivalency of ligand presentation.